├── .github └── workflows │ ├── deploy-book.yml │ └── push-translations.yml ├── .gitignore ├── 01_Sample_preparation ├── Considerations.md ├── Experimental_design.md ├── Introduction.md ├── Reproducibility.md └── Resources.md ├── 02_Sample_acquisition ├── Introduction.md ├── Picking.md ├── Practical_considerations.md ├── Resources.md └── _notinyet_Setting_up.md ├── 03_Image_analysis ├── Classification.md ├── Colocalization.md ├── Common_types_of_analysis.md ├── Data_management.md ├── GeneralUseSoftware.md ├── Intensity.md ├── Introduction.md ├── Resources.md ├── Shape.md ├── Software.md ├── SpecificUseSoftware.md ├── Tracking.md ├── _notinyet_Common_pitfalls.md ├── _notinyet_Image_processing.md └── _notinyet_Image_segmentation.md ├── 04_Data_presentation ├── Introduction.md ├── Presentation_images.md ├── Resources.md ├── Statistics.md └── _notinyet_Presentation_graphs.md ├── BBBC_montage.png ├── CITATION.cff ├── Glossary.md ├── LICENSE ├── QuantitativeBioimaging.md ├── README.md ├── _build └── gettext │ ├── 01_Sample_preparation.pot │ ├── 02_Sample_acquisition.pot │ ├── 03_Image_analysis.pot │ ├── 04_Data_presentation.pot │ ├── Glossary.pot │ ├── QuantitativeBioimaging.pot │ ├── README.pot │ ├── bibliography.pot │ ├── community_resources.pot │ ├── contributors.pot │ ├── genindex.pot │ └── welcome.pot ├── _config.yml ├── _static └── myfile.css ├── _toc.yml ├── bibliography.md ├── community_resources.md ├── contributors.md ├── favicon.png ├── genindex.md ├── images ├── 10TipsHowToNotLieWithImages.png ├── Flow-chart-to-help-choose-which-type-of-microscope-to-use.png ├── colocalization.png ├── crosstalk.png ├── data_management.png ├── discrete_classes.png ├── inversion.png ├── mounting_media.png ├── multichannel.png ├── processing_images_cheatsheet.gif ├── rotation.png ├── sdr_fig1.png └── wavelength_resolution.png ├── intl_requirements.txt ├── locale ├── cs │ └── LC_MESSAGES │ │ ├── 01_Sample_preparation.po │ │ ├── 02_Sample_acquisition.po │ │ ├── 03_Image_analysis.po │ │ ├── 04_Data_presentation.po │ │ ├── Glossary.po │ │ ├── QuantitativeBioimaging.po │ │ ├── README.po │ │ ├── bibliography.po │ │ ├── community_resources.po │ │ ├── contributors.po │ │ ├── genindex.po │ │ └── welcome.po ├── de │ └── LC_MESSAGES │ │ ├── 01_Sample_preparation.po │ │ ├── 02_Sample_acquisition.po │ │ ├── 03_Image_analysis.po │ │ ├── 04_Data_presentation.po │ │ ├── Glossary.po │ │ ├── QuantitativeBioimaging.po │ │ ├── README.po │ │ ├── bibliography.po │ │ ├── community_resources.po │ │ ├── contributors.po │ │ ├── genindex.po │ │ └── welcome.po ├── es │ └── LC_MESSAGES │ │ ├── 01_Sample_preparation.po │ │ ├── 02_Sample_acquisition.po │ │ ├── 03_Image_analysis.po │ │ ├── 04_Data_presentation.po │ │ ├── Glossary.po │ │ ├── QuantitativeBioimaging.po │ │ ├── README.po │ │ ├── bibliography.po │ │ ├── community_resources.po │ │ ├── contributors.po │ │ ├── genindex.po │ │ └── welcome.po ├── fi │ └── LC_MESSAGES │ │ ├── 01_Sample_preparation.po │ │ ├── 02_Sample_acquisition.po │ │ ├── 03_Image_analysis.po │ │ ├── 04_Data_presentation.po │ │ ├── Glossary.po │ │ ├── QuantitativeBioimaging.po │ │ ├── README.po │ │ ├── bibliography.po │ │ ├── community_resources.po │ │ ├── contributors.po │ │ ├── genindex.po │ │ └── welcome.po ├── fr │ └── LC_MESSAGES │ │ ├── 01_Sample_preparation.po │ │ ├── 02_Sample_acquisition.po │ │ ├── 03_Image_analysis.po │ │ ├── 04_Data_presentation.po │ │ ├── Glossary.po │ │ ├── QuantitativeBioimaging.po │ │ ├── README.po │ │ ├── bibliography.po │ │ ├── community_resources.po │ │ ├── contributors.po │ │ ├── genindex.po │ │ └── welcome.po ├── it │ └── LC_MESSAGES │ │ ├── 01_Sample_preparation.po │ │ ├── 02_Sample_acquisition.po │ │ ├── 03_Image_analysis.po │ │ ├── 04_Data_presentation.po │ │ ├── Glossary.po │ │ ├── QuantitativeBioimaging.po │ │ ├── README.po │ │ ├── bibliography.po │ │ ├── community_resources.po │ │ ├── contributors.po │ │ ├── genindex.po │ │ └── welcome.po ├── ja │ └── LC_MESSAGES │ │ ├── 01_Sample_preparation.po │ │ ├── 02_Sample_acquisition.po │ │ ├── 03_Image_analysis.po │ │ ├── 04_Data_presentation.po │ │ ├── Glossary.po │ │ ├── QuantitativeBioimaging.po │ │ ├── README.po │ │ ├── bibliography.po │ │ ├── community_resources.po │ │ ├── contributors.po │ │ ├── genindex.po │ │ └── welcome.po ├── pl │ └── LC_MESSAGES │ │ ├── 01_Sample_preparation.po │ │ ├── 02_Sample_acquisition.po │ │ ├── 03_Image_analysis.po │ │ ├── 04_Data_presentation.po │ │ ├── Glossary.po │ │ ├── QuantitativeBioimaging.po │ │ ├── README.po │ │ ├── bibliography.po │ │ ├── community_resources.po │ │ ├── contributors.po │ │ ├── genindex.po │ │ └── welcome.po └── pt │ └── LC_MESSAGES │ ├── 01_Sample_preparation.po │ ├── 02_Sample_acquisition.po │ ├── 03_Image_analysis.po │ ├── 04_Data_presentation.po │ ├── Glossary.po │ ├── QuantitativeBioimaging.po │ ├── README.po │ ├── bibliography.po │ ├── community_resources.po │ ├── contributors.po │ ├── genindex.po │ └── welcome.po ├── logo.png ├── references.bib ├── requirements.txt ├── transifex.yml └── welcome.md /.github/workflows/deploy-book.yml: -------------------------------------------------------------------------------- 1 | name: deploy-book 2 | 3 | # Only run this when the master branch changes 4 | on: 5 | push: 6 | branches: 7 | - main 8 | # don't rebuild English if we're just pushing translation files 9 | paths-ignore: 10 | - _build/gettext/** 11 | - locale/** 12 | 13 | # This job installs dependencies, builds the book, and pushes it to `gh-pages` 14 | jobs: 15 | deploy-book: 16 | runs-on: ubuntu-latest 17 | steps: 18 | - uses: actions/checkout@v2 19 | 20 | # Install dependencies 21 | - name: Set up Python 3.8 22 | uses: actions/setup-python@v2 23 | with: 24 | python-version: 3.8 25 | 26 | - name: Install dependencies 27 | run: | 28 | pip install -r requirements.txt 29 | 30 | # Build the book 31 | - name: Build the book 32 | run: | 33 | jupyter-book build . 34 | 35 | # Push the book's HTML to github-pages 36 | - name: GitHub Pages action 37 | uses: peaceiris/actions-gh-pages@v3.6.1 38 | with: 39 | github_token: ${{ secrets.GITHUB_TOKEN }} 40 | publish_dir: ./_build/html 41 | cname: www.bioimagingguide.org 42 | -------------------------------------------------------------------------------- /.github/workflows/push-translations.yml: -------------------------------------------------------------------------------- 1 | name: push-translations 2 | 3 | # Only run this when the main branch changes a markdown file or a top level config file 4 | on: 5 | push: 6 | branches: 7 | - main 8 | paths: 9 | - '**.md' 10 | - '_*.yml' 11 | 12 | permissions: 13 | contents: write 14 | pull-requests: write 15 | 16 | jobs: 17 | push-translations: 18 | env: 19 | GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} 20 | runs-on: ubuntu-latest 21 | steps: 22 | - uses: actions/checkout@v2 23 | 24 | # Install dependencies 25 | - name: Set up Python 3.8 26 | uses: actions/setup-python@v2 27 | with: 28 | python-version: 3.8 29 | 30 | - name: Install dependencies 31 | run: | 32 | pip install -r requirements.txt 33 | pip install -r intl_requirements.txt 34 | 35 | # Update the files 36 | - name: Update the files 37 | run: | 38 | jb config sphinx . 39 | sphinx-build -b gettext . _build/gettext 40 | sphinx-intl update -p _build/gettext 41 | rm conf.py 42 | 43 | - name: Push translations to a branch (branch protection) 44 | run: | 45 | git config user.name github-actions 46 | git config user.email github-actions@github.com 47 | git checkout -b auto_translation 48 | git add "**.pot" 49 | git commit -m "auto generated translation file updates" 50 | git push -u origin auto_translation 51 | gh pr create --title "Auto-translations" --body "Made by GH Actions" 52 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | **.DS_Store 2 | _build/html** 3 | _build/gettext/.** 4 | _build/gettext/_** 5 | _build/.doctrees** 6 | 7 | */.ipynb_checkpoints/* 8 | .ipynb_checkpoints/* 9 | -------------------------------------------------------------------------------- /01_Sample_preparation/Experimental_design.md: -------------------------------------------------------------------------------- 1 | # Experimental design decisions 2 | 3 | A number of critical decisions must be made when designing a quantitative bioimaging experiment. Many of these decisions will be deeply dependent on what is possible given the biology you wish to study, for example: 4 | - You will always prefer live imaging to fixed imaging if it is important to assess the dynamics of a given process 5 | - You may need to perform special processes such as tissue clearing if it is important to image deep into a relatively opaque specimen 6 | - You cannot rely on genetic tagging with fluorescent proteins if your model system is not genetically tractable to such manipulations 7 | - You have to image at a particularly high resolution to confidently assess interactions between two molecules imaged in the same system 8 | 9 | It is therefore _**extremely**_ important to think through all of the aspects of your biological question before ever picking up a pipette or a slide. Many sample preparation decisions are deeply entwined with the availability and suitability of particular microscopes; see [that section](content/microscope_selection) for more information. 10 | 11 | ## Mounting 12 | 13 | ### Glass coverslips 14 | 15 | Many imaging applications involve mounting on glass coverslips, either directly or using a coverslip mounted into a dish. While there is a wide range of coverslip sizes and shapes, the most important attribute is the coverslip thickness. Coverslip grade dictates the expected thickness and tolerance. These factors are important because most microscope manufacturers assume a specific coverslip thickness (0.17mm) in the design of objective lenses to minimize aberrations. These aberrations tend to affect the brightness and axial resolution, reducing signal to noise ratio, sharpness, and resolution. The tolerance of the coverslip (to minimize the variability in thickness) is essential for super-resolution techniques or intensity measurements in images collected with high numerical aperture objectives. Other applications do not require the mounting of samples onto glass or plastic but instead have the sample and the objective lens immersed in the same medium. 16 | 17 | ```{list-table} Comparison of coverslip grades 18 | :header-rows: 1 19 | :name: coverslip-grades 20 | 21 | * - Grade 22 | - Nominal thickness [mm] 23 | - Thickness range [mm] 24 | * - #1.5 25 | - 0.17 26 | - 0.16 - 0.19 27 | * - #1.5H 28 | - 0.17 29 | - 0.165 - 0.175 30 | ``` 31 | 32 | ### Mounting media 33 | 34 | The {term}`refractive index` the sample is placed in, as well as the refractive index of the glass and the medium between the objective and the sample are all critical to determining the achievable resolution. The {term}`mounting media` can have other important optical and/or experimental properties; it is important to use the correct mounting media for experiment planned. 35 | 36 | ```{figure} ../images/mounting_media.png 37 | --- 38 | alt: effects of mounting media 39 | width: 75% 40 | align: center 41 | name: mounting-media-dependence 42 | --- 43 | **Effects of mounting media on staining with various fluorophores**. Adapted from Jonkman J., Brown C.M., Wright G.D _et al_. Tutorial: guidance for quantitative confocal microscopy. _Nat Prot_ **15**, (2020) {cite}`Jonkman2020-bo` 44 | ``` 45 | 46 | ## Fluorophore selection 47 | 48 | Fluorophores are molecules that are able to emit light upon absorption of a photon, typically of shorter wavelength. The fluorophores relevant to biomedical research can be small molecules organic dyes (FITC, Alexa Fluor 488) that bind specific cell structure (e.g., DAPI, MitoTracker), fluorescent analogues of small molecules (e.g., phalloidin, fluorescent amino acids) or fluorescent proteins. Some of the important properties to consider when choosing fluorophores are listed below: 49 | 50 | - Excitation/emission spectra of each fluorophore 51 | - Brightness (dyes tend to be brighter than proteins) 52 | - Photostability 53 | - Propensity to oligomerize (in the case of fluorescent proteins) 54 | - Phototoxicity (when imaging in live samples) 55 | 56 | Understanding fluorophores, microscope specifications (light source, filters, detector), and analysis goals are key in selecting the appropriate fluorophore(s) to address a scientific question. See the section on [reproducibility](content/reproducibility) for more information. 57 | 58 | 62 | -------------------------------------------------------------------------------- /01_Sample_preparation/Introduction.md: -------------------------------------------------------------------------------- 1 | # Introduction 2 | 3 | A good image starts at the bench. The best performing instrument will not produce rigorous, reproducible or high quality data unless sample preparation has been optimized. To design a rigorous and reproducible microscopy experiment, it is critical to identify the goal of the experiment and understand the factors that impact the image. This information informs researchers about how to prepare the sample, what minimal controls and corrections are needed, how to choose the appropriate instrumentation, optimize acquisition, analyze and present microscopy data. 4 | 5 | Here we will discuss some of the key choices you will make during sample preparation, including selecting your sample type and fluorophore (if you're performing fluorescence microscopy). We also discuss some minimal controls necessary for interpreting your results. 6 | 7 | 8 | -------------------------------------------------------------------------------- /01_Sample_preparation/Reproducibility.md: -------------------------------------------------------------------------------- 1 | # Reproducibility 2 | 3 | (content/reproducibility)= 4 | 5 | A number of factors are critical in designing a reproducible microscopy experiment. A few critical factors are laid out here; see other works such as {cite}`Jost2019-nx` 6 | 7 | ## Antibody validation 8 | 9 | While in a perfect world, antibodies would always be specific to a particular target, unfortunately, this cannot always be relied upon when performing {term}`immunolabeling`. {cite}`Uhlen2016-wy` When possible, one should perform knockout and/or knockdown controls to confirm antibody specificity; where not, look for availability of another antibody to a different part of the target molecule (sometimes called the _epitope_) and confirm you get consistent localization. 10 | 11 | Optimizing your {term}`blocking` and {term}`permeabilization` conditions for the particular antibody and protocol can reduce non-specific background. No-primary-antibody controls should always be performed as well, as they are essential for validating signal specificity. 12 | 13 | ## Fluorescent protein localization validation 14 | 15 | Expression of fluorescently-tagged proteins can make localization of a molecule or structure possible, especially when no good antibody exist for immunolabeling and/or it will be helpful to observe the molecule's behavior in live cells. While a study comparing overlap between the same molecular targets with fluorescent proteins vs antibodies found 80% overlap, they also found that some considerations (such as whether the C- or N- terminus of a protein is tagged) may cause changes in localization. {cite}`Stadler2013`. A recent paper {cite}`Sittewelle2023` surveys considerations for genetic tagging of molecules for live microscopy. 16 | 17 | (content/bleedthrough)= 18 | ## Bleedthrough 19 | 20 | When performing multicolor fluorescence microscopy, it is critical to choose fluorophores with sufficiently distinct excitation and emission spectra; online tools such as FPbase {cite}`Lambert2019-xl` can help with such selections, especially if you know the various optical components of the microscope on which you will be imaging your samples (these configurations can be saved and shared on FPbase; ask the maintainer of the microscope you plan to use if such a configuration file is already online). Even if you believe your fluorophores are sufficiently separated, it is critical to check single-color fluorescent controls using the same imaging conditions (and preferably on the same day) as your multicolor controls to be certain no bleedthrough is occurring; it is _mandatory_ to do this if you are planning to measure [colocalization](content/colocalization). -------------------------------------------------------------------------------- /01_Sample_preparation/Resources.md: -------------------------------------------------------------------------------- 1 | # Resources for learning more 2 | 3 | ```{list-table} 4 | :header-rows: 1 5 | :name: sample-preparation-resource-table 6 | 7 | * - **Resource Name** 8 | - **Link** 9 | - **Brief description** 10 | * - 🌐 Microforum 11 | - [link](https://forum.microlist.org/) 12 | - An online forum for discussing issues with and getting advice on sample preparation and microscopy 13 | * - 🌐 FPbase {cite}`Lambert2019-xl` 14 | - [link](https://www.fpbase.org/) 15 | - Database for identifying fluorophores by brightness, spectra and assessing compatibility with other fluorophores and with microscope filters 16 | * - 🌐 Bio-protocol 17 | - [link](https://bio-protocol.org/en/about ) 18 | - Website to search for protocols across biological disciplines, including protocols associated with work published elsewhere. All protocols are available under an open access license (CC BY or CC BY-NC) 19 | * - 🌐 protocols.io 20 | - [link](https://www.protocols.io/) 21 | - A secure platform for developing and sharing reproducible methods 22 | * - 📄 Designing a rigorous microscopy experiment: Validating methods and avoiding bias {cite}`Jost2019-nx` 23 | - [link](https://rupress.org/jcb/article/218/5/1452/120908/Designing-a-rigorous-microscopy-experiment) 24 | - Review of aspects of designing a rigorous light microscopy experiment, including validation of samples and imaging, identification and correction of errors, and strategies to avoid biases 25 | * - 📄 Tutorial: guidance for quantitative confocal microscopy {cite}`Jonkman2020-bo` 26 | - [link](https://doi.org/10.1038/s41596-020-0313-9) 27 | - Step-by-step guidance on practical considerations for sample preparation, acquisition, and image analysis; primarily though not exclusively aimed at users of confocal microscopy 28 | 29 | ``` 30 | -------------------------------------------------------------------------------- /02_Sample_acquisition/Introduction.md: -------------------------------------------------------------------------------- 1 | # Introduction 2 | 3 | Microscopes are optical instruments, and as such, they are composed of different optical components and devices. As a beginner, it is important to recognize the experimental parameters that can affect the quality and rigor of the imaging data, and by extension, its interpretation. 4 | 5 | A foundational concept is the “light path,” which can be used to trace out light’s trajectory from the light source to the detector. When working with microscopes, whether it is a cell culture microscope or a cutting-edge superresolution system, it is important to take the time to trace out the different light paths in the system. By approaching the system as a sum of its parts means that optimizing and troubleshooting become systematic processes compared to when the system is treated as a black box. This [interactive tutorial at MicroscopyU](https://www.microscopyu.com/tutorials/tepaths) shows the light paths in a standard inverted microscope; [this view](https://www.microscopyu.com/microscopy-basics/components) gives more detail about the various parts. 6 | 7 | ## Types of microscopes 8 | 9 | While far from a comprehensive list of what is available, a few of the most common types of microscopes are listed below. 10 | - **Widefield**, sometimes called _epifluorescence_, microscopes that take in all the light available to them in a single light path; this approach requires the least complex hardware, and also is often advantageous when imaging dim samples. {term}`Deconvolution` is sometimes performed after imaging on a widefield microscope to remove blur. 11 | - **Confocal** - microscopes that remove out-of-focus light in the light path, typically using one or many pinholes to physically block this light. Several variants of confocal microscopy exist; spinning-disk confocal microscopes are often preferred for live-cell imaging applications as they tend to minimize toxicity to the sample. 12 | - **Multiphoton** microscopes utilize multiple pulses of longer-wavelength (lower energy) light to penetrate deep into tissue, since tissues are less likely to scatter these wavelengths; once there, multiple low-engergy photons hitting the fluorphore at the same time will use their combined energy to activate a fluorophore that each photon alone would be too weak to do. Because the benefit of these systems is in their deeper penetration, they are often used for performing live-animal imaging. 13 | - **Superresolution** microscopes that are designed to allows the user to bypass the minimum optical resolution limit (typically 200 nm, depending on sample consideration) to resolve very small structures. Sometimes this is achieved with specialized hardware (such as in STED and SIM) and sometimes with specialized probes (such as in PALM and STORM). 14 | - **Light sheet** microscopes that illuminate the sample perpendicular to the axis of imaging, often by a second, orthogonal set of objective lenses. This allows for thin optical sectioning across large volumes, but introduces more considerations around sample mounting. Many variations on light sheet microscopes have emerged in recent years. 15 | 16 | ```{important} 17 | No matter which kind of microscope you use, scientific microscopes are complex instruments with many working parts, all of which typically must be in good working order and calibrated/aligned properly for quantitative imaging to take place. The maintainer of your microscope will typically ensure this, but speak with them regularly about questions you may have and about how changes to the microscope configuration may affect your ability to accurately make certain measurements. Your microscope maintainer may be maintaining a large number of microscopes with a large number of independent users, so if something looks "off", make sure to talk with them before proceeding! 18 | ``` 19 | 20 | 24 | -------------------------------------------------------------------------------- /02_Sample_acquisition/Picking.md: -------------------------------------------------------------------------------- 1 | # Choosing the right microscopy modality 2 | 3 | ## Introduction 4 | (content/microscope_selection)= 5 | Choosing the right microscope for your experiment will be a factor both of what the experiment dictates and what the researcher can access. The image below (from [Fundamentals of Microscopy by Jermey Sanderson](http://dx.doi.org/10.1002/cpmo.76) {cite}`Sanderson2020-qz`) gives a sense of the sorts of decisions one should consider when choosing a microscope; a more thorough description of the pros and cons of various kinds of microscopes can be found in [this tutorial](https://doi.org/10.1038/s41596-020-0313-9){cite}`Jonkman2020-bo`. 6 | 7 | ```{figure} ../images/Flow-chart-to-help-choose-which-type-of-microscope-to-use.png 8 | --- 9 | alt: BBBC image montage 10 | width: 100% 11 | align: center 12 | name: microscope-selection-flowchart 13 | --- 14 | **Flow chart to help choose which type of microscope to use.** Figure by Jeremy Sanderson. [Source](https://www.researchgate.net/figure/Flow-chart-to-help-choose-which-type-of-microscope-to-use_fig5_341918746) {cite}`Sanderson2020-qz` 15 | ``` 16 | 17 | ## Opportunities for microscopy resource access 18 | 19 | While some imaging facilities are open only to members of a single institution, others allow outside visitors or even sponsor visitors to travel to them. 20 | 21 | * **Advanced Imaging Center - Janelia Research Campus.** The AIC was created to give access to the broad scientific community to new imaging instruments that are not commercially available. Proposals can be submitted during open calls at [their website](https://www.aicjanelia.org/apply). 22 | 23 | 24 | -------------------------------------------------------------------------------- /02_Sample_acquisition/Practical_considerations.md: -------------------------------------------------------------------------------- 1 | # Practical considerations 2 | 3 | We recommend checking out [Microtutor](https://microtutor.globalbioimaging.org/) and [MyScope](https://myscope.training/) for interactive explanations of many of these concepts! 4 | 5 | ## Objective selection 6 | 7 | Microscope objectives have a number of features that must be considered when deciding which objective is right for your experiment 8 | 9 | - Magnification and resolution: the higher the numerical aperture (NA) of the lens, the finer the resolution one can obtain in one's sample. The NA is calculated as {math}`NA=RI * sin(θ)`, relating both to the {term}`refractive index` of the sample, glass, and {term}`immersion media` as well as the range of angles of emitted light that can be collected into the lens. Unless special techniques are used, the typical limit of resultion is calculated as {math}`d = λ / 2NA`, meaning the resolution is set both by the NA of the lens but also by the wavelength of light used for imaging. 10 | 11 | ```{figure} ../images/wavelength_resolution.png 12 | --- 13 | alt: microtubules imaged at 488nm and 647nm 14 | width: 50% 15 | align: center 16 | name: resolution-wavelength-dependence 17 | --- 18 | **Decreased resolution at longer wavelengths of light**. Microtubules imaged at a shorter wavelength of light show higher resolution than those imaged at longer wavelengths. Adapted from Jonkman J., Brown C.M., Wright G.D _et al_. Tutorial: guidance for quantitative confocal microscopy. _Nat Prot_ **15**, (2020) {cite}`Jonkman2020-bo` 19 | ``` 20 | 21 | - Color correction: When performing multicolor microscopy, it is important to choose an objective lens that is labeled as `Apo` or `Super Apo`, as such lenses are corrected to focus 3 to 6 colors in the same plane at the same time. `Fluor` lenses will typically focus two colors at once. 22 | - Working distance: The working distance (WD) gives the distance in millimeters that the lens can focus into the sample. This distance includes the coverslip and mounting media as well. If imaging a thick sample, and/or if needing to image away from the surface of the sample, it is important to ensure the lens has a sufficient working distance. 23 | 24 | ## Filter sets 25 | 26 | It is important to make sure that the microscope that you want to image on has the correct filter sets for the fluorphores you wish to use. See the [section on bleedthrough](content/bleedthrough) for more information. 27 | 28 | ## Z sampling 29 | 30 | - If you wish to capture multiple z sections, the spacing of these setions is important if you wish to be able to perform an accurate 3D reconstruction. SVI has a [fuller mathematical explanation of this](https://svi.nl/NyquistRate),as well as an easy-to-use [online calculator](https://svi.nl/NyquistCalculator) that you can use to calculate the optimal z section spacing for your imaging conditions. 31 | 32 | ## Acquisition power/speed 33 | 34 | The amount of signal captured from any fluorophore will be related not just to the intrinsic brightness of the fluorophore, but also the amount of excitation light it is exposed to (due to duration, power, or both) as well as amount of time and signal multiplication that happens at the detector (typically a camera or a photomultiplier tube (PMT)). An optimal experiment is typically one that minimizes the amount of light hitting the sample (to reduce photobleaching and/or phototoxicity) while acheiving adequate fluorescent signal and in minimal time on the equipment. How exactly to balance these competing factors will depend on the exact biology being studied and the researcher's constraints. 35 | 36 | -------------------------------------------------------------------------------- /02_Sample_acquisition/Resources.md: -------------------------------------------------------------------------------- 1 | # Resources for learning more 2 | 3 | ```{list-table} 4 | :header-rows: 1 5 | :name: sample-acquisition-resource-table 6 | 7 | * - **Resource Name** 8 | - **Link** 9 | - **Brief description** 10 | * - 🌐 Nikon MicroscopyU 11 | - [link](https://www.microscopyu.com/microscopy-basics) 12 | - Fundamentals of microscopy explained for beginners with lots of images and plain language descriptions of terms used in microscopy 13 | * - 🌐 Microtutor 14 | - [link](https://microtutor.globalbioimaging.org/) 15 | - A fantastic interactive course on fluorescence microscopy, created by the team at [Harvard CITE](https://cite.hms.harvard.edu/) 16 | * - 🌐 MyScope 17 | - [link](https://myscope.training/) 18 | - An interactive microscope simulator and learning environment developed by MicroscopyAustralia, covering a number of types of microscopy. 19 | * - 📖 Visualizing Cells Through Microscopy 20 | - [link](https://open.oregonstate.education/cellbiology/chapter/microscopy/) 21 | - An open textbook chapter from the "Fundamentals of Cell Biology" book from Oregon State University, a great introductory guide to concepts in microscopy. 22 | * - 📄 Seeing is believing? A beginners' guide to practical pitfalls in image acquisition {cite}`North2006-sb` 23 | - [link](https://doi.org/10.1083/jcb.200507103) 24 | - An overview of common concerns to check for during sample preparation and image acquisition 25 | * - 📄 Fluorescence microscopy - avoiding the pitfalls {cite}`Brown2007-ou` 26 | - [link](https://journals.biologists.com/jcs/article/120/10/1703/29404/Fluorescence-microscopy-avoiding-the-pitfalls) 27 | - Short overview of some of the most common pitfalls for beginners to fluorescence microscopy 28 | * - 📄 Tutorial: guidance for quantitative confocal microscopy {cite}`Jonkman2020-bo` 29 | - [link](https://doi.org/10.1038/s41596-020-0313-9) 30 | - Step-by-step guidance on practical considerations for sample preparation, acquisition, and image analysis; primarily though not exclusively aimed at users of confocal microscopy 31 | * - 📄 Best practices and tools for reporting reproducible fluorescence microscopy methods {cite}`Montero_Llopis2021-nb` 32 | - [link](https://www.nature.com/articles/s41592-021-01156-w) 33 | - Guidelines and resources for accurate reporting of the most common fluorescence light microscopy techniques, emphasizing the impact of accurate microscopy metadata on data interpretation. 34 | * - 📄 Believing is seeing - the deceptive influence of bias in quantitative microscopy{cite}`Lee2024-zu` 35 | - [link](https://doi.org/10.1242/jcs.261567) 36 | - Thoughtful review on technological and especially psychological factors that can lead to biased microscopy results 37 | * - 🎥 iBiology Microscopy Short Course 38 | - [link](https://www.youtube.com/watch?v=4c5ILWQmqRY&list=PLQFc-Dxlf4pSRaEk8Xi9BzS0r8-LYmwRQ) 39 | - An 8 hour video series consisting of 14 videos introducting major concepts in microscopy. A longer course with >70 videos is also available. 40 | * - 🎥 Microcourses 41 | - [link](https://www.youtube.com/@Microcourses) 42 | - Videos about microscopy from the microscopy cores at Harvard Medical School 43 | * - 🌐 Advanced Imaging Center 44 | - [link](https://www.aicjanelia.org/apply) 45 | - Access to the state of the art microscopy instruments and imaging experts 46 | * - 🌐 Africa Microscopy Initiative 47 | - [link](https://www.microscopy.africa/ ) 48 | - Access to advanced microscopes, molecular biology and cell culture equipment for scientists in Africa 49 | * - 🌐 Euro-Bioimaging 50 | - [link](https://www.eurobioimaging.eu) 51 | - Access to microcopy instruments and training for scientists in Europe 52 | ``` 53 | 54 | -------------------------------------------------------------------------------- /02_Sample_acquisition/_notinyet_Setting_up.md: -------------------------------------------------------------------------------- 1 | # Setting up your acquisition 2 | 3 | ## Introduction 4 | 5 | -------------------------------------------------------------------------------- /03_Image_analysis/Colocalization.md: -------------------------------------------------------------------------------- 1 | # Colocalization 2 | 3 | (content/colocalization)= 4 | ## What is colocalization? 5 | 6 | Colocalization is when two or more different labels (e.g., eGFP and mCherry) spatially overlap in your image (also called co-occurrence). Another component of colocalization is that the fluorescent labels often correlate in intensity (i.e., pixels with brighter eGFP also have brighter mCherry). It is very important to measure colocalization quantitatively–**do not just trust your eyes!** 7 | 8 | It is also important to recognize that co-ocurrence does not _necessarily_ imply interaction. 9 | 10 | ```{margin} 11 | As an example, it is possible for two people to work in the same building and never interact. 12 | ``` 13 | 14 | ```{figure} ../images/colocalization.png 15 | --- 16 | alt: degrees of colocalization 17 | width: 100% 18 | align: center 19 | name: colocalization-fig 20 | --- 21 | **Colocalization is about intensity and spatial overlap of labels** 22 | ``` 23 | 24 |
25 | 26 | ````{dropdown} 📏 How do I measure it? 27 | 28 | There are two main branches for how to look at colocalization: Object-based and correlation-based. 29 | 30 | * **Object-based colocalization** is appropriate when you want to be able to say something about a fraction of objects being positive for multiple labels (e.g., 99% of eGFP+ cells were also mCherry+). Here’s a sample workflow: 31 | 32 | ```{mermaid} 33 | flowchart LR 34 | A[Raw image Label #1] -->|Segmentation| B((Identified objects \n eGFP+ cells)) 35 | C[Raw image Label #2] --> |Segmentation| D((Identified objects \n mCherry+ cells)) 36 | 37 | B & D -->E(Measure overlap per cell \n if overlap > threshold %, say colocalized )--> G(Fraction of eGFP+ cells also mCherry+) 38 | E --> H(Fraction of mCherry+ cells also eGFP+) 39 | 40 | classDef empty width:0px,height:0px; 41 | 42 | style A fill:#D0F1E3,stroke:#57CC99 43 | style B fill:#D0F1E3,stroke:#57CC99 44 | 45 | style C fill:#FFF4d6,stroke:#FFBE0B 46 | 47 | style C fill:#FFD6E8,stroke:#F5006A 48 | style D fill:#FFD6E8,stroke:#F5006A 49 | ``` 50 | 51 | * **Correlation-based colocalization** is more appropriate when the labels you’re measuring are not found in discrete objects or when you predict that the signal in the labels should correlate. Correlation-based colocalization is simpler to measure as it does not require any {term}`segmentation` of objects. Pearson correlation coefficients are readily measurable in most image analysis softwares (e.g., FIJI, CellProfiler, etc.). 52 | ```` 53 | 54 | ````{dropdown} ⚠️ Where can things go wrong? 55 | * **Not having adequate controls** (e.g., single label controls where only one fluorescent label is present). Noise, uneven illumination, and other technical artifacts can cause correlation between two channels 56 | * **Not correcting for shift between channels** It’s common to have some degree of shift between different imaging channels due to differences in optics (e.g., different filter cubes). Not correcting for this shift (e.g., by measuring it and applying the corresponding correction to the channels) can limit your ability to detect colocalization. 57 | * **Bleedthrough** Sometimes signal from one fluorescent channel bleeds into another, which can falsely increase your detected colocalization. This happens most commonly with fluorophores that are similar in spectra (e.g., GFP and YFP). This is caused by fluorophore in one channel being weakly excited by light used to excite a different fluorophore and the resulting emitted fluorescence makes it through the emission filter (e.g., your green objects show up in the yellow channel as well). Assess this with single label controls. 58 | * **Improper interpretation of your colocalization metric** The details of the metric chosen here are very important - they vary widely in terms of their inclusion of background pixels, their sensitivity to signal-to-noise, etc. Consultation with an expert and the inclusion of proper controls can help you be assured that your measurement is truly what you think it is. 59 | ```` 60 | 61 | ```{dropdown} 📚🤷‍♀️ Where can I learn more? 62 | 63 | * 🔢 [Theoretical background on colocalization](https://svi.nl/ColocalizationTheory) 64 | * 📄 [Image co-localization - co-occurrence versus correlation](https://journals.biologists.com/jcs/article/131/3/jcs211847/77151/Image-co-localization-co-occurrence-versus) {cite}`Aaron2018-qi` 65 | ``` 66 | -------------------------------------------------------------------------------- /03_Image_analysis/Common_types_of_analysis.md: -------------------------------------------------------------------------------- 1 | # Common types of analysis 2 | 3 | In this section, we detail information and tips about some common, very useful types of image analysis. We first describe two aspects of morphological analysis. **Morphology** is the study of the appearance, form, and structure of an object and morphological measurements include those based on object **shape** (e.g. cell area) as well as **intensity** (e.g. mean brightness of GFP). After describing shape-based and intensity-based analyses, we also present tips for measuring **colocalization**, **tracking objects**, and **classifying objects**. 4 | -------------------------------------------------------------------------------- /03_Image_analysis/Data_management.md: -------------------------------------------------------------------------------- 1 | # Data management and sharing 2 | 3 | ## What is it? 4 | 5 | Both journals and scientific funders have placed more emphasis in recent years on the fact that it is critical to save both the raw data generated during the course of scientific discovery as well as the workflows used to process such data. While mandates to publicly deposit raw image data have recently gone into place in several countries, it can be difficult for researchers to know where to store images, code, and metadata associated with their bioimaging experiments. 6 | 7 | ````{dropdown} 🤔 What are my options? 8 | 9 | There are many options for storing image data in online repositories. These services make it easy to share and reuse data. The best option will depend on the size of the dataset, the budget for storage, whether there is related non-image data, and how much metadata is available for the dataset. Some options are summarized below: 10 | 11 | ```{figure} ../images/data_management.png 12 | --- 13 | alt: Comparison of various data respositories 14 | width: 100% 15 | align: center 16 | name: data-repository-chart 17 | --- 18 | **Options for storing bioimaging data** Figure by Beth Cimini (2023) [Source](https://doi.org/10.5281/zenodo.7628604) 19 | ``` 20 | ```` 21 | 22 | ```{dropdown} ⚠️ Where can things go wrong? 23 | 24 | * **Not storing original versions of images**. It is critical that the raw image data be saved and stored. It is very important that these files are not compressed formats (e.g., '.jpeg') or modified from the original files on which analysis was performed. If files are modified, measurements will change and the analysis pipeline will not be reproducible to anyone else. 25 | 26 | * **Necessary imaging metadata is unavailable**. In order to properly calibrate measurement data, it's critical that information like pixel size (e.g., in microns), the microscope manufacturer and model, and acquisition settings are included alongside the data. If this isn't included, it will be very difficult to reproduce results or use the combine the data with other datasets. 27 | 28 | ``` 29 | 30 | ```{dropdown} 📚🤷‍♀️ Where can I learn more? 31 | 32 | * 🌐 [Zenodo](https://zenodo.org/) 33 | * 🌐 [Figshare](https://figshare.com) 34 | * 🌐 [Dryad](https://datadryad.org) 35 | * 🌐 [Bioimage Archive](https://www.ebi.ac.uk/bioimage-archive/) {cite}`Hartley2022-mt` 36 | * 🌐 [Image Data Resource (IDR)](https://idr.openmicroscopy.org/) {cite}`Williams2017-yy` 37 | * 🌐 [BBBC](https://bbbc.broadinstitute.org/) {cite}`Ljosa2012-fr` 38 | * 🌐 [Cell Painting Gallery](https://registry.opendata.aws/cellpainting-gallery/) 39 | 40 | ``` 41 | 42 | -------------------------------------------------------------------------------- /03_Image_analysis/Intensity.md: -------------------------------------------------------------------------------- 1 | # Intensity measurements 2 | 3 | ## What are intensity measurements? 4 | Intensity refers to the brightness of signal for a fluorescent label. Using intensity measurements, we can infer a relative amount of fluorophore or stain. So for instance, if you have a protein tagged with a fluorophore, you can measure the intensity of that fluorophore to get a relative measure of how much protein is present in your sample. Intensity measurements include the following (non-exhaustive) and can be measured within an image, in a object like a cell, in subregions of an object: 5 | * **Mean intensity**: the average intensity across all pixels 6 | * **Integrated intensity**: the sum of pixel intensities, a proxy for the total amount of that marker in an object 7 | * **Texture measurements**: the smoothness of the intensities 8 | 9 |
10 | 11 | ````{dropdown} 📏 How do I measure it? 12 | 13 | Intensity is relatively straightforward to measure, but can be quite tricky to do _correctly_ (see below). We strongly suggest you contact an image analysis expert before proceeding with this type of analysis because there are so many places things can go wrong. In general, you want to measure on either raw images, or illumination-corrected images, but in general with minimal {term}`image processing`. Illumination-correction is a form of {term}`image processing` to compensate for the uneven pattern of illumination produced by most light sources where the middle of the field of illumination is brighter than the edges. Then intensity measurements can be made in any standard image analysis software, either across the whole image or in identified objects. See below for an example workflow: 14 | 15 | ```{mermaid} 16 | flowchart LR 17 | A[Raw image] -->|"Correct uneven illumination\n (optional, but best practice)" | B[Corrected image]-->|Segmentation|C((Identified objects \n e.g., cells)) 18 | 19 | B -->|Measure intensity| E(Image-level intensity \nmeasurements) 20 | C -->|Measure intensity| F(Object-level intensity \nmeasurements) 21 | 22 | classDef empty width:0px,height:0px; 23 | 24 | style A fill:#D0F1E3,stroke:#57CC99 25 | style B fill:#D0F1E3,stroke:#57CC99 26 | 27 | style C fill:#FFF4d6,stroke:#FFBE0B 28 | 29 | style C fill:#FFD6E8,stroke:#F5006A 30 | ``` 31 | ```` 32 | 33 | ````{dropdown} ⚠️ Where can things go wrong? 34 | ```{margin} 35 | To understand saturation another way, imagine you’re trying to measure average male height with a 2 meter tape measure. If our sample contains men that are taller than 2 meters, we can’t tell _how much taller_ than 6 feet they are; they’re like saturated pixels that exceed the intensity we can detect. This saturation of our measurement tool means we can’t accurately report average height. 36 | ``` 37 | 38 | * **Saturation** Saturated pixels are so bright their intensity values max out our detector (camera). If you have saturated pixels in the cells you’re trying to measure, you really can’t do most intensity measurements. This is because for saturated pixels, you don’t know how bright they really are, just that they’re brighter than you can detect. There are some intensity measurements that are robust to some saturation. For example, the median intensity of an image won’t be affected by saturation unless you have >½ the image saturated. But measurements like mean intensity will be affected by saturation. 39 | 40 | * **Inadequate controls** In most cases, the exact intensity measures you get don’t mean anything biologically in isolation. It’s only by comparison of conditions that we can generate some biological insight. A control condition is therefore **very** important to compare to your experimental condition. 41 | 42 | * **Not matching imaging conditions across experimental conditions** Because intensity measures are affected by exposure time, light source intensity, and other factors, it’s very important to match imaging settings across your samples. Relatedly, you should make sure you don’t separate imaging your experimental and control conditions to different days if this can be in any way avoided. Fluorophores can become dimmer over time in samples, which complicates interpretation if different sample types were imaged on different days. 43 | 44 | ```` 45 | 46 | ```{dropdown} 📚🤷‍♀️ Where can I learn more? 47 | 48 | * 🎓 [Neubias training resource on intensity measures](https://neubias.github.io/training-resources/measure_intensities/index.html) 49 | 50 | ``` 51 | -------------------------------------------------------------------------------- /03_Image_analysis/Introduction.md: -------------------------------------------------------------------------------- 1 | # Introduction 2 | 3 | Microscopy images are inherently quantitative, which makes them a very powerful data source. As a biologist, image analysis allows you to translate these numbers into insights that answer biological questions. For our purposes, **image analysis** is the process of measuring aspects of biological phenomena captured in microscopy images. Microscopy images are already _inherently quantitative_ in that they are matrices (i.e., grids) of numbers. However, image analysis is the process of turning these raw numbers into biologically interpretable measurements. Image analysis typically involves a series of steps that can be collected into a pipeline or analysis workflow. A simple example workflow is shown below: 4 | 5 | ```{mermaid} 6 | 7 | flowchart LR 8 | A[Raw image] -->|Illumination correction| B[Corrected image] 9 | B -->|Segmentation| C((Identified objects \n e.g., cells, nuclei)) 10 | C -->|Measure size and shape| D(Size and shape measurements \n e.g., Average cell area) 11 | 12 | B & C-->|Measure intensity|G(Intensity measurements \n e.g., Average eGFP intensity) 13 | classDef empty width:0px,height:0px; 14 | 15 | style G fill:#DCC7FA, stroke:#8338EC 16 | 17 | style C fill:#FFF4d6,stroke:#FFBE0B 18 | 19 | style A fill:#FFD6E8,stroke:#F5006A 20 | style B fill:#FFD6E8,stroke:#F5006A 21 | 22 | style D fill:#D6E6FF,stroke:#3A86FF 23 | style G fill:#D6E6FF,stroke:#3A86FF 24 | ``` 25 | 26 | The specifics of your workflow depend on your biological question. Below we present a few common types of analysis for fluorescence microscopy experiments. For each, we’ll explain key ideas to understand before you begin, common pitfalls, and links to a few key resources to learn more. We encourage you to think about your analysis strategy even before beginning sample preparation. While not always possible, speaking with an image analysis expert{cite}`Cimini2024-uh` in your local core facility or asking a question on the [image.sc](https://image.sc) forum _before you begin_ can save you a ton of time and headache when it comes to designing an image analysis strategy. Some general concepts are also covered in a recent short review{cite}`. 27 | 28 | Note that "automated" and "quantified" are not at all the same as "accurate" "unbiased" - see {cite}`Jost2019-nx` and {cite}`Lee2024-zu` for further treatment of these issues. -------------------------------------------------------------------------------- /03_Image_analysis/Resources.md: -------------------------------------------------------------------------------- 1 | # Resources for learning more 2 | 3 | ```{list-table} 4 | :header-rows: 1 5 | :name: image-analysis-resource-table 6 | 7 | * - **Resource Name** 8 | - **Link** 9 | - **Brief description** 10 | * - 🌐 Image.sc {cite}`Rueden2019-qp` 11 | - [link](https://forum.image.sc/) 12 | - Discussion forum for bioimage analysis software 13 | * - 🌐 GloBIAS Bioimage Analyst Database 14 | - [link](https://www.globias.org/resources/bioimage-analyst-db) 15 | - Find the friendly local bioimage analyst near you! 16 | * - 🌐 Peter Bankhead’s Intro to Bioimage Analysis 17 | - [link](https://bioimagebook.github.io/) 18 | - Guide for absolute beginners to image analysis, including embedded questions/answers, exercises with Python and ImageJ, and videos to check understanding 19 | * - 📖 Bioimage Data Analysis {cite}`Miura2016-wq` 20 | - [link](https://analyticalscience.wiley.com/do/10.1002/was.00050003/full/bioimagedataanalysis.pdf) 21 | - A free online textbook introducing various topics by Bioimage Analysis experts, edited by Kota Miura 22 | * - 📄 Reproducible image handling and analysis {cite}`Miura2021-mb` 23 | - [link](https://www.embopress.org/doi/full/10.15252/embj.2020105889) 24 | - An article reviewing major pitfalls in image handling and how to avoid them and create reproducible analysis workflows 25 | * - 📄 Made to measure: an introduction to quantification in microscopy data 26 | - [link](https://arxiv.org/abs/2302.01657#) {cite}`Culley2023-dj` 27 | - An article describing several common classes of measurements made in microscopy data, as well as technical factors that may affect the results 28 | * - 🌐 Metrics Reloaded {cite}`Maier-Hein2024-cp,Reinke2024-aj,reinke2023common` 29 | - [link](https://metrics-reloaded.dkfz.de/) 30 | - An interactive guide to choosing the right metric for your scientific question 31 | * - 📄 A Hitchhiker's guide through the bio-image analysis software universe {cite}`Haase2022-ad` 32 | - [link](https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14451) 33 | - An article that gives guidance and a glossary of available image analysis software and packages 34 | * - 🌐 BioImage Informatics Index 35 | - [link](https://biii.eu/) 36 | - Repository platform for searching bioimage analysis tools and workflows based on the problem, method or software of choice 37 | * - 🎥 iBiology Bioimage Analysis video series 38 | - [link](https://youtu.be/1xo4vi6Ub4I) 39 | - Video series that introduces Bioimage analysis, including overviews of {term}`image processing`, {term}`segmentation`, tracking, making and interpreting measurements, tips and pitfalls 40 | * - 🌐 Bioimage ANalysis Desktop (BAND) 41 | - [link](https://band.embl.de) 42 | - Access to virtual desktops allowing access to bioimage analysis software from a browser 43 | * - 🌐 Galaxy Imaging Node 44 | - [link](https://imaging.usegalaxy.eu/) 45 | - A Galaxy node prepopulated with a number of open-source image analysis tools and workflows, making it easy to create and share reproducible FAIR workflows 46 | * - 🌐 Image Analysis Training Resources 47 | - [link](https://neubias.github.io/training-resources/index.html) 48 | - Image analysis traning resources collected by NEUBIAS, styled based on The Carpentries 49 | * - 🌐 Bioimage Analysis AwesomeList 50 | - [link](https://github.com/hallvaaw/awesome-biological-image-analysis) 51 | - A curated [AwesomeList](https://github.com/sindresorhus/awesome) of resources related to bioimage analysis 52 | * - 🌐 Bioimage Analysis Notebooks 53 | - [link](https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/) 54 | - A collection of Python Jupyter notebooks for BioImageAnalysis, GPU-accelerated image processing, bio-image data science and more 55 | * - 📄 Believing is seeing - the deceptive influence of bias in quantitative microscopy{cite}`Lee2024-zu` 56 | - [link](https://doi.org/10.1242/jcs.261567) 57 | - Thoughtful review on technological and especially psychological factors that can lead to biased microscopy results 58 | ``` 59 | -------------------------------------------------------------------------------- /03_Image_analysis/Shape.md: -------------------------------------------------------------------------------- 1 | # Size and Shape measurements 2 | 3 | ## What are size measurements? 4 | Size measurements describe the dimensions of objects in your image. Common size measurements include: 5 | 6 | * **Area**: the 2D space an object takes up in the image or the 3D surface area of an object 7 | * **Volume**: the 3D space an object takes up in a 3D image 8 | * **Perimeter**: the distance around the edge of an object 9 | 10 | ## What are shape measurements? 11 | Shape measurements describe the 2D or 3D form of objects in our sample. Common shape measurements include: 12 | 13 | * **Circularity**: How round vs. elongated an object is. Formally defined as $circularity = 4pi*{area}/{perimeter}^2$ where 1 is a perfect circle and circularity <1 is a more elongated polygon. 14 | * **Solidity**: how dense vs. wispy/holey an object is. Formally defined as $solidity = area/convex area$ where _convex area_ is akin to the area inside a shape formed by stretching a rubber band around the object. 15 | 16 |
17 | 18 | ```{dropdown} 📏 How do I measure it? 19 | 20 | After segmenting an image to locate the pixels belonging to different objects, morphology can be measured readily in many image analysis softwares, like FIJI and CellProfiler. For example, in {term}`Fiji`, after identifying your objects as {term}`ROIs`, be sure to **Analyze > Set Measurements…** and select “Shape Descriptors” then simply measure your {term}`ROIs` with **Analyze > Measure**. In CellProfiler, this is accomplished using the module MeasureObjectSizeShape. 21 | ``` 22 | 23 | ```{dropdown} ⚠️ Where can things go wrong? 24 | 25 | * **Not understanding the limitations of your images**. All biological structures are 3D, but we often analyze 2D images. Often this is still very useful! But the larger and more complex your objects (e.g., neurons in a tissue section), the more limited a 2D view becomes. 26 | * **Failing to use calibrated units**. Be sure to properly calibrate your images and present final measurements in microns (or similar units). If measuring 3D images, be sure to take into account the z-step, which is likely larger than the xy pixel size. 27 | ``` 28 | 29 | ```{dropdown} 📚🤷‍♀️ Where can I learn more? 30 | 31 | * 📄 [Current Methods and Pipelines for Image-Based Quantitation of Nuclear Shape and Nuclear Envelope Abnormalities](https://www.mdpi.com/2073-4409/11/3/347/htm) {cite}`Janssen2022-bm` 32 | * 🌐 [Description of morphological measurements made by CellProfiler](https://cellprofiler-manual.s3.amazonaws.com/CellProfiler-4.2.4/modules/measurement.html#id20) 33 | * 🎓 [Plain language description of various morphological measures by Michael Wirth](http://www.cyto.purdue.edu/cdroms/micro2/content/education/wirth10.pdf) 34 | ``` 35 | -------------------------------------------------------------------------------- /03_Image_analysis/SpecificUseSoftware.md: -------------------------------------------------------------------------------- 1 | # Specific Use Software 2 | 3 | Tools on this page tend to be extremely good at certain tasks, but are less intended for a wide range of use cases. For tools with broader areas of focus, see the [General Use Software](./GeneralUseSoftware.md) page. 4 | 5 | (content/cellpose)= 6 | ## logo Cellpose 7 | 8 | [Cellpose](https://www.cellpose.org/) {cite}`Stringer2021-uq` is a {term}`segmentation` algorithm, it provides a graphical user interface that allows users to use trained models or train their own using their images and annotations. 9 | 10 | 11 | ```{dropdown} What type of image analysis problem is it best at? 12 | 13 | Object {term}`segmentation`, most trained models are for cell {term}`segmentation` but could be applied to segment other similar objects 14 | ``` 15 | 16 | ```{dropdown} What are its disadvantages? 17 | 18 | 19 | 20 | * Its use requires some computational knowledge. 21 | * Training a new model requires manual annotation correction that can be time consuming, but is likely less time consuming than other methods of training models. 22 | ``` 23 | 24 | ```{dropdown} How to download/install and learn more? 25 | 26 | 27 | 28 | * 🌐 [Installation instructions](https://cellpose.readthedocs.io/en/latest/installation.html) 29 | * 🎥 [How to use tutorial](https://www.youtube.com/watch?v=5qANHWoubZU) 30 | ``` 31 | 32 | (content/ilastik)= 33 | ## logo ilastik 34 | 35 | [ilastik](https://www.ilastik.org/) {cite}`Berg2019-no` is a tool for interactive image classification, {term}`segmentation` and analysis. It leverages machine-learning algorithms to perform pixel and object-level classification. Using it requires no experience in {term}`image processing`. 36 | 37 | 38 | ```{dropdown} What type of image analysis problem is it best at? 39 | 40 | It can be used for both instance {term}`segmentation` and semantic {term}`segmentation`. It does also perform {term}`segmentation` and tracking, though with somewhat fewer tunable parameters than some other tools offer. 41 | ``` 42 | 43 | ```{dropdown} What are its disadvantages? 44 | 45 | 46 | 47 | * Sometimes loading or exporting images can require a bit of troubleshooting to get the dimensions correct. 48 | * ilastik is limited by your computer’s RAM so training a model with lots of features or working with very large images is likely to slow you down. 49 | ``` 50 | 51 | ```{dropdown} How to download/install and learn more? 52 | 53 | To download ilastik: 54 | 55 | 56 | 57 | * 🌐 [ilastik download ](https://www.ilastik.org/download.html) 58 | 59 | For documentation examples and tutorials. 60 | 61 | 62 | 63 | * 🌐 [User guide](https://www.ilastik.org/documentation/index.html#user-documentation) 64 | ``` 65 | 66 | (content/piximi)= 67 | ## logo Piximi 68 | 69 | 70 | [Piximi](https://www.piximi.app/) {cite}`Moser2024-vt` is an application for annotation and classification that runs entirely from your browser and requires no installation and minimal setup. 71 | 72 | 73 | ```{dropdown} What type of image analysis problem is it best at? 74 | 75 | Piximi can do image classification using machine learning 76 | ``` 77 | 78 | ```{dropdown} What are its disadvantages? 79 | 80 | 81 | 82 | * It is still in the developing phases and some of its proposed features are not available yet 83 | ``` 84 | 85 | ```{dropdown} How to download/install and learn more? 86 | 87 | 88 | 89 | * 🌐 [Piximi website ](https://www.piximi.app/) 90 | * 🌐 [Piximi user guide ](https://documentation.piximi.app/intro.html) 91 | ``` -------------------------------------------------------------------------------- /03_Image_analysis/Tracking.md: -------------------------------------------------------------------------------- 1 | # Object tracking 2 | 3 | ## What is tracking? 4 | Tracking, or _object tracking_, refers to the ability to estimate the location of objects in motion from one frame of video to the next. Practically, object tracking in microscopy involves identifying your objects in each frame of your video, then relating objects from frame to frame to be able to identify the same cell as it moves in space. 5 | 6 |
7 | 8 | ```{dropdown} 📏 How do I measure it? 9 | 10 | There are several options for tracking objects, like the [TrackMate](https://imagej.net/plugins/trackmate/) {cite}`Tinevez2017-fb` plugin in Fiji, but tracking is somewhat more complex to setup than the previous analyses. In addition to just identifying objects in the movie/time series, tracking also allows you to identify splitting (e.g. mitosis) and merging events. There are many measurements that come out of tracking, including spatial measures like where the objects move to, speed measurements, distance traveled (length of track), and rate of splitting events (e.g., mitotic events) and merging events. 11 | 12 | ``` 13 | 14 | ````{dropdown} ⚠️ Where can things go wrong? 15 | * **Poor {term}`segmentation`** If objects are dropping out from frame to frame, this makes it more difficult to track them over time. Accurate {term}`segmentation` is the foundation of good tracking results. This can become more difficult if your objects are also changing in shape or intensity (due to things such as bleaching) over the course of the video. It’s important to find a {term}`segmentation` strategy that can work well across your frames. 16 | * **Inadequate frame rate** If objects are highly dynamic but the images were not taken at a high frequency, tracking can be difficult because objects might have moved too much for the algorithm to relate them from one frame to the next. It is important to match the image acquisition frequency to how dynamic your cells or objects are. 17 | 18 | ```` 19 | 20 | ```{dropdown} 📚🤷‍♀️ Where can I learn more? 21 | 22 | * 📄 [Computerized Cell Tracking](https://www.sciencedirect.com/science/article/pii/S2468502X20300711) 23 | * 🌐 [TrackMate Manual](https://imagej.net/media/plugins/trackmate/trackmate-manual.pdf) 24 | ``` 25 | -------------------------------------------------------------------------------- /03_Image_analysis/_notinyet_Common_pitfalls.md: -------------------------------------------------------------------------------- 1 | # Common pitfalls 2 | 3 | In addition to the mistakes we summarize for common image analysis tasks, here we present a general list of common mistakes for beginners to image analysis. For each, we explain why this is a problem and make suggestions for how to avoid these issues. 4 | 5 | 1. Changing your image bit depth 6 | 7 | Let's say you've opened your image in {term}`Fiji` and you want to process it in some way (e.g., maximum intensity projection, splitting channels, etc.) before saving it out to measure somewhere else. You go to `Image` > `Type` > `RGB (Color)` since you want a color image to import into your next analysis software and then save the resulting image. What's the problem with this? By making this change, even if the image looks exactly the same to your eyes, you've actually inadvertently changed the intensity values quite a bit! Let's take a look at an example. In Fiji there are several built-in example images. Let's open neuron.tif (you can follow along by going to `File` > `Open Samples...` > `Neuron (5 channels)`. 8 | 9 | Here's how the image opens. There are 5 channels, but let's just look at the first one: 10 | ![image](https://user-images.githubusercontent.com/28116530/206793825-364998d4-6043-4b1d-8438-0a5b37b97232.png) 11 | 12 | 13 | -------------------------------------------------------------------------------- /03_Image_analysis/_notinyet_Image_processing.md: -------------------------------------------------------------------------------- 1 | # Image Processing 2 | 3 | ## Introduction 4 | 5 | -------------------------------------------------------------------------------- /03_Image_analysis/_notinyet_Image_segmentation.md: -------------------------------------------------------------------------------- 1 | # Image Segmentation 2 | 3 | ## Introduction 4 | 5 | -------------------------------------------------------------------------------- /04_Data_presentation/Introduction.md: -------------------------------------------------------------------------------- 1 | # Introduction 2 | 3 | When presenting microscopy image data in biology and biomedicine, it's important to consider the quality of the images, the labeling and annotation of important features, and the overall visual appeal. This also applies to diagrams and plots which convey numerical data derived from microscopy images. Chart types must in addition be suitable for the specific data that is being conveyed to not mislead audiences. This applies to image data in scientific posters, talk-slides, or publications. 4 | 5 | -------------------------------------------------------------------------------- /04_Data_presentation/Resources.md: -------------------------------------------------------------------------------- 1 | # Resources for learning more 2 | 3 | ```{list-table} 4 | :header-rows: 1 5 | :name: data-presentation-resource-table 6 | 7 | * - **Resource Name** 8 | - **Link** 9 | - **Brief description** 10 | * - 📄 Creating clear and informative image-based figures for scientific publications {cite}`Jambor2021-qe` 11 | - [link](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001161 ) 12 | - Review article on how to create accessible, fair scientific figures, including guidelines for microscopy images 13 | * - 📄 Community-developed checklists for publishing images and image analysis {cite}`Schmied2024-et` 14 | - [link](https://doi.org/10.1038/s41592-023-01987-9) 15 | - A paper recommending checklists and best practices for publishing image data. [It also has a JupyterBook](https://quarep-limi.github.io/WG12_checklists_for_image_publishing/intro.html) 16 | * - 📖 Modern Statistics for Modern Biology {cite}`Holmes2019-no` 17 | - [link](https://www.huber.embl.de/msmb/) 18 | - Online statistics for biologists textbook with code examples (in R) 19 | 20 | ``` 21 | 22 | 26 | -------------------------------------------------------------------------------- /04_Data_presentation/_notinyet_Presentation_graphs.md: -------------------------------------------------------------------------------- 1 | # Presentation of graphs 2 | 3 | ## Introduction 4 | 5 | -------------------------------------------------------------------------------- /BBBC_montage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/COBA-NIH/MicroscopyForBeginnersReferenceGuide/76e48826ded54fdd505832e7328b78c31f1c3f07/BBBC_montage.png -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- 1 | date-released: "2023-jun-01" 2 | repository-code: "https://github.com/COBA-NIH/MicroscopyForBeginnersReferenceGuide" 3 | message: "If you use this software, please cite it as below." 4 | title: "A biologist's guide to planning and performing quantitative 5 | bioimaging experiments" 6 | cff-version: "1.2.0" 7 | authors: 8 | - family-names: "Senft" 9 | given-names: "Rebecca A" 10 | orcid: "https://orcid.org/0000-0003-0081-4170" 11 | - family-names: "Diaz-Rohrer" 12 | given-names: "Barbara" 13 | orcid: "https://orcid.org/0000-0002-4748-7077" 14 | - family-names: "Colarusso" 15 | given-names: "Pina" 16 | orcid: "https://orcid.org/0000-0002-2875-3579" 17 | - family-names: "Swift" 18 | given-names: "Lucy" 19 | orcid: "https://orcid.org/0000-0003-2447-1774" 20 | - family-names: "Jamali" 21 | given-names: "Nasim" 22 | orcid: "https://orcid.org/0000-0003-1851-6585" 23 | - family-names: "Jambor" 24 | given-names: "Helena" 25 | orcid: "https://orcid.org/0000-0003-3397-1842" 26 | - family-names: "Pengo" 27 | given-names: "Thomas" 28 | orcid: "https://orcid.org/0000-0002-9632-918X" 29 | - family-names: "Brideau" 30 | given-names: "Craig" 31 | orcid: "https://orcid.org/0000-0001-7992-0413" 32 | - family-names: "Llopis" 33 | given-names: "Paula Montero" 34 | orcid: "https://orcid.org/0000-0002-5983-2296" 35 | - family-names: "Uhlmann" 36 | given-names: "Virginie" 37 | orcid: "https://orcid.org/0000-0002-2859-9241" 38 | - family-names: "Kirk" 39 | given-names: "Jason" 40 | - family-names: "Gonzales" 41 | given-names: "Kevin Andrew" 42 | orcid: "https://orcid.org/0000-0001-7418-965X" 43 | - family-names: "Bankhead" 44 | given-names: "Peter" 45 | orcid: "https://orcid.org/0000-0003-4851-8813" 46 | - family-names: "Evans 3rd" 47 | given-names: "Edward L" 48 | orcid: "https://orcid.org/0000-0003-0278-4227" 49 | - family-names: "Giang" 50 | given-names: "William" 51 | - family-names: "Haase" 52 | given-names: "Robert" 53 | orcid: "https://orcid.org/0000-0001-5949-2327" 54 | - family-names: "Costa Cruz" 55 | given-names: "Mario" 56 | orcid: "https://orcid.org/0000-0003-0362-1323" 57 | - family-names: "Schätz" 58 | given-names: "Martin" 59 | orcid: "https://orcid.org/0000-0003-0931-4017" 60 | - family-names: "Eliceiri" 61 | given-names: "Kevin W" 62 | orcid: "https://orcid.org/0000-0001-8678-670X" 63 | - family-names: "Cimini" 64 | given-names: "Beth A" 65 | orcid: "https://orcid.org/0000-0001-9640-9318" 66 | preferred-citation: 67 | type: "article" 68 | publisher: 69 | name: "Public Library of Science" 70 | date-released: "2023-jun-01" 71 | volume: "21" 72 | journal: "PLoS Biol." 73 | title: "A biologist's guide to planning and performing quantitative 74 | bioimaging experiments" 75 | publisher: "Public Library of Science" 76 | start: "e3002167" 77 | authors: 78 | - family-names: "Senft" 79 | given-names: "Rebecca A" 80 | orcid: "https://orcid.org/0000-0003-0081-4170" 81 | - family-names: "Diaz-Rohrer" 82 | given-names: "Barbara" 83 | orcid: "https://orcid.org/0000-0002-4748-7077" 84 | - family-names: "Colarusso" 85 | given-names: "Pina" 86 | orcid: "https://orcid.org/0000-0002-2875-3579" 87 | - family-names: "Swift" 88 | given-names: "Lucy" 89 | orcid: "https://orcid.org/0000-0003-2447-1774" 90 | - family-names: "Jamali" 91 | given-names: "Nasim" 92 | orcid: "https://orcid.org/0000-0003-1851-6585" 93 | - family-names: "Jambor" 94 | given-names: "Helena" 95 | orcid: "https://orcid.org/0000-0003-3397-1842" 96 | - family-names: "Pengo" 97 | given-names: "Thomas" 98 | orcid: "https://orcid.org/0000-0002-9632-918X" 99 | - family-names: "Brideau" 100 | given-names: "Craig" 101 | orcid: "https://orcid.org/0000-0001-7992-0413" 102 | - family-names: "Llopis" 103 | given-names: "Paula Montero" 104 | orcid: "https://orcid.org/0000-0002-5983-2296" 105 | - family-names: "Uhlmann" 106 | given-names: "Virginie" 107 | orcid: "https://orcid.org/0000-0002-2859-9241" 108 | - family-names: "Kirk" 109 | given-names: "Jason" 110 | - family-names: "Gonzales" 111 | given-names: "Kevin Andrew" 112 | orcid: "https://orcid.org/0000-0001-7418-965X" 113 | - family-names: "Bankhead" 114 | given-names: "Peter" 115 | orcid: "https://orcid.org/0000-0003-4851-8813" 116 | - family-names: "Evans 3rd" 117 | given-names: "Edward L" 118 | orcid: "https://orcid.org/0000-0003-0278-4227" 119 | - family-names: "Eliceiri" 120 | given-names: "Kevin W" 121 | orcid: "https://orcid.org/0000-0001-8678-670X" 122 | - family-names: "Cimini" 123 | given-names: "Beth A" 124 | orcid: "https://orcid.org/0000-0001-9640-9318" 125 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | BSD 3-Clause License 2 | 3 | Copyright (c) 2023, Center for Open Bioimage Analysis 4 | 5 | Redistribution and use in source and binary forms, with or without 6 | modification, are permitted provided that the following conditions are met: 7 | 8 | 1. Redistributions of source code must retain the above copyright notice, this 9 | list of conditions and the following disclaimer. 10 | 11 | 2. Redistributions in binary form must reproduce the above copyright notice, 12 | this list of conditions and the following disclaimer in the documentation 13 | and/or other materials provided with the distribution. 14 | 15 | 3. Neither the name of the copyright holder nor the names of its 16 | contributors may be used to endorse or promote products derived from 17 | this software without specific prior written permission. 18 | 19 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 20 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 21 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 22 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 23 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 24 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 25 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 26 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 27 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 28 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 29 | -------------------------------------------------------------------------------- /QuantitativeBioimaging.md: -------------------------------------------------------------------------------- 1 | # Quantitative Bioimaging 2 | 3 | ## What do we mean by quantitative bioimaging? 4 | 5 | While microscopy was by necessity a qualitative science for most of its history, we now live in an era where microscope images can be used to precisely quantify observable phenotypes. 6 | 7 | The ability to draw accurate quantitative answers from these experiments relies on certain best practices being followed. If one can confidently say "Yes" to each of the following 4 questions, one is likely to be able to quantify their sample. 8 | 9 | - Have I prepared my sample in a way that minimizes technical artifacts and lets me understand exactly which molecule(s) I am observing? 10 | - Have I conducted my microscopy so that I minimize technical artifacts and am in the quantitative range of the detector attached to my microscope? 11 | - Have I selected analysis metric(s) that truly answer my biological question and measured them in a way that minimizes technical artifacts? 12 | - Have I chosen appropriate statistical comparisons and data presentation approaches so that the distribution of my metric(s) can be fairly compared across samples, answering my biolgical question? 13 | 14 | Answering each of these questions requires thought, expertise, and often a fair amount of trial and error; it can feel overwhelming to grapple with all the technical aspects and caveats present in a bioimaging experiment. These questions **_can_** be answered, however, though often not in a single pass - [continuous optimization through multiple rounds of answering these questions](qb-decision-cycle) is typically needed for best results. 15 | 16 | The resources linked in this guide are designed to help a reader develop skills in each or all of these areas, helping them get the most from their microscopy data. 17 | 18 | ```{figure} images/sdr_fig1.png 19 | --- 20 | alt: cycle 21 | width: 80% 22 | align: center 23 | name: qb-decision-cycle 24 | --- 25 | **The decision cycle of quantitative bioimaging {cite}`Senft2023-zy`** Reproduced from Senft and Diaz-Rohrer et al, [**_A biologist’s guide to planning and performing quantitative bioimaging experiments_**](https://doi.org/10.1371/journal.pbio.3002167). 26 | ``` -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | [![DOI](https://zenodo.org/badge/568954740.svg)](https://zenodo.org/doi/10.5281/zenodo.10675608) 2 | 3 | # Microscopy For Beginners Reference Guide 4 | Website :link: :arrow_right: [CLICK HERE](https://bioimagingguide.org) 5 | 6 | A Beginner's guide to microscopy, from sample prep to acquisition, image analysis, and data interpretation. See the paper [here](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167) (original preprint [here](https://doi.org/10.5281/zenodo.7439283)) 7 | -------------------------------------------------------------------------------- /_build/gettext/QuantitativeBioimaging.pot: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2024 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , YEAR. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=UTF-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | 19 | #: ../../QuantitativeBioimaging.md:1 20 | msgid "Quantitative Bioimaging" 21 | msgstr "" 22 | 23 | #: ../../QuantitativeBioimaging.md:3 24 | msgid "What do we mean by quantitative bioimaging?" 25 | msgstr "" 26 | 27 | #: ../../QuantitativeBioimaging.md:5 28 | msgid "While microscopy was by necessity a qualitative science for most of its history, we now live in an era where microscope images can be used to precisely quantify observable phenotypes." 29 | msgstr "" 30 | 31 | #: ../../QuantitativeBioimaging.md:7 32 | msgid "The ability to draw accurate quantitative answers from these experiments relies on certain best practices being followed. If one can confidently say \"Yes\" to each of the following 4 questions, one is likely to be able to quantify their sample." 33 | msgstr "" 34 | 35 | #: ../../QuantitativeBioimaging.md:9 36 | msgid "Have I prepared my sample in a way that minimizes technical artifacts and lets me understand exactly which molecule(s) I am observing?" 37 | msgstr "" 38 | 39 | #: ../../QuantitativeBioimaging.md:10 40 | msgid "Have I conducted my microscopy so that I minimize technical artifacts and am in the quantitative range of the detector attached to my microscope?" 41 | msgstr "" 42 | 43 | #: ../../QuantitativeBioimaging.md:11 44 | msgid "Have I selected analysis metric(s) that truly answer my biological question and measured them in a way that minimizes technical artifacts?" 45 | msgstr "" 46 | 47 | #: ../../QuantitativeBioimaging.md:12 48 | msgid "Have I chosen appropriate statistical comparisons and data presentation approaches so that the distribution of my metric(s) can be fairly compared across samples, answering my biolgical question?" 49 | msgstr "" 50 | 51 | #: ../../QuantitativeBioimaging.md:14 52 | msgid "Answering each of these questions requires thought, expertise, and often a fair amount of trial and error; it can feel overwhelming to grapple with all the technical aspects and caveats present in a bioimaging experiment. These questions **_can_** be answered, however, though often not in a single pass - [continuous optimization through multiple rounds of answering these questions](qb-decision-cycle) is typically needed for best results." 53 | msgstr "" 54 | 55 | #: ../../QuantitativeBioimaging.md:16 56 | msgid "The resources linked in this guide are designed to help a reader develop skills in each or all of these areas, helping them get the most from their microscopy data." 57 | msgstr "" 58 | 59 | #: ../../QuantitativeBioimaging.md:25 60 | msgid "cycle" 61 | msgstr "" 62 | 63 | #: ../../QuantitativeBioimaging.md:25 64 | msgid "**The decision cycle of quantitative bioimaging {cite}`Senft2023-zy`** Reproduced from Senft and Diaz-Rohrer et al, [**_A biologist’s guide to planning and performing quantitative bioimaging experiments_**](https://doi.org/10.1371/journal.pbio.3002167)." 65 | msgstr "" 66 | -------------------------------------------------------------------------------- /_build/gettext/README.pot: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2024 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , YEAR. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=UTF-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | 19 | #: ../../README.md:1 20 | msgid "[![DOI](https://zenodo.org/badge/568954740.svg)](https://zenodo.org/doi/10.5281/zenodo.10675608)" 21 | msgstr "" 22 | 23 | #: ../../README.md:1 24 | msgid "DOI" 25 | msgstr "" 26 | 27 | #: ../../README.md:3 28 | msgid "Microscopy For Beginners Reference Guide" 29 | msgstr "" 30 | 31 | #: ../../README.md:4 32 | msgid "Website :link: :arrow_right: [CLICK HERE](https://bioimagingguide.org)" 33 | msgstr "" 34 | 35 | #: ../../README.md:6 36 | msgid "A Beginner's guide to microscopy, from sample prep to acquisition, image analysis, and data interpretation. See the paper [here](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167) (original preprint [here](https://doi.org/10.5281/zenodo.7439283))" 37 | msgstr "" 38 | -------------------------------------------------------------------------------- /_build/gettext/bibliography.pot: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2024 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , YEAR. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=UTF-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | 19 | #: ../../bibliography.md:1 20 | msgid "Bibliography" 21 | msgstr "" 22 | -------------------------------------------------------------------------------- /_build/gettext/community_resources.pot: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2024 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , YEAR. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2025-05-23 21:07+0000\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=UTF-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | 19 | #: ../../community_resources.md:1 20 | msgid "Community resources" 21 | msgstr "" 22 | 23 | #: ../../community_resources.md:3 24 | msgid "Below are globally and locally available community resources" 25 | msgstr "" 26 | 27 | #: ../../community_resources.md:5 28 | msgid "Global and online resources" 29 | msgstr "" 30 | 31 | #: ../../community_resources.md:12 32 | #: ../../community_resources.md:41 33 | msgid "**Resource Name**" 34 | msgstr "" 35 | 36 | #: ../../community_resources.md:13 37 | #: ../../community_resources.md:42 38 | msgid "**Link**" 39 | msgstr "" 40 | 41 | #: ../../community_resources.md:14 42 | msgid "**Brief description**" 43 | msgstr "" 44 | 45 | #: ../../community_resources.md:15 46 | msgid "Global BioImaging" 47 | msgstr "" 48 | 49 | #: ../../community_resources.md:16 50 | msgid "[link](https://globalbioimaging.org/)" 51 | msgstr "" 52 | 53 | #: ../../community_resources.md:17 54 | msgid "Training resources, working groups, recommendations for standardization and research reproducibility for global bioimaging efforts" 55 | msgstr "" 56 | 57 | #: ../../community_resources.md:18 58 | msgid "GloBIAS" 59 | msgstr "" 60 | 61 | #: ../../community_resources.md:19 62 | msgid "[link](https://www.globias.org/home)" 63 | msgstr "" 64 | 65 | #: ../../community_resources.md:20 66 | msgid "Connections, training, and more for bioimage analysts across the world" 67 | msgstr "" 68 | 69 | #: ../../community_resources.md:21 70 | msgid "Microforum" 71 | msgstr "" 72 | 73 | #: ../../community_resources.md:22 74 | msgid "[link](https://forum.microlist.org/)" 75 | msgstr "" 76 | 77 | #: ../../community_resources.md:23 78 | msgid "Discussion forum for bioimaging sample preparation and acquisition" 79 | msgstr "" 80 | 81 | #: ../../community_resources.md:24 82 | msgid "Scientific Community Image Forum (Image . sc)" 83 | msgstr "" 84 | 85 | #: ../../community_resources.md:25 86 | msgid "[link](https://forum.image.sc/)" 87 | msgstr "" 88 | 89 | #: ../../community_resources.md:26 90 | msgid "Discussion forum for bioimage analysis software {cite}`Rueden2019-qp`" 91 | msgstr "" 92 | 93 | #: ../../community_resources.md:27 94 | msgid "Microtutor" 95 | msgstr "" 96 | 97 | #: ../../community_resources.md:28 98 | msgid "[link](https://microtutor.globalbioimaging.org/)" 99 | msgstr "" 100 | 101 | #: ../../community_resources.md:29 102 | msgid "A fantastic interactive course on fluorescence microscopy, created by the team at [Harvard CITE](https://cite.hms.harvard.edu/)" 103 | msgstr "" 104 | 105 | #: ../../community_resources.md:30 106 | msgid "HMS Nikon Imaging Center \"Favorite References\"" 107 | msgstr "" 108 | 109 | #: ../../community_resources.md:31 110 | msgid "[link](https://nic.med.harvard.edu/fav_references/)" 111 | msgstr "" 112 | 113 | #: ../../community_resources.md:32 114 | msgid "A curated list of references related to many aspects of microscopy and image analysis" 115 | msgstr "" 116 | 117 | #: ../../community_resources.md:35 118 | msgid "Local resources" 119 | msgstr "" 120 | 121 | #: ../../community_resources.md:43 122 | msgid "BioImaging North America (BINA)" 123 | msgstr "" 124 | 125 | #: ../../community_resources.md:44 126 | msgid "[link](https://www.bioimagingnorthamerica.org/)" 127 | msgstr "" 128 | 129 | #: ../../community_resources.md:45 130 | msgid "Latin America BioImaging" 131 | msgstr "" 132 | 133 | #: ../../community_resources.md:46 134 | msgid "[link](https://www.latambioimaging.org/ )" 135 | msgstr "" 136 | 137 | #: ../../community_resources.md:47 138 | msgid "African BioImaging Consortium" 139 | msgstr "" 140 | 141 | #: ../../community_resources.md:48 142 | msgid "[link](https://www.africanbioimaging.org/)" 143 | msgstr "" 144 | 145 | #: ../../community_resources.md:49 146 | msgid "South Africa BioImaging" 147 | msgstr "" 148 | 149 | #: ../../community_resources.md:50 150 | msgid "[link](https://www.sabioimaging.org/)" 151 | msgstr "" 152 | 153 | #: ../../community_resources.md:51 154 | msgid "Euro-bioimaging" 155 | msgstr "" 156 | 157 | #: ../../community_resources.md:52 158 | msgid "[link](https://www.eurobioimaging.eu/)" 159 | msgstr "" 160 | 161 | #: ../../community_resources.md:53 162 | msgid "Advanced BioImaging support (Japan)" 163 | msgstr "" 164 | 165 | #: ../../community_resources.md:54 166 | msgid "[link](https://www.nibb.ac.jp/abis/)" 167 | msgstr "" 168 | 169 | #: ../../community_resources.md:55 170 | msgid "Microscopy Australia" 171 | msgstr "" 172 | 173 | #: ../../community_resources.md:56 174 | msgid "[link](https://micro.org.au/)" 175 | msgstr "" 176 | 177 | #: ../../community_resources.md:57 178 | msgid "Canada BioImaging" 179 | msgstr "" 180 | 181 | #: ../../community_resources.md:58 182 | msgid "[link](https://www.canadabioimaging.org/)" 183 | msgstr "" 184 | 185 | #: ../../community_resources.md:59 186 | msgid "Singapore Microscopy Infrastructure Network" 187 | msgstr "" 188 | 189 | #: ../../community_resources.md:60 190 | msgid "[link](https://www.singascope.sg/)" 191 | msgstr "" 192 | -------------------------------------------------------------------------------- /_build/gettext/contributors.pot: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2024 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , YEAR. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 15:22+0000\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=UTF-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | 19 | #: ../../contributors.md:1 20 | msgid "Contributing to this guide" 21 | msgstr "" 22 | 23 | #: ../../contributors.md:3 24 | msgid "Contributors" 25 | msgstr "" 26 | 27 | #: ../../contributors.md:5 28 | msgid "The original material for this book was created as part of the paper \"[**_A biologist’s guide to planning and performing quantitative bioimaging experiments_**](https://doi.org/10.1371/journal.pbio.3002167)\" {cite}`Senft2023-zy`. by Rebecca A. Senft*, Barbara Diaz-Rohrer*, Pina Colarusso, Lucy Swift, Nasim Jamali, Helena Jambor, Thomas Pengo, Craig Brideau, Paula Montero Llopis, Virginie Uhlmann, Jason Kirk, Kevin Andrew Gonzales, Peter Bankhead, Edward L. Evans III, Kevin W Eliceiri and Beth A. Cimini." 29 | msgstr "" 30 | 31 | #: ../../contributors.md:7 32 | msgid "This project was initiated by the [Center for Open Bioimage Analysis](https://openbioimageanalysis.org/) .We are grateful to [Bioimaging North America](https://www.bioimagingnorthamerica.org/) (especially its [Image Informatics](https://www.bioimagingnorthamerica.org/image-informatics-wg/) and [Training and Education](https://www.bioimagingnorthamerica.org/te-wg/) Working Groups) for both initial and ongoing support of this project." 33 | msgstr "" 34 | 35 | #: ../../contributors.md:9 36 | msgid "Since this guide has become available, we gratefully acknowledge contributions from the following members of the microscopy and bioimage analysis community!" 37 | msgstr "" 38 | 39 | #: ../../contributors.md:10 40 | msgid "William Giang" 41 | msgstr "" 42 | 43 | #: ../../contributors.md:11 44 | msgid "Robert Haase" 45 | msgstr "" 46 | 47 | #: ../../contributors.md:13 48 | msgid "Improvements to the build and maintenance system for this book have come from" 49 | msgstr "" 50 | 51 | #: ../../contributors.md:14 52 | msgid "Pete Bankhead" 53 | msgstr "" 54 | 55 | #: ../../contributors.md:16 56 | msgid "How can I become a contributor?" 57 | msgstr "" 58 | 59 | #: ../../contributors.md:18 60 | msgid "Please feel free to open an [issue](https://github.com/broadinstitute/MicroscopyForBeginnersReferenceGuide/issues) or pull request to contribute! We hope for this to be a living document reflecting the best practices and resources available." 61 | msgstr "" 62 | 63 | #: ../../contributors.md:20 64 | msgid "We currently also offer a [Google Form](https://docs.google.com/forms/d/e/1FAIpQLScWQbemviI2OkvVkeTKUOozAzKNndcZpXIB_nE0qFMl72lqvQ/viewform) for contributions, though note these may be responded to more slowly than direct contributions to the GitHub repository." 65 | msgstr "" 66 | 67 | #: ../../contributors.md:23 68 | msgid "Translation" 69 | msgstr "" 70 | 71 | #: ../../contributors.md:25 72 | msgid "This guide is available in [English](https://www.bioimagingguide.org) as well as [Czech](https://cs.bioimagingguide.org), [Portuguese](https://pt.bioimagingguide.org), and [Spanish](https://es.bioimagingguide.org)." 73 | msgstr "" 74 | 75 | #: ../../contributors.md:27 76 | msgid "Work is underway to translate this guide into other languages - translation is planned or has begun in French, German, Finnish, Italian, Japanese, Polish, and Farsi. To help translate into one of these languages, or another language not listed here, please contact bcimini AT broadinstitute DOT org." 77 | msgstr "" 78 | 79 | #: ../../contributors.md:29 80 | msgid "Translations are gratefully acknowledged from:" 81 | msgstr "" 82 | 83 | #: ../../contributors.md:31 84 | msgid "Czech : Martin Schätz" 85 | msgstr "" 86 | 87 | #: ../../contributors.md:32 88 | msgid "Portuguese: Mario Costa Cruz" 89 | msgstr "" 90 | 91 | #: ../../contributors.md:33 92 | msgid "Spanish: Mariana De Niz" 93 | msgstr "" 94 | -------------------------------------------------------------------------------- /_build/gettext/genindex.pot: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2024 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , YEAR. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=UTF-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | 19 | #: ../../genindex.md:1 20 | msgid "Index" 21 | msgstr "" 22 | -------------------------------------------------------------------------------- /_build/gettext/welcome.pot: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2024 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , YEAR. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=UTF-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | 19 | #: ../../welcome.md:1 20 | msgid "" 21 | msgstr "" 22 | 23 | #: ../../welcome.md:1 24 | msgid "Sample Preparation" 25 | msgstr "" 26 | 27 | #: ../../welcome.md:1 28 | msgid "Sample Acquisition" 29 | msgstr "" 30 | 31 | #: ../../welcome.md:1 32 | msgid "Image Analysis and Data Handling" 33 | msgstr "" 34 | 35 | #: ../../welcome.md:1 36 | msgid "Data Interpretation" 37 | msgstr "" 38 | 39 | #: ../../welcome.md:1 40 | msgid "Additional Resources" 41 | msgstr "" 42 | 43 | #: ../../welcome.md:1 44 | msgid "Welcome" 45 | msgstr "" 46 | 47 | #: ../../welcome.md:3 48 | msgid "Welcome to the world of bioimaging and bioimage analysis! 🎉" 49 | msgstr "" 50 | 51 | #: ../../welcome.md:11 52 | msgid "BBBC image montage" 53 | msgstr "" 54 | 55 | #: ../../welcome.md:11 56 | msgid "**Montage of fluorescence microscopy images from [BBBC](https://bbbc.broadinstitute.org/) {cite}`Ljosa2012-fr` (Broad Institute).** Images shown are from experiments BBBC007, BBBC008, BBBC034, BBBC038, BBBC039, and BBBC020 from left to right, top to bottom." 57 | msgstr "" 58 | 59 | #: ../../welcome.md:13 60 | msgid "What is this book?" 61 | msgstr "" 62 | 63 | #: ../../welcome.md:15 64 | msgid "This book is a companion website to our paper \"[**_A biologist’s guide to planning and performing quantitative bioimaging experiments_**](https://doi.org/10.1371/journal.pbio.3002167)\" {cite}`Senft2023-zy`. Our goal is to provide recommendations and a curated set of resources for biologists looking to understand the factors that impact their fluorescence microscopy experiments." 65 | msgstr "" 66 | 67 | #: ../../welcome.md:17 68 | msgid "This book is a collaborative effort from experts in biology, imaging, image analysis, and data management, interpretation, and presentation. Our tips and recommendations come from real experiences training and working with biologists who are beginners to bioimaging and bioimage analysis. When starting out in a new field, you often don't know what you don't know. Here we provide context, tips for avoiding common beginner errors, and a focused list of high-quality, open source resources (full list available [here](bibliography)). We use icons to indicate the type of resource:" 69 | msgstr "" 70 | 71 | #: ../../welcome.md:39 72 | msgid "What **isn't** this book?" 73 | msgstr "" 74 | 75 | #: ../../welcome.md:41 76 | msgid "This book is **not** meant to be an exhaustive list of all resources. Many others have curated excellent such resources(see [here](https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14451) {cite}`Haase2022-ad` and [here](https://www.bioimagingnorthamerica.org/training-education-resources/) and [here](https://biii.eu/) {cite}`Paul-Gilloteaux2021-vw`). Our goal is to create a more streamlined, beginner-accessible guide." 77 | msgstr "" 78 | 79 | #: ../../welcome.md:42 80 | msgid "This book is **not** a protocol or step by step guide, though certain resources we link to might be. Each subsection from sample prep to data interpretation are massive topics that we can't exhaustively cover in a guide for beginners." 81 | msgstr "" 82 | 83 | #: ../../welcome.md:45 84 | msgid "How to use this book:" 85 | msgstr "" 86 | 87 | #: ../../welcome.md:46 88 | msgid "Please select a section using the navigation panel on the left to get started or begin with sample preparation by clicking the \"Next\" button below ↘️." 89 | msgstr "" 90 | 91 | #: ../../welcome.md:48 92 | msgid "Most sections will guide you through individual subtopics using some or all of the following list of questions:" 93 | msgstr "" 94 | 95 | #: ../../welcome.md:49 96 | msgid "What is it?" 97 | msgstr "" 98 | 99 | #: ../../welcome.md:50 100 | msgid "What are my options?" 101 | msgstr "" 102 | 103 | #: ../../welcome.md:51 104 | msgid "How do I do it?" 105 | msgstr "" 106 | 107 | #: ../../welcome.md:52 108 | msgid "Where can things go wrong?" 109 | msgstr "" 110 | 111 | #: ../../welcome.md:53 112 | msgid "Where can I learn more? (links to resources)" 113 | msgstr "" 114 | 115 | #: ../../welcome.md:55 116 | msgid "Which questions are used and the exact phrasing may vary by section, but we hope this structure helps guide users to a deeper understanding of each subtopic." 117 | msgstr "" 118 | 119 | #: ../../welcome.md:57 120 | msgid "What if my resource/topic is not included?" 121 | msgstr "" 122 | 123 | #: ../../welcome.md:58 124 | msgid "Please feel free to open an [issue](https://github.com/broadinstitute/MicroscopyForBeginnersReferenceGuide/issues) or pull request to contribute! We hope for this to be a living document reflecting the best practices and resources available." 125 | msgstr "" 126 | -------------------------------------------------------------------------------- /_config.yml: -------------------------------------------------------------------------------- 1 | # Book settings 2 | # Learn more at https://jupyterbook.org/customize/config.html 3 | 4 | title: Microscopy for Beginners reference guide 5 | author: "" 6 | copyright : "2024" # Copyright year to be placed in the footer 7 | logo : "logo.png" # A path to the book logo 8 | # Patterns to skip when building the book. Can be glob-style (e.g. "*skip.ipynb") 9 | exclude_patterns : [_build, Thumbs.db, .DS_Store, "**.ipynb_checkpoints"] 10 | # Auto-exclude files not in the toc 11 | only_build_toc_files : false 12 | 13 | 14 | # Force re-execution of notebooks on each build. 15 | # See https://jupyterbook.org/content/execute.html 16 | execute: 17 | execute_notebooks: force 18 | 19 | # Define the name of the latex output file for PDF builds 20 | latex: 21 | latex_documents: 22 | targetname: book.tex 23 | 24 | # Add a bibtex file so that we can create citations 25 | bibtex_bibfiles: 26 | - references.bib 27 | 28 | # Information about where the book exists on the web 29 | repository: 30 | url: https://github.com/broadinstitute/MicroscopyForBeginnersReferenceGuide # Online location of your book 31 | branch: main # Which branch of the repository should be used when creating links (optional) 32 | 33 | # Add GitHub buttons to your book 34 | # See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository 35 | html: 36 | use_issues_button: true 37 | use_repository_button: true 38 | use_edit_page_button: true # Whether to add an "edit this page" button to pages. If `true`, repository information in repository: must be filled in 39 | favicon : "favicon.png" # A path to a favicon image 40 | google_analytics_id: G-LDZ3MLCB50 41 | comments: 42 | hypothesis: true 43 | extra_footer: | 44 |

45 | English česky português español 46 |

47 | 48 | sphinx: 49 | extra_extensions: 50 | - sphinxcontrib.mermaid 51 | config: 52 | bibtex_reference_style: super 53 | locale_dirs: ["locale/"] 54 | gettext_compact: true 55 | -------------------------------------------------------------------------------- /_static/myfile.css: -------------------------------------------------------------------------------- 1 | summary.summary-title.card-header { 2 | font-size: 20px; 3 | padding: 0.75em; 4 | } 5 | 6 | p { 7 | font-weight: 400; 8 | } 9 | h2 { 10 | font-size: 30px; 11 | } 12 | 13 | h3 { 14 | font-size: 24px; 15 | } 16 | 17 | h4 { 18 | font-size: 20px; 19 | } 20 | h3 { 21 | font-size: 18px; 22 | } 23 | h4 { 24 | font-size: 16px; 25 | } 26 | body, h1, h2, h3, h4 ,h5, h6 { 27 | font-family: "HelveticaNeue-Light", "Arial", sans-serif !important; 28 | } 29 | #main-content li { 30 | margin-top: 0px; 31 | padding-top: 0px; 32 | margin-bottom: 4px; 33 | padding-bottom: 4px; 34 | } 35 | .mermaid { 36 | padding-bottom: 30px; 37 | } 38 | 39 | #site-navigation a { 40 | margin-top: 0px; 41 | padding-top: 0px; 42 | margin-bottom: 0px; 43 | padding-bottom: 0px; 44 | } 45 | .toctree-wrapper.compound p,ul { 46 | margin-top: 0px; 47 | padding-top: 0px; 48 | margin-bottom: 0px; 49 | padding-bottom: 0px; 50 | } 51 | li.toctree-l1 { 52 | margin-top: 0px; 53 | padding-top: 0px; 54 | margin-bottom: 0px !important; 55 | padding-bottom: 0px !important; 56 | } 57 | .bd-sidebar { 58 | min-width: 300px; 59 | } 60 | 61 | /* grid text sizing and padding */ 62 | #open-source-software .sd-card-text{ 63 | font-size: 0.9em; 64 | } 65 | #open-source-software .sd-card-body.docutils{ 66 | padding: 0.6em; 67 | } 68 | 69 | /* 70 | #main-content ul.simple { 71 | margin-bottom: 6px; 72 | padding-bottom: 6px 73 | } 74 | .topbar>div { 75 | padding-left: 20px; 76 | } 77 | #navbar-toggler { 78 | position: relative; 79 | } 80 | -------------------------------------------------------------------------------- /_toc.yml: -------------------------------------------------------------------------------- 1 | format: jb-book 2 | root: welcome 3 | defaults: 4 | caption: Default Caption 5 | parts: 6 | - caption: 7 | chapters: 8 | - file: QuantitativeBioimaging 9 | - caption: Sample Preparation 10 | chapters: 11 | - file: 01_Sample_preparation/Introduction 12 | - file: 01_Sample_preparation/Experimental_design 13 | - file: 01_Sample_preparation/Considerations 14 | - file: 01_Sample_preparation/Reproducibility 15 | - file: 01_Sample_preparation/Resources 16 | - caption: Sample Acquisition 17 | chapters: 18 | - file: 02_Sample_acquisition/Introduction 19 | - file: 02_Sample_acquisition/Picking 20 | - file: 02_Sample_acquisition/Practical_considerations 21 | - file: 02_Sample_acquisition/Resources 22 | - caption: Image Analysis and Data Handling 23 | chapters: 24 | - file: 03_Image_analysis/Introduction 25 | - file: 03_Image_analysis/Common_types_of_analysis.md 26 | sections: 27 | - file: 03_Image_analysis/Shape 28 | - file: 03_Image_analysis/Intensity 29 | - file: 03_Image_analysis/Colocalization 30 | - file: 03_Image_analysis/Tracking 31 | - file: 03_Image_analysis/Classification 32 | - file: 03_Image_analysis/Software 33 | sections: 34 | - file: 03_Image_analysis/GeneralUseSoftware 35 | - file: 03_Image_analysis/SpecificUseSoftware 36 | - file: 03_Image_analysis/Data_management 37 | - file: 03_Image_analysis/Resources 38 | - caption: Data Interpretation 39 | chapters: 40 | - file: 04_Data_presentation/Introduction 41 | - file: 04_Data_presentation/Presentation_images 42 | - file: 04_Data_presentation/Statistics 43 | - file: 04_Data_presentation/Resources 44 | - caption: Additional Resources 45 | chapters: 46 | - file: community_resources 47 | - file: contributors 48 | - file: Glossary 49 | - file: bibliography 50 | - file: genindex 51 | -------------------------------------------------------------------------------- /bibliography.md: -------------------------------------------------------------------------------- 1 | # Bibliography 2 | (bibliography)= 3 | ```{bibliography} 4 | :style: unsrt 5 | ``` 6 | 7 | -------------------------------------------------------------------------------- /community_resources.md: -------------------------------------------------------------------------------- 1 | # Community resources 2 | 3 | Below are globally and locally available community resources 4 | 5 | ## Global and online resources 6 | 7 | ```{list-table} 8 | :header-rows: 1 9 | :name: global-resource-table 10 | 11 | * - **Resource Name** 12 | - **Link** 13 | - **Brief description** 14 | * - Global BioImaging 15 | - [link](https://globalbioimaging.org/) 16 | - Training resources, working groups, recommendations for standardization and research reproducibility for global bioimaging efforts 17 | * - GloBIAS 18 | - [link](https://www.globias.org/home) 19 | - Connections, training, and more for bioimage analysts across the world 20 | * - Microforum 21 | - [link](https://forum.microlist.org/) 22 | - Discussion forum for bioimaging sample preparation and acquisition 23 | * - Scientific Community Image Forum (Image . sc) 24 | - [link](https://forum.image.sc/) 25 | - Discussion forum for bioimage analysis software {cite}`Rueden2019-qp` 26 | * - Microtutor 27 | - [link](https://microtutor.globalbioimaging.org/) 28 | - A fantastic interactive course on fluorescence microscopy, created by the team at [Harvard CITE](https://cite.hms.harvard.edu/) 29 | * - HMS Nikon Imaging Center "Favorite References" 30 | - [link](https://nic.med.harvard.edu/fav_references/) 31 | - A curated list of references related to many aspects of microscopy and image analysis 32 | 33 | ``` 34 | 35 | ## Local resources 36 | 37 | ```{list-table} 38 | :header-rows: 1 39 | :name: local-resource-table 40 | 41 | * - **Resource Name** 42 | - **Link** 43 | * - BioImaging North America (BINA) 44 | - [link](https://www.bioimagingnorthamerica.org/) 45 | * - Latin America BioImaging 46 | - [link](https://www.latambioimaging.org/ ) 47 | * - African BioImaging Consortium 48 | - [link](https://www.africanbioimaging.org/) 49 | * - South Africa BioImaging 50 | - [link](https://www.sabioimaging.org/) 51 | * - Euro-bioimaging 52 | - [link](https://www.eurobioimaging.eu/) 53 | * - Advanced BioImaging support (Japan) 54 | - [link](https://www.nibb.ac.jp/abis/) 55 | * - Microscopy Australia 56 | - [link](https://micro.org.au/) 57 | * - Canada BioImaging 58 | - [link](https://www.canadabioimaging.org/) 59 | * - Singapore Microscopy Infrastructure Network 60 | - [link](https://www.singascope.sg/) 61 | ``` 62 | -------------------------------------------------------------------------------- /contributors.md: -------------------------------------------------------------------------------- 1 | # Contributing to this guide 2 | 3 | ## Contributors 4 | 5 | The original material for this book was created as part of the paper "[**_A biologist’s guide to planning and performing quantitative bioimaging experiments_**](https://doi.org/10.1371/journal.pbio.3002167)" {cite}`Senft2023-zy`. by Rebecca A. Senft*, Barbara Diaz-Rohrer*, Pina Colarusso, Lucy Swift, Nasim Jamali, Helena Jambor, Thomas Pengo, Craig Brideau, Paula Montero Llopis, Virginie Uhlmann, Jason Kirk, Kevin Andrew Gonzales, Peter Bankhead, Edward L. Evans III, Kevin W Eliceiri and Beth A. Cimini. 6 | 7 | This project was initiated by the [Center for Open Bioimage Analysis](https://openbioimageanalysis.org/) .We are grateful to [Bioimaging North America](https://www.bioimagingnorthamerica.org/) (especially its [Image Informatics](https://www.bioimagingnorthamerica.org/image-informatics-wg/) and [Training and Education](https://www.bioimagingnorthamerica.org/te-wg/) Working Groups) for both initial and ongoing support of this project. 8 | 9 | Since this guide has become available, we gratefully acknowledge contributions from the following members of the microscopy and bioimage analysis community! 10 | - William Giang 11 | - Robert Haase 12 | 13 | Improvements to the build and maintenance system for this book have come from 14 | - Pete Bankhead 15 | 16 | ## How can I become a contributor? 17 | 18 | Please feel free to open an [issue](https://github.com/broadinstitute/MicroscopyForBeginnersReferenceGuide/issues) or pull request to contribute! We hope for this to be a living document reflecting the best practices and resources available. 19 | 20 | We currently also offer a [Google Form](https://docs.google.com/forms/d/e/1FAIpQLScWQbemviI2OkvVkeTKUOozAzKNndcZpXIB_nE0qFMl72lqvQ/viewform) for contributions, though note these may be responded to more slowly than direct contributions to the GitHub repository. 21 | 22 | 23 | ## Translation 24 | 25 | This guide is available in [English](https://www.bioimagingguide.org) as well as [Czech](https://cs.bioimagingguide.org), [Portuguese](https://pt.bioimagingguide.org), and [Spanish](https://es.bioimagingguide.org). 26 | 27 | Work is underway to translate this guide into other languages - translation is planned or has begun in French, German, Finnish, Italian, Japanese, Polish, and Farsi. To help translate into one of these languages, or another language not listed here, please contact bcimini AT broadinstitute DOT org. 28 | 29 | Translations are gratefully acknowledged from: 30 | 31 | - Czech : Martin Schätz 32 | - Portuguese: Mario Costa Cruz 33 | - Spanish: Mariana De Niz 34 | -------------------------------------------------------------------------------- /favicon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/COBA-NIH/MicroscopyForBeginnersReferenceGuide/76e48826ded54fdd505832e7328b78c31f1c3f07/favicon.png -------------------------------------------------------------------------------- /genindex.md: -------------------------------------------------------------------------------- 1 | # Index -------------------------------------------------------------------------------- /images/10TipsHowToNotLieWithImages.png: -------------------------------------------------------------------------------- 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license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=utf-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | "Generated-By: Babel 2.13.1\n" 19 | 20 | #: ../../README.md:1 21 | msgid "[![DOI](https://zenodo.org/badge/568954740.svg)](https://zenodo.org/doi/10.5281/zenodo.10675608)" 22 | msgstr "" 23 | 24 | #: ../../README.md:1 25 | msgid "DOI" 26 | msgstr "" 27 | 28 | #: ../../README.md:3 29 | msgid "Microscopy For Beginners Reference Guide" 30 | msgstr "" 31 | 32 | #: ../../README.md:4 33 | msgid "Website :link: :arrow_right: [CLICK HERE](https://bioimagingguide.org)" 34 | msgstr "" 35 | 36 | #: ../../README.md:6 37 | msgid "" 38 | "A Beginner's guide to microscopy, from sample prep to acquisition, image " 39 | "analysis, and data interpretation. See the paper " 40 | "[here](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167)" 41 | " (original preprint [here](https://doi.org/10.5281/zenodo.7439283))" 42 | msgstr "" 43 | 44 | #~ msgid "" 45 | #~ "A Beginner's guide to microscopy, from" 46 | #~ " sample prep to acquisition, image " 47 | #~ "analysis, and data interpretation. See " 48 | #~ "the related preprint " 49 | #~ "[here](https://doi.org/10.5281/zenodo.7439283)" 50 | #~ msgstr "" 51 | 52 | -------------------------------------------------------------------------------- /locale/cs/LC_MESSAGES/bibliography.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , YEAR. 5 | # 6 | # Translators: 7 | # Beth Cimini, 2023 8 | # 9 | #, fuzzy 10 | msgid "" 11 | msgstr "" 12 | "Project-Id-Version: Python\n" 13 | "Report-Msgid-Bugs-To: \n" 14 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 15 | "PO-Revision-Date: 2023-05-02 18:49+0000\n" 16 | "Last-Translator: Beth Cimini, 2023\n" 17 | "Language-Team: Czech (https://app.transifex.com/center-for-open-bioimage-analysis/teams/169123/cs/)\n" 18 | "MIME-Version: 1.0\n" 19 | "Content-Type: text/plain; charset=UTF-8\n" 20 | "Content-Transfer-Encoding: 8bit\n" 21 | "Language: cs\n" 22 | "Plural-Forms: nplurals=4; plural=(n == 1 && n % 1 == 0) ? 0 : (n >= 2 && n <= 4 && n % 1 == 0) ? 1: (n % 1 != 0 ) ? 2 : 3;\n" 23 | 24 | #: ../../bibliography.md:1 25 | msgid "Bibliography" 26 | msgstr "Bibliografie" 27 | -------------------------------------------------------------------------------- /locale/cs/LC_MESSAGES/genindex.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , YEAR. 5 | # 6 | # Translators: 7 | # Beth Cimini, 2023 8 | # 9 | #, fuzzy 10 | msgid "" 11 | msgstr "" 12 | "Project-Id-Version: Python\n" 13 | "Report-Msgid-Bugs-To: \n" 14 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 15 | "PO-Revision-Date: 2023-05-02 18:49+0000\n" 16 | "Last-Translator: Beth Cimini, 2023\n" 17 | "Language-Team: Czech (https://app.transifex.com/center-for-open-bioimage-analysis/teams/169123/cs/)\n" 18 | "MIME-Version: 1.0\n" 19 | "Content-Type: text/plain; charset=UTF-8\n" 20 | "Content-Transfer-Encoding: 8bit\n" 21 | "Language: cs\n" 22 | "Plural-Forms: nplurals=4; plural=(n == 1 && n % 1 == 0) ? 0 : (n >= 2 && n <= 4 && n % 1 == 0) ? 1: (n % 1 != 0 ) ? 2 : 3;\n" 23 | 24 | #: ../../genindex.md:1 25 | msgid "Index" 26 | msgstr "Index" 27 | -------------------------------------------------------------------------------- /locale/de/LC_MESSAGES/QuantitativeBioimaging.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-06-28 07:29-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: de\n" 15 | "Language-Team: de \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.12.1\n" 21 | 22 | #: ../../QuantitativeBioimaging.md:1 23 | msgid "Quantitative Bioimaging" 24 | msgstr "" 25 | 26 | #: ../../QuantitativeBioimaging.md:3 27 | msgid "What do we mean by quantitative bioimaging?" 28 | msgstr "" 29 | 30 | #: ../../QuantitativeBioimaging.md:5 31 | msgid "" 32 | "While microscopy was by necessity a qualitative science for most of its " 33 | "history, we now live in an era where microscope images can be used to " 34 | "precisely quantify observable phenotypes." 35 | msgstr "" 36 | 37 | #: ../../QuantitativeBioimaging.md:7 38 | msgid "" 39 | "The ability to draw accurate quantitative answers from these experiments " 40 | "relies on certain best practices being followed. If one can confidently " 41 | "say \"Yes\" to each of the following 4 questions, one is likely to be " 42 | "able to quantify their sample." 43 | msgstr "" 44 | 45 | #: ../../QuantitativeBioimaging.md:9 46 | msgid "" 47 | "Have I prepared my sample in a way that minimizes technical artifacts and" 48 | " lets me understand exactly which molecule(s) I am observing?" 49 | msgstr "" 50 | 51 | #: ../../QuantitativeBioimaging.md:10 52 | msgid "" 53 | "Have I conducted my microscopy so that I minimize technical artifacts and" 54 | " am in the quantitative range of the detector attached to my microscope?" 55 | msgstr "" 56 | 57 | #: ../../QuantitativeBioimaging.md:11 58 | msgid "" 59 | "Have I selected analysis metric(s) that truly answer my biological " 60 | "question and measured them in a way that minimizes technical artifacts?" 61 | msgstr "" 62 | 63 | #: ../../QuantitativeBioimaging.md:12 64 | msgid "" 65 | "Have I chosen appropriate statistical comparisons and data presentation " 66 | "approaches so that the distribution of my metric(s) can be fairly " 67 | "compared across samples, answering my biolgical question?" 68 | msgstr "" 69 | 70 | #: ../../QuantitativeBioimaging.md:14 71 | msgid "" 72 | "Answering each of these questions requires thought, expertise, and often " 73 | "a fair amount of trial and error; it can feel overwhelming to grapple " 74 | "with all the technical aspects and caveats present in a bioimaging " 75 | "experiment. These questions **_can_** be answered, however, though often " 76 | "not in a single pass - [continuous optimization through multiple rounds " 77 | "of answering these questions](qb-decision-cycle) is typically needed for " 78 | "best results." 79 | msgstr "" 80 | 81 | #: ../../QuantitativeBioimaging.md:16 82 | msgid "" 83 | "The resources linked in this guide are designed to help a reader develop " 84 | "skills in each or all of these areas, helping them get the most from " 85 | "their microscopy data." 86 | msgstr "" 87 | 88 | #: ../../QuantitativeBioimaging.md:25 89 | msgid "cycle" 90 | msgstr "" 91 | 92 | #: ../../QuantitativeBioimaging.md:25 93 | msgid "" 94 | "**The decision cycle of quantitative bioimaging {cite}`Senft2023-zy`** " 95 | "Reproduced from Senft and Diaz-Rohrer et al, [**_A biologist’s guide to " 96 | "planning and performing quantitative bioimaging " 97 | "experiments_**](https://doi.org/10.1371/journal.pbio.3002167)." 98 | msgstr "" 99 | 100 | -------------------------------------------------------------------------------- /locale/de/LC_MESSAGES/README.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: de\n" 15 | "Language-Team: de \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.13.1\n" 21 | 22 | #: ../../README.md:1 23 | msgid "[![DOI](https://zenodo.org/badge/568954740.svg)](https://zenodo.org/doi/10.5281/zenodo.10675608)" 24 | msgstr "" 25 | 26 | #: ../../README.md:1 27 | msgid "DOI" 28 | msgstr "" 29 | 30 | #: ../../README.md:3 31 | msgid "Microscopy For Beginners Reference Guide" 32 | msgstr "" 33 | 34 | #: ../../README.md:4 35 | msgid "Website :link: :arrow_right: [CLICK HERE](https://bioimagingguide.org)" 36 | msgstr "" 37 | 38 | #: ../../README.md:6 39 | msgid "" 40 | "A Beginner's guide to microscopy, from sample prep to acquisition, image " 41 | "analysis, and data interpretation. See the paper " 42 | "[here](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167)" 43 | " (original preprint [here](https://doi.org/10.5281/zenodo.7439283))" 44 | msgstr "" 45 | 46 | -------------------------------------------------------------------------------- /locale/de/LC_MESSAGES/bibliography.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: de\n" 15 | "Language-Team: de \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.12.1\n" 21 | 22 | #: ../../bibliography.md:1 23 | msgid "Bibliography" 24 | msgstr "" 25 | 26 | -------------------------------------------------------------------------------- /locale/de/LC_MESSAGES/community_resources.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: de\n" 15 | "Language-Team: de \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.13.1\n" 21 | 22 | #: ../../community_resources.md:1 23 | msgid "Community resources" 24 | msgstr "" 25 | 26 | #: ../../community_resources.md:3 27 | msgid "Below are globally and locally available community resources" 28 | msgstr "" 29 | 30 | #: ../../community_resources.md:5 31 | msgid "Global and online resources" 32 | msgstr "" 33 | 34 | #: ../../community_resources.md:12 ../../community_resources.md:38 35 | msgid "**Resource Name**" 36 | msgstr "" 37 | 38 | #: ../../community_resources.md:13 ../../community_resources.md:39 39 | msgid "**Link**" 40 | msgstr "" 41 | 42 | #: ../../community_resources.md:14 43 | msgid "**Brief description**" 44 | msgstr "" 45 | 46 | #: ../../community_resources.md:15 47 | msgid "Global BioImaging" 48 | msgstr "" 49 | 50 | #: ../../community_resources.md:16 51 | msgid "[link](https://globalbioimaging.org/)" 52 | msgstr "" 53 | 54 | #: ../../community_resources.md:17 55 | msgid "" 56 | "Training resources, working groups, recommendations for standardization " 57 | "and research reproducibility for global bioimaging efforts" 58 | msgstr "" 59 | 60 | #: ../../community_resources.md:18 61 | msgid "GloBIAS" 62 | msgstr "" 63 | 64 | #: ../../community_resources.md:19 65 | msgid "[link](https://www.globias.org/home)" 66 | msgstr "" 67 | 68 | #: ../../community_resources.md:20 69 | msgid "Connections, training, and more for bioimage analysts across the world" 70 | msgstr "" 71 | 72 | #: ../../community_resources.md:21 73 | msgid "Microforum" 74 | msgstr "" 75 | 76 | #: ../../community_resources.md:22 77 | msgid "[link](https://forum.microlist.org/)" 78 | msgstr "" 79 | 80 | #: ../../community_resources.md:23 81 | msgid "Discussion forum for bioimaging sample preparation and acquisition" 82 | msgstr "" 83 | 84 | #: ../../community_resources.md:24 85 | msgid "Scientific Community Image Forum (Image . sc)" 86 | msgstr "" 87 | 88 | #: ../../community_resources.md:25 89 | msgid "[link](https://forum.image.sc/)" 90 | msgstr "" 91 | 92 | #: ../../community_resources.md:26 93 | msgid "Discussion forum for bioimage analysis software {cite}`Rueden2019-qp`" 94 | msgstr "" 95 | 96 | #: ../../community_resources.md:27 97 | msgid "HMS Nikon Imaging Center \"Favorite References\"" 98 | msgstr "" 99 | 100 | #: ../../community_resources.md:28 101 | msgid "[link](https://nic.med.harvard.edu/fav_references/)" 102 | msgstr "" 103 | 104 | #: ../../community_resources.md:29 105 | msgid "" 106 | "A curated list of references related to many aspects of microscopy and " 107 | "image analysis" 108 | msgstr "" 109 | 110 | #: ../../community_resources.md:32 111 | msgid "Local resources" 112 | msgstr "" 113 | 114 | #: ../../community_resources.md:40 115 | msgid "BioImaging North America (BINA)" 116 | msgstr "" 117 | 118 | #: ../../community_resources.md:41 119 | msgid "[link](https://www.bioimagingnorthamerica.org/)" 120 | msgstr "" 121 | 122 | #: ../../community_resources.md:42 123 | msgid "Latin America BioImaging" 124 | msgstr "" 125 | 126 | #: ../../community_resources.md:43 127 | msgid "[link](https://www.latambioimaging.org/ )" 128 | msgstr "" 129 | 130 | #: ../../community_resources.md:44 131 | msgid "African BioImaging Consortium" 132 | msgstr "" 133 | 134 | #: ../../community_resources.md:45 135 | msgid "[link](https://www.africanbioimaging.org/)" 136 | msgstr "" 137 | 138 | #: ../../community_resources.md:46 139 | msgid "South Africa BioImaging" 140 | msgstr "" 141 | 142 | #: ../../community_resources.md:47 143 | msgid "[link](https://www.sabioimaging.org/)" 144 | msgstr "" 145 | 146 | #: ../../community_resources.md:48 147 | msgid "Euro-bioimaging" 148 | msgstr "" 149 | 150 | #: ../../community_resources.md:49 151 | msgid "[link](https://www.eurobioimaging.eu/)" 152 | msgstr "" 153 | 154 | #: ../../community_resources.md:50 155 | msgid "Advanced BioImaging support (Japan)" 156 | msgstr "" 157 | 158 | #: ../../community_resources.md:51 159 | msgid "[link](https://www.nibb.ac.jp/abis/)" 160 | msgstr "" 161 | 162 | #: ../../community_resources.md:52 163 | msgid "Microscopy Australia" 164 | msgstr "" 165 | 166 | #: ../../community_resources.md:53 167 | msgid "[link](https://micro.org.au/)" 168 | msgstr "" 169 | 170 | #: ../../community_resources.md:54 171 | msgid "Canada BioImaging" 172 | msgstr "" 173 | 174 | #: ../../community_resources.md:55 175 | msgid "[link](https://www.canadabioimaging.org/)" 176 | msgstr "" 177 | 178 | #: ../../community_resources.md:56 179 | msgid "Singapore Microscopy Infrastructure Network" 180 | msgstr "" 181 | 182 | #: ../../community_resources.md:57 183 | msgid "[link](https://www.singascope.sg/)" 184 | msgstr "" 185 | 186 | -------------------------------------------------------------------------------- /locale/de/LC_MESSAGES/genindex.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: de\n" 15 | "Language-Team: de \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.12.1\n" 21 | 22 | #: ../../genindex.md:1 23 | msgid "Index" 24 | msgstr "" 25 | 26 | -------------------------------------------------------------------------------- /locale/de/LC_MESSAGES/welcome.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-06-28 07:29-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: de\n" 15 | "Language-Team: de \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.12.1\n" 21 | 22 | #: ../../welcome.md:1 23 | msgid "Sample Preparation" 24 | msgstr "" 25 | 26 | #: ../../welcome.md:1 27 | msgid "Sample Acquisition" 28 | msgstr "" 29 | 30 | #: ../../welcome.md:1 31 | msgid "Image Analysis and Data Handling" 32 | msgstr "" 33 | 34 | #: ../../welcome.md:1 35 | msgid "Data Interpretation" 36 | msgstr "" 37 | 38 | #: ../../welcome.md:1 39 | msgid "Additional Resources" 40 | msgstr "" 41 | 42 | #: ../../welcome.md:1 43 | msgid "Welcome" 44 | msgstr "" 45 | 46 | #: ../../welcome.md:3 47 | msgid "Welcome to the world of bioimaging and bioimage analysis! 🎉" 48 | msgstr "" 49 | 50 | #: ../../welcome.md:11 51 | msgid "BBBC image montage" 52 | msgstr "" 53 | 54 | #: ../../welcome.md:11 55 | msgid "" 56 | "**Montage of fluorescence microscopy images from " 57 | "[BBBC](https://bbbc.broadinstitute.org/) {cite}`Ljosa2012-fr` (Broad " 58 | "Institute).** Images shown are from experiments BBBC007, BBBC008, " 59 | "BBBC034, BBBC038, BBBC039, and BBBC020 from left to right, top to bottom." 60 | msgstr "" 61 | 62 | #: ../../welcome.md:13 63 | msgid "What is this book?" 64 | msgstr "" 65 | 66 | #: ../../welcome.md:15 67 | msgid "" 68 | "This book is a companion website to our paper \"[**_A biologist’s guide " 69 | "to planning and performing quantitative bioimaging " 70 | "experiments_**](https://doi.org/10.1371/journal.pbio.3002167)\" " 71 | "{cite}`Senft2023-zy`. Our goal is to provide recommendations and a " 72 | "curated set of resources for biologists looking to understand the factors" 73 | " that impact their fluorescence microscopy experiments." 74 | msgstr "" 75 | 76 | #: ../../welcome.md:17 77 | msgid "" 78 | "This book is a collaborative effort from experts in biology, imaging, " 79 | "image analysis, and data management, interpretation, and presentation. " 80 | "Our tips and recommendations come from real experiences training and " 81 | "working with biologists who are beginners to bioimaging and bioimage " 82 | "analysis. When starting out in a new field, you often don't know what you" 83 | " don't know. Here we provide context, tips for avoiding common beginner " 84 | "errors, and a focused list of high-quality, open source resources (full " 85 | "list available [here](bibliography)). We use icons to indicate the type " 86 | "of resource:" 87 | msgstr "" 88 | 89 | #: ../../welcome.md:39 90 | msgid "What **isn't** this book?" 91 | msgstr "" 92 | 93 | #: ../../welcome.md:41 94 | msgid "" 95 | "This book is **not** meant to be an exhaustive list of all resources. " 96 | "Many others have curated excellent such resources(see " 97 | "[here](https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14451) " 98 | "{cite}`Haase2022-ad` and [here](https://www.bioimagingnorthamerica.org" 99 | "/training-education-resources/) and [here](https://biii.eu/) {cite}`Paul-" 100 | "Gilloteaux2021-vw`). Our goal is to create a more streamlined, beginner-" 101 | "accessible guide." 102 | msgstr "" 103 | 104 | #: ../../welcome.md:42 105 | msgid "" 106 | "This book is **not** a protocol or step by step guide, though certain " 107 | "resources we link to might be. Each subsection from sample prep to data " 108 | "interpretation are massive topics that we can't exhaustively cover in a " 109 | "guide for beginners." 110 | msgstr "" 111 | 112 | #: ../../welcome.md:45 113 | msgid "How to use this book:" 114 | msgstr "" 115 | 116 | #: ../../welcome.md:46 117 | msgid "" 118 | "Please select a section using the navigation panel on the left to get " 119 | "started or begin with sample preparation by clicking the \"Next\" button " 120 | "below ↘️." 121 | msgstr "" 122 | 123 | #: ../../welcome.md:48 124 | msgid "" 125 | "Most sections will guide you through individual subtopics using some or " 126 | "all of the following list of questions:" 127 | msgstr "" 128 | 129 | #: ../../welcome.md:49 130 | msgid "What is it?" 131 | msgstr "" 132 | 133 | #: ../../welcome.md:50 134 | msgid "What are my options?" 135 | msgstr "" 136 | 137 | #: ../../welcome.md:51 138 | msgid "How do I do it?" 139 | msgstr "" 140 | 141 | #: ../../welcome.md:52 142 | msgid "Where can things go wrong?" 143 | msgstr "" 144 | 145 | #: ../../welcome.md:53 146 | msgid "Where can I learn more? (links to resources)" 147 | msgstr "" 148 | 149 | #: ../../welcome.md:55 150 | msgid "" 151 | "Which questions are used and the exact phrasing may vary by section, but " 152 | "we hope this structure helps guide users to a deeper understanding of " 153 | "each subtopic." 154 | msgstr "" 155 | 156 | #: ../../welcome.md:57 157 | msgid "What if my resource/topic is not included?" 158 | msgstr "" 159 | 160 | #: ../../welcome.md:58 161 | msgid "" 162 | "Please feel free to open an " 163 | "[issue](https://github.com/broadinstitute/MicroscopyForBeginnersReferenceGuide/issues)" 164 | " or pull request to contribute! We hope for this to be a living document " 165 | "reflecting the best practices and resources available." 166 | msgstr "" 167 | 168 | -------------------------------------------------------------------------------- /locale/es/LC_MESSAGES/README.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=utf-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | "Generated-By: Babel 2.13.1\n" 19 | 20 | #: ../../README.md:1 21 | msgid "[![DOI](https://zenodo.org/badge/568954740.svg)](https://zenodo.org/doi/10.5281/zenodo.10675608)" 22 | msgstr "" 23 | 24 | #: ../../README.md:1 25 | msgid "DOI" 26 | msgstr "" 27 | 28 | #: ../../README.md:3 29 | msgid "Microscopy For Beginners Reference Guide" 30 | msgstr "" 31 | 32 | #: ../../README.md:4 33 | msgid "Website :link: :arrow_right: [CLICK HERE](https://bioimagingguide.org)" 34 | msgstr "" 35 | 36 | #: ../../README.md:6 37 | msgid "" 38 | "A Beginner's guide to microscopy, from sample prep to acquisition, image " 39 | "analysis, and data interpretation. See the paper " 40 | "[here](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167)" 41 | " (original preprint [here](https://doi.org/10.5281/zenodo.7439283))" 42 | msgstr "" 43 | 44 | #~ msgid "" 45 | #~ "A Beginner's guide to microscopy, from" 46 | #~ " sample prep to acquisition, image " 47 | #~ "analysis, and data interpretation" 48 | #~ msgstr "" 49 | 50 | #~ msgid "" 51 | #~ "A Beginner's guide to microscopy, from" 52 | #~ " sample prep to acquisition, image " 53 | #~ "analysis, and data interpretation. See " 54 | #~ "the related preprint " 55 | #~ "[here](https://doi.org/10.5281/zenodo.7439283)" 56 | #~ msgstr "" 57 | 58 | -------------------------------------------------------------------------------- /locale/es/LC_MESSAGES/bibliography.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , YEAR. 5 | # 6 | # Translators: 7 | # Beth Cimini, 2023 8 | # 9 | #, fuzzy 10 | msgid "" 11 | msgstr "" 12 | "Project-Id-Version: Python\n" 13 | "Report-Msgid-Bugs-To: \n" 14 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 15 | "PO-Revision-Date: 2023-05-02 18:49+0000\n" 16 | "Last-Translator: Beth Cimini, 2023\n" 17 | "Language-Team: Spanish (https://app.transifex.com/center-for-open-bioimage-analysis/teams/169123/es/)\n" 18 | "MIME-Version: 1.0\n" 19 | "Content-Type: text/plain; charset=UTF-8\n" 20 | "Content-Transfer-Encoding: 8bit\n" 21 | "Language: es\n" 22 | "Plural-Forms: nplurals=3; plural=n == 1 ? 0 : n != 0 && n % 1000000 == 0 ? 1 : 2;\n" 23 | 24 | #: ../../bibliography.md:1 25 | msgid "Bibliography" 26 | msgstr "Bibliografía" 27 | -------------------------------------------------------------------------------- /locale/es/LC_MESSAGES/genindex.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , YEAR. 5 | # 6 | # Translators: 7 | # Beth Cimini, 2023 8 | # 9 | #, fuzzy 10 | msgid "" 11 | msgstr "" 12 | "Project-Id-Version: Python\n" 13 | "Report-Msgid-Bugs-To: \n" 14 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 15 | "PO-Revision-Date: 2023-05-02 18:49+0000\n" 16 | "Last-Translator: Beth Cimini, 2023\n" 17 | "Language-Team: Spanish (https://app.transifex.com/center-for-open-bioimage-analysis/teams/169123/es/)\n" 18 | "MIME-Version: 1.0\n" 19 | "Content-Type: text/plain; charset=UTF-8\n" 20 | "Content-Transfer-Encoding: 8bit\n" 21 | "Language: es\n" 22 | "Plural-Forms: nplurals=3; plural=n == 1 ? 0 : n != 0 && n % 1000000 == 0 ? 1 : 2;\n" 23 | 24 | #: ../../genindex.md:1 25 | msgid "Index" 26 | msgstr "Índice" 27 | -------------------------------------------------------------------------------- /locale/fi/LC_MESSAGES/QuantitativeBioimaging.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-06-28 07:29-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: fi\n" 15 | "Language-Team: fi \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.12.1\n" 21 | 22 | #: ../../QuantitativeBioimaging.md:1 23 | msgid "Quantitative Bioimaging" 24 | msgstr "" 25 | 26 | #: ../../QuantitativeBioimaging.md:3 27 | msgid "What do we mean by quantitative bioimaging?" 28 | msgstr "" 29 | 30 | #: ../../QuantitativeBioimaging.md:5 31 | msgid "" 32 | "While microscopy was by necessity a qualitative science for most of its " 33 | "history, we now live in an era where microscope images can be used to " 34 | "precisely quantify observable phenotypes." 35 | msgstr "" 36 | 37 | #: ../../QuantitativeBioimaging.md:7 38 | msgid "" 39 | "The ability to draw accurate quantitative answers from these experiments " 40 | "relies on certain best practices being followed. If one can confidently " 41 | "say \"Yes\" to each of the following 4 questions, one is likely to be " 42 | "able to quantify their sample." 43 | msgstr "" 44 | 45 | #: ../../QuantitativeBioimaging.md:9 46 | msgid "" 47 | "Have I prepared my sample in a way that minimizes technical artifacts and" 48 | " lets me understand exactly which molecule(s) I am observing?" 49 | msgstr "" 50 | 51 | #: ../../QuantitativeBioimaging.md:10 52 | msgid "" 53 | "Have I conducted my microscopy so that I minimize technical artifacts and" 54 | " am in the quantitative range of the detector attached to my microscope?" 55 | msgstr "" 56 | 57 | #: ../../QuantitativeBioimaging.md:11 58 | msgid "" 59 | "Have I selected analysis metric(s) that truly answer my biological " 60 | "question and measured them in a way that minimizes technical artifacts?" 61 | msgstr "" 62 | 63 | #: ../../QuantitativeBioimaging.md:12 64 | msgid "" 65 | "Have I chosen appropriate statistical comparisons and data presentation " 66 | "approaches so that the distribution of my metric(s) can be fairly " 67 | "compared across samples, answering my biolgical question?" 68 | msgstr "" 69 | 70 | #: ../../QuantitativeBioimaging.md:14 71 | msgid "" 72 | "Answering each of these questions requires thought, expertise, and often " 73 | "a fair amount of trial and error; it can feel overwhelming to grapple " 74 | "with all the technical aspects and caveats present in a bioimaging " 75 | "experiment. These questions **_can_** be answered, however, though often " 76 | "not in a single pass - [continuous optimization through multiple rounds " 77 | "of answering these questions](qb-decision-cycle) is typically needed for " 78 | "best results." 79 | msgstr "" 80 | 81 | #: ../../QuantitativeBioimaging.md:16 82 | msgid "" 83 | "The resources linked in this guide are designed to help a reader develop " 84 | "skills in each or all of these areas, helping them get the most from " 85 | "their microscopy data." 86 | msgstr "" 87 | 88 | #: ../../QuantitativeBioimaging.md:25 89 | msgid "cycle" 90 | msgstr "" 91 | 92 | #: ../../QuantitativeBioimaging.md:25 93 | msgid "" 94 | "**The decision cycle of quantitative bioimaging {cite}`Senft2023-zy`** " 95 | "Reproduced from Senft and Diaz-Rohrer et al, [**_A biologist’s guide to " 96 | "planning and performing quantitative bioimaging " 97 | "experiments_**](https://doi.org/10.1371/journal.pbio.3002167)." 98 | msgstr "" 99 | 100 | -------------------------------------------------------------------------------- /locale/fi/LC_MESSAGES/README.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: fi\n" 15 | "Language-Team: fi \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.13.1\n" 21 | 22 | #: ../../README.md:1 23 | msgid "[![DOI](https://zenodo.org/badge/568954740.svg)](https://zenodo.org/doi/10.5281/zenodo.10675608)" 24 | msgstr "" 25 | 26 | #: ../../README.md:1 27 | msgid "DOI" 28 | msgstr "" 29 | 30 | #: ../../README.md:3 31 | msgid "Microscopy For Beginners Reference Guide" 32 | msgstr "" 33 | 34 | #: ../../README.md:4 35 | msgid "Website :link: :arrow_right: [CLICK HERE](https://bioimagingguide.org)" 36 | msgstr "" 37 | 38 | #: ../../README.md:6 39 | msgid "" 40 | "A Beginner's guide to microscopy, from sample prep to acquisition, image " 41 | "analysis, and data interpretation. See the paper " 42 | "[here](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167)" 43 | " (original preprint [here](https://doi.org/10.5281/zenodo.7439283))" 44 | msgstr "" 45 | 46 | -------------------------------------------------------------------------------- /locale/fi/LC_MESSAGES/bibliography.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: fi\n" 15 | "Language-Team: fi \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.12.1\n" 21 | 22 | #: ../../bibliography.md:1 23 | msgid "Bibliography" 24 | msgstr "" 25 | 26 | -------------------------------------------------------------------------------- /locale/fi/LC_MESSAGES/community_resources.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: fi\n" 15 | "Language-Team: fi \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.13.1\n" 21 | 22 | #: ../../community_resources.md:1 23 | msgid "Community resources" 24 | msgstr "" 25 | 26 | #: ../../community_resources.md:3 27 | msgid "Below are globally and locally available community resources" 28 | msgstr "" 29 | 30 | #: ../../community_resources.md:5 31 | msgid "Global and online resources" 32 | msgstr "" 33 | 34 | #: ../../community_resources.md:12 ../../community_resources.md:38 35 | msgid "**Resource Name**" 36 | msgstr "" 37 | 38 | #: ../../community_resources.md:13 ../../community_resources.md:39 39 | msgid "**Link**" 40 | msgstr "" 41 | 42 | #: ../../community_resources.md:14 43 | msgid "**Brief description**" 44 | msgstr "" 45 | 46 | #: ../../community_resources.md:15 47 | msgid "Global BioImaging" 48 | msgstr "" 49 | 50 | #: ../../community_resources.md:16 51 | msgid "[link](https://globalbioimaging.org/)" 52 | msgstr "" 53 | 54 | #: ../../community_resources.md:17 55 | msgid "" 56 | "Training resources, working groups, recommendations for standardization " 57 | "and research reproducibility for global bioimaging efforts" 58 | msgstr "" 59 | 60 | #: ../../community_resources.md:18 61 | msgid "GloBIAS" 62 | msgstr "" 63 | 64 | #: ../../community_resources.md:19 65 | msgid "[link](https://www.globias.org/home)" 66 | msgstr "" 67 | 68 | #: ../../community_resources.md:20 69 | msgid "Connections, training, and more for bioimage analysts across the world" 70 | msgstr "" 71 | 72 | #: ../../community_resources.md:21 73 | msgid "Microforum" 74 | msgstr "" 75 | 76 | #: ../../community_resources.md:22 77 | msgid "[link](https://forum.microlist.org/)" 78 | msgstr "" 79 | 80 | #: ../../community_resources.md:23 81 | msgid "Discussion forum for bioimaging sample preparation and acquisition" 82 | msgstr "" 83 | 84 | #: ../../community_resources.md:24 85 | msgid "Scientific Community Image Forum (Image . sc)" 86 | msgstr "" 87 | 88 | #: ../../community_resources.md:25 89 | msgid "[link](https://forum.image.sc/)" 90 | msgstr "" 91 | 92 | #: ../../community_resources.md:26 93 | msgid "Discussion forum for bioimage analysis software {cite}`Rueden2019-qp`" 94 | msgstr "" 95 | 96 | #: ../../community_resources.md:27 97 | msgid "HMS Nikon Imaging Center \"Favorite References\"" 98 | msgstr "" 99 | 100 | #: ../../community_resources.md:28 101 | msgid "[link](https://nic.med.harvard.edu/fav_references/)" 102 | msgstr "" 103 | 104 | #: ../../community_resources.md:29 105 | msgid "" 106 | "A curated list of references related to many aspects of microscopy and " 107 | "image analysis" 108 | msgstr "" 109 | 110 | #: ../../community_resources.md:32 111 | msgid "Local resources" 112 | msgstr "" 113 | 114 | #: ../../community_resources.md:40 115 | msgid "BioImaging North America (BINA)" 116 | msgstr "" 117 | 118 | #: ../../community_resources.md:41 119 | msgid "[link](https://www.bioimagingnorthamerica.org/)" 120 | msgstr "" 121 | 122 | #: ../../community_resources.md:42 123 | msgid "Latin America BioImaging" 124 | msgstr "" 125 | 126 | #: ../../community_resources.md:43 127 | msgid "[link](https://www.latambioimaging.org/ )" 128 | msgstr "" 129 | 130 | #: ../../community_resources.md:44 131 | msgid "African BioImaging Consortium" 132 | msgstr "" 133 | 134 | #: ../../community_resources.md:45 135 | msgid "[link](https://www.africanbioimaging.org/)" 136 | msgstr "" 137 | 138 | #: ../../community_resources.md:46 139 | msgid "South Africa BioImaging" 140 | msgstr "" 141 | 142 | #: ../../community_resources.md:47 143 | msgid "[link](https://www.sabioimaging.org/)" 144 | msgstr "" 145 | 146 | #: ../../community_resources.md:48 147 | msgid "Euro-bioimaging" 148 | msgstr "" 149 | 150 | #: ../../community_resources.md:49 151 | msgid "[link](https://www.eurobioimaging.eu/)" 152 | msgstr "" 153 | 154 | #: ../../community_resources.md:50 155 | msgid "Advanced BioImaging support (Japan)" 156 | msgstr "" 157 | 158 | #: ../../community_resources.md:51 159 | msgid "[link](https://www.nibb.ac.jp/abis/)" 160 | msgstr "" 161 | 162 | #: ../../community_resources.md:52 163 | msgid "Microscopy Australia" 164 | msgstr "" 165 | 166 | #: ../../community_resources.md:53 167 | msgid "[link](https://micro.org.au/)" 168 | msgstr "" 169 | 170 | #: ../../community_resources.md:54 171 | msgid "Canada BioImaging" 172 | msgstr "" 173 | 174 | #: ../../community_resources.md:55 175 | msgid "[link](https://www.canadabioimaging.org/)" 176 | msgstr "" 177 | 178 | #: ../../community_resources.md:56 179 | msgid "Singapore Microscopy Infrastructure Network" 180 | msgstr "" 181 | 182 | #: ../../community_resources.md:57 183 | msgid "[link](https://www.singascope.sg/)" 184 | msgstr "" 185 | 186 | -------------------------------------------------------------------------------- /locale/fi/LC_MESSAGES/genindex.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: fi\n" 15 | "Language-Team: fi \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.12.1\n" 21 | 22 | #: ../../genindex.md:1 23 | msgid "Index" 24 | msgstr "" 25 | 26 | -------------------------------------------------------------------------------- /locale/fr/LC_MESSAGES/QuantitativeBioimaging.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-06-28 07:29-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=utf-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | "Generated-By: Babel 2.10.3\n" 19 | 20 | #: ../../QuantitativeBioimaging.md:1 21 | msgid "Quantitative Bioimaging" 22 | msgstr "" 23 | 24 | #: ../../QuantitativeBioimaging.md:3 25 | msgid "What do we mean by quantitative bioimaging?" 26 | msgstr "" 27 | 28 | #: ../../QuantitativeBioimaging.md:5 29 | msgid "" 30 | "While microscopy was by necessity a qualitative science for most of its " 31 | "history, we now live in an era where microscope images can be used to " 32 | "precisely quantify observable phenotypes." 33 | msgstr "" 34 | 35 | #: ../../QuantitativeBioimaging.md:7 36 | msgid "" 37 | "The ability to draw accurate quantitative answers from these experiments " 38 | "relies on certain best practices being followed. If one can confidently " 39 | "say \"Yes\" to each of the following 4 questions, one is likely to be " 40 | "able to quantify their sample." 41 | msgstr "" 42 | 43 | #: ../../QuantitativeBioimaging.md:9 44 | msgid "" 45 | "Have I prepared my sample in a way that minimizes technical artifacts and" 46 | " lets me understand exactly which molecule(s) I am observing?" 47 | msgstr "" 48 | 49 | #: ../../QuantitativeBioimaging.md:10 50 | msgid "" 51 | "Have I conducted my microscopy so that I minimize technical artifacts and" 52 | " am in the quantitative range of the detector attached to my microscope?" 53 | msgstr "" 54 | 55 | #: ../../QuantitativeBioimaging.md:11 56 | msgid "" 57 | "Have I selected analysis metric(s) that truly answer my biological " 58 | "question and measured them in a way that minimizes technical artifacts?" 59 | msgstr "" 60 | 61 | #: ../../QuantitativeBioimaging.md:12 62 | msgid "" 63 | "Have I chosen appropriate statistical comparisons and data presentation " 64 | "approaches so that the distribution of my metric(s) can be fairly " 65 | "compared across samples, answering my biolgical question?" 66 | msgstr "" 67 | 68 | #: ../../QuantitativeBioimaging.md:14 69 | msgid "" 70 | "Answering each of these questions requires thought, expertise, and often " 71 | "a fair amount of trial and error; it can feel overwhelming to grapple " 72 | "with all the technical aspects and caveats present in a bioimaging " 73 | "experiment. These questions **_can_** be answered, however, though often " 74 | "not in a single pass - [continuous optimization through multiple rounds " 75 | "of answering these questions](qb-decision-cycle) is typically needed for " 76 | "best results." 77 | msgstr "" 78 | 79 | #: ../../QuantitativeBioimaging.md:16 80 | msgid "" 81 | "The resources linked in this guide are designed to help a reader develop " 82 | "skills in each or all of these areas, helping them get the most from " 83 | "their microscopy data." 84 | msgstr "" 85 | 86 | #: ../../QuantitativeBioimaging.md:25 87 | msgid "cycle" 88 | msgstr "" 89 | 90 | #: ../../QuantitativeBioimaging.md:25 91 | msgid "" 92 | "**The decision cycle of quantitative bioimaging {cite}`Senft2023-zy`** " 93 | "Reproduced from Senft and Diaz-Rohrer et al, [**_A biologist’s guide to " 94 | "planning and performing quantitative bioimaging " 95 | "experiments_**](https://doi.org/10.1371/journal.pbio.3002167)." 96 | msgstr "" 97 | 98 | #~ msgid "" 99 | #~ "**The decision cycle of quantitative " 100 | #~ "bioimaging {cite}`Senft2023-cb`** Reproduced from" 101 | #~ " Senft and Diaz-Rohrer et al, " 102 | #~ "[**_A biologist’s guide to the field " 103 | #~ "of quantitative " 104 | #~ "bioimaging_**](https://doi.org/10.5281/zenodo.7439283)." 105 | #~ msgstr "" 106 | 107 | -------------------------------------------------------------------------------- /locale/fr/LC_MESSAGES/README.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=utf-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | "Generated-By: Babel 2.13.1\n" 19 | 20 | #: ../../README.md:1 21 | msgid "[![DOI](https://zenodo.org/badge/568954740.svg)](https://zenodo.org/doi/10.5281/zenodo.10675608)" 22 | msgstr "" 23 | 24 | #: ../../README.md:1 25 | msgid "DOI" 26 | msgstr "" 27 | 28 | #: ../../README.md:3 29 | msgid "Microscopy For Beginners Reference Guide" 30 | msgstr "" 31 | 32 | #: ../../README.md:4 33 | msgid "Website :link: :arrow_right: [CLICK HERE](https://bioimagingguide.org)" 34 | msgstr "" 35 | 36 | #: ../../README.md:6 37 | msgid "" 38 | "A Beginner's guide to microscopy, from sample prep to acquisition, image " 39 | "analysis, and data interpretation. See the paper " 40 | "[here](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167)" 41 | " (original preprint [here](https://doi.org/10.5281/zenodo.7439283))" 42 | msgstr "" 43 | 44 | #~ msgid "" 45 | #~ "A Beginner's guide to microscopy, from" 46 | #~ " sample prep to acquisition, image " 47 | #~ "analysis, and data interpretation. See " 48 | #~ "the related preprint " 49 | #~ "[here](https://doi.org/10.5281/zenodo.7439283)" 50 | #~ msgstr "" 51 | 52 | -------------------------------------------------------------------------------- /locale/fr/LC_MESSAGES/bibliography.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=utf-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | "Generated-By: Babel 2.10.3\n" 19 | 20 | #: ../../bibliography.md:1 21 | msgid "Bibliography" 22 | msgstr "" 23 | 24 | -------------------------------------------------------------------------------- /locale/fr/LC_MESSAGES/community_resources.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=utf-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | "Generated-By: Babel 2.13.1\n" 19 | 20 | #: ../../community_resources.md:1 21 | msgid "Community resources" 22 | msgstr "" 23 | 24 | #: ../../community_resources.md:3 25 | msgid "Below are globally and locally available community resources" 26 | msgstr "" 27 | 28 | #: ../../community_resources.md:5 29 | msgid "Global and online resources" 30 | msgstr "" 31 | 32 | #: ../../community_resources.md:12 ../../community_resources.md:38 33 | msgid "**Resource Name**" 34 | msgstr "" 35 | 36 | #: ../../community_resources.md:13 ../../community_resources.md:39 37 | msgid "**Link**" 38 | msgstr "" 39 | 40 | #: ../../community_resources.md:14 41 | msgid "**Brief description**" 42 | msgstr "" 43 | 44 | #: ../../community_resources.md:15 45 | msgid "Global BioImaging" 46 | msgstr "" 47 | 48 | #: ../../community_resources.md:16 49 | msgid "[link](https://globalbioimaging.org/)" 50 | msgstr "" 51 | 52 | #: ../../community_resources.md:17 53 | msgid "" 54 | "Training resources, working groups, recommendations for standardization " 55 | "and research reproducibility for global bioimaging efforts" 56 | msgstr "" 57 | 58 | #: ../../community_resources.md:18 59 | msgid "GloBIAS" 60 | msgstr "" 61 | 62 | #: ../../community_resources.md:19 63 | msgid "[link](https://www.globias.org/home)" 64 | msgstr "" 65 | 66 | #: ../../community_resources.md:20 67 | msgid "Connections, training, and more for bioimage analysts across the world" 68 | msgstr "" 69 | 70 | #: ../../community_resources.md:21 71 | msgid "Microforum" 72 | msgstr "" 73 | 74 | #: ../../community_resources.md:22 75 | msgid "[link](https://forum.microlist.org/)" 76 | msgstr "" 77 | 78 | #: ../../community_resources.md:23 79 | msgid "Discussion forum for bioimaging sample preparation and acquisition" 80 | msgstr "" 81 | 82 | #: ../../community_resources.md:24 83 | msgid "Scientific Community Image Forum (Image . sc)" 84 | msgstr "" 85 | 86 | #: ../../community_resources.md:25 87 | msgid "[link](https://forum.image.sc/)" 88 | msgstr "" 89 | 90 | #: ../../community_resources.md:26 91 | msgid "Discussion forum for bioimage analysis software {cite}`Rueden2019-qp`" 92 | msgstr "" 93 | 94 | #: ../../community_resources.md:27 95 | msgid "HMS Nikon Imaging Center \"Favorite References\"" 96 | msgstr "" 97 | 98 | #: ../../community_resources.md:28 99 | msgid "[link](https://nic.med.harvard.edu/fav_references/)" 100 | msgstr "" 101 | 102 | #: ../../community_resources.md:29 103 | msgid "" 104 | "A curated list of references related to many aspects of microscopy and " 105 | "image analysis" 106 | msgstr "" 107 | 108 | #: ../../community_resources.md:32 109 | msgid "Local resources" 110 | msgstr "" 111 | 112 | #: ../../community_resources.md:40 113 | msgid "BioImaging North America (BINA)" 114 | msgstr "" 115 | 116 | #: ../../community_resources.md:41 117 | msgid "[link](https://www.bioimagingnorthamerica.org/)" 118 | msgstr "" 119 | 120 | #: ../../community_resources.md:42 121 | msgid "Latin America BioImaging" 122 | msgstr "" 123 | 124 | #: ../../community_resources.md:43 125 | msgid "[link](https://www.latambioimaging.org/ )" 126 | msgstr "" 127 | 128 | #: ../../community_resources.md:44 129 | msgid "African BioImaging Consortium" 130 | msgstr "" 131 | 132 | #: ../../community_resources.md:45 133 | msgid "[link](https://www.africanbioimaging.org/)" 134 | msgstr "" 135 | 136 | #: ../../community_resources.md:46 137 | msgid "South Africa BioImaging" 138 | msgstr "" 139 | 140 | #: ../../community_resources.md:47 141 | msgid "[link](https://www.sabioimaging.org/)" 142 | msgstr "" 143 | 144 | #: ../../community_resources.md:48 145 | msgid "Euro-bioimaging" 146 | msgstr "" 147 | 148 | #: ../../community_resources.md:49 149 | msgid "[link](https://www.eurobioimaging.eu/)" 150 | msgstr "" 151 | 152 | #: ../../community_resources.md:50 153 | msgid "Advanced BioImaging support (Japan)" 154 | msgstr "" 155 | 156 | #: ../../community_resources.md:51 157 | msgid "[link](https://www.nibb.ac.jp/abis/)" 158 | msgstr "" 159 | 160 | #: ../../community_resources.md:52 161 | msgid "Microscopy Australia" 162 | msgstr "" 163 | 164 | #: ../../community_resources.md:53 165 | msgid "[link](https://micro.org.au/)" 166 | msgstr "" 167 | 168 | #: ../../community_resources.md:54 169 | msgid "Canada BioImaging" 170 | msgstr "" 171 | 172 | #: ../../community_resources.md:55 173 | msgid "[link](https://www.canadabioimaging.org/)" 174 | msgstr "" 175 | 176 | #: ../../community_resources.md:56 177 | msgid "Singapore Microscopy Infrastructure Network" 178 | msgstr "" 179 | 180 | #: ../../community_resources.md:57 181 | msgid "[link](https://www.singascope.sg/)" 182 | msgstr "" 183 | 184 | -------------------------------------------------------------------------------- /locale/fr/LC_MESSAGES/genindex.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=utf-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | "Generated-By: Babel 2.10.3\n" 19 | 20 | #: ../../genindex.md:1 21 | msgid "Index" 22 | msgstr "" 23 | 24 | -------------------------------------------------------------------------------- /locale/it/LC_MESSAGES/QuantitativeBioimaging.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-06-28 07:29-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: it\n" 15 | "Language-Team: it \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.12.1\n" 21 | 22 | #: ../../QuantitativeBioimaging.md:1 23 | msgid "Quantitative Bioimaging" 24 | msgstr "" 25 | 26 | #: ../../QuantitativeBioimaging.md:3 27 | msgid "What do we mean by quantitative bioimaging?" 28 | msgstr "" 29 | 30 | #: ../../QuantitativeBioimaging.md:5 31 | msgid "" 32 | "While microscopy was by necessity a qualitative science for most of its " 33 | "history, we now live in an era where microscope images can be used to " 34 | "precisely quantify observable phenotypes." 35 | msgstr "" 36 | 37 | #: ../../QuantitativeBioimaging.md:7 38 | msgid "" 39 | "The ability to draw accurate quantitative answers from these experiments " 40 | "relies on certain best practices being followed. If one can confidently " 41 | "say \"Yes\" to each of the following 4 questions, one is likely to be " 42 | "able to quantify their sample." 43 | msgstr "" 44 | 45 | #: ../../QuantitativeBioimaging.md:9 46 | msgid "" 47 | "Have I prepared my sample in a way that minimizes technical artifacts and" 48 | " lets me understand exactly which molecule(s) I am observing?" 49 | msgstr "" 50 | 51 | #: ../../QuantitativeBioimaging.md:10 52 | msgid "" 53 | "Have I conducted my microscopy so that I minimize technical artifacts and" 54 | " am in the quantitative range of the detector attached to my microscope?" 55 | msgstr "" 56 | 57 | #: ../../QuantitativeBioimaging.md:11 58 | msgid "" 59 | "Have I selected analysis metric(s) that truly answer my biological " 60 | "question and measured them in a way that minimizes technical artifacts?" 61 | msgstr "" 62 | 63 | #: ../../QuantitativeBioimaging.md:12 64 | msgid "" 65 | "Have I chosen appropriate statistical comparisons and data presentation " 66 | "approaches so that the distribution of my metric(s) can be fairly " 67 | "compared across samples, answering my biolgical question?" 68 | msgstr "" 69 | 70 | #: ../../QuantitativeBioimaging.md:14 71 | msgid "" 72 | "Answering each of these questions requires thought, expertise, and often " 73 | "a fair amount of trial and error; it can feel overwhelming to grapple " 74 | "with all the technical aspects and caveats present in a bioimaging " 75 | "experiment. These questions **_can_** be answered, however, though often " 76 | "not in a single pass - [continuous optimization through multiple rounds " 77 | "of answering these questions](qb-decision-cycle) is typically needed for " 78 | "best results." 79 | msgstr "" 80 | 81 | #: ../../QuantitativeBioimaging.md:16 82 | msgid "" 83 | "The resources linked in this guide are designed to help a reader develop " 84 | "skills in each or all of these areas, helping them get the most from " 85 | "their microscopy data." 86 | msgstr "" 87 | 88 | #: ../../QuantitativeBioimaging.md:25 89 | msgid "cycle" 90 | msgstr "" 91 | 92 | #: ../../QuantitativeBioimaging.md:25 93 | msgid "" 94 | "**The decision cycle of quantitative bioimaging {cite}`Senft2023-zy`** " 95 | "Reproduced from Senft and Diaz-Rohrer et al, [**_A biologist’s guide to " 96 | "planning and performing quantitative bioimaging " 97 | "experiments_**](https://doi.org/10.1371/journal.pbio.3002167)." 98 | msgstr "" 99 | 100 | -------------------------------------------------------------------------------- /locale/it/LC_MESSAGES/README.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: it\n" 15 | "Language-Team: it \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.13.1\n" 21 | 22 | #: ../../README.md:1 23 | msgid "[![DOI](https://zenodo.org/badge/568954740.svg)](https://zenodo.org/doi/10.5281/zenodo.10675608)" 24 | msgstr "" 25 | 26 | #: ../../README.md:1 27 | msgid "DOI" 28 | msgstr "" 29 | 30 | #: ../../README.md:3 31 | msgid "Microscopy For Beginners Reference Guide" 32 | msgstr "" 33 | 34 | #: ../../README.md:4 35 | msgid "Website :link: :arrow_right: [CLICK HERE](https://bioimagingguide.org)" 36 | msgstr "" 37 | 38 | #: ../../README.md:6 39 | msgid "" 40 | "A Beginner's guide to microscopy, from sample prep to acquisition, image " 41 | "analysis, and data interpretation. See the paper " 42 | "[here](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167)" 43 | " (original preprint [here](https://doi.org/10.5281/zenodo.7439283))" 44 | msgstr "" 45 | 46 | -------------------------------------------------------------------------------- /locale/it/LC_MESSAGES/bibliography.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: it\n" 15 | "Language-Team: it \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.12.1\n" 21 | 22 | #: ../../bibliography.md:1 23 | msgid "Bibliography" 24 | msgstr "" 25 | 26 | -------------------------------------------------------------------------------- /locale/it/LC_MESSAGES/community_resources.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: it\n" 15 | "Language-Team: it \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.13.1\n" 21 | 22 | #: ../../community_resources.md:1 23 | msgid "Community resources" 24 | msgstr "" 25 | 26 | #: ../../community_resources.md:3 27 | msgid "Below are globally and locally available community resources" 28 | msgstr "" 29 | 30 | #: ../../community_resources.md:5 31 | msgid "Global and online resources" 32 | msgstr "" 33 | 34 | #: ../../community_resources.md:12 ../../community_resources.md:38 35 | msgid "**Resource Name**" 36 | msgstr "" 37 | 38 | #: ../../community_resources.md:13 ../../community_resources.md:39 39 | msgid "**Link**" 40 | msgstr "" 41 | 42 | #: ../../community_resources.md:14 43 | msgid "**Brief description**" 44 | msgstr "" 45 | 46 | #: ../../community_resources.md:15 47 | msgid "Global BioImaging" 48 | msgstr "" 49 | 50 | #: ../../community_resources.md:16 51 | msgid "[link](https://globalbioimaging.org/)" 52 | msgstr "" 53 | 54 | #: ../../community_resources.md:17 55 | msgid "" 56 | "Training resources, working groups, recommendations for standardization " 57 | "and research reproducibility for global bioimaging efforts" 58 | msgstr "" 59 | 60 | #: ../../community_resources.md:18 61 | msgid "GloBIAS" 62 | msgstr "" 63 | 64 | #: ../../community_resources.md:19 65 | msgid "[link](https://www.globias.org/home)" 66 | msgstr "" 67 | 68 | #: ../../community_resources.md:20 69 | msgid "Connections, training, and more for bioimage analysts across the world" 70 | msgstr "" 71 | 72 | #: ../../community_resources.md:21 73 | msgid "Microforum" 74 | msgstr "" 75 | 76 | #: ../../community_resources.md:22 77 | msgid "[link](https://forum.microlist.org/)" 78 | msgstr "" 79 | 80 | #: ../../community_resources.md:23 81 | msgid "Discussion forum for bioimaging sample preparation and acquisition" 82 | msgstr "" 83 | 84 | #: ../../community_resources.md:24 85 | msgid "Scientific Community Image Forum (Image . sc)" 86 | msgstr "" 87 | 88 | #: ../../community_resources.md:25 89 | msgid "[link](https://forum.image.sc/)" 90 | msgstr "" 91 | 92 | #: ../../community_resources.md:26 93 | msgid "Discussion forum for bioimage analysis software {cite}`Rueden2019-qp`" 94 | msgstr "" 95 | 96 | #: ../../community_resources.md:27 97 | msgid "HMS Nikon Imaging Center \"Favorite References\"" 98 | msgstr "" 99 | 100 | #: ../../community_resources.md:28 101 | msgid "[link](https://nic.med.harvard.edu/fav_references/)" 102 | msgstr "" 103 | 104 | #: ../../community_resources.md:29 105 | msgid "" 106 | "A curated list of references related to many aspects of microscopy and " 107 | "image analysis" 108 | msgstr "" 109 | 110 | #: ../../community_resources.md:32 111 | msgid "Local resources" 112 | msgstr "" 113 | 114 | #: ../../community_resources.md:40 115 | msgid "BioImaging North America (BINA)" 116 | msgstr "" 117 | 118 | #: ../../community_resources.md:41 119 | msgid "[link](https://www.bioimagingnorthamerica.org/)" 120 | msgstr "" 121 | 122 | #: ../../community_resources.md:42 123 | msgid "Latin America BioImaging" 124 | msgstr "" 125 | 126 | #: ../../community_resources.md:43 127 | msgid "[link](https://www.latambioimaging.org/ )" 128 | msgstr "" 129 | 130 | #: ../../community_resources.md:44 131 | msgid "African BioImaging Consortium" 132 | msgstr "" 133 | 134 | #: ../../community_resources.md:45 135 | msgid "[link](https://www.africanbioimaging.org/)" 136 | msgstr "" 137 | 138 | #: ../../community_resources.md:46 139 | msgid "South Africa BioImaging" 140 | msgstr "" 141 | 142 | #: ../../community_resources.md:47 143 | msgid "[link](https://www.sabioimaging.org/)" 144 | msgstr "" 145 | 146 | #: ../../community_resources.md:48 147 | msgid "Euro-bioimaging" 148 | msgstr "" 149 | 150 | #: ../../community_resources.md:49 151 | msgid "[link](https://www.eurobioimaging.eu/)" 152 | msgstr "" 153 | 154 | #: ../../community_resources.md:50 155 | msgid "Advanced BioImaging support (Japan)" 156 | msgstr "" 157 | 158 | #: ../../community_resources.md:51 159 | msgid "[link](https://www.nibb.ac.jp/abis/)" 160 | msgstr "" 161 | 162 | #: ../../community_resources.md:52 163 | msgid "Microscopy Australia" 164 | msgstr "" 165 | 166 | #: ../../community_resources.md:53 167 | msgid "[link](https://micro.org.au/)" 168 | msgstr "" 169 | 170 | #: ../../community_resources.md:54 171 | msgid "Canada BioImaging" 172 | msgstr "" 173 | 174 | #: ../../community_resources.md:55 175 | msgid "[link](https://www.canadabioimaging.org/)" 176 | msgstr "" 177 | 178 | #: ../../community_resources.md:56 179 | msgid "Singapore Microscopy Infrastructure Network" 180 | msgstr "" 181 | 182 | #: ../../community_resources.md:57 183 | msgid "[link](https://www.singascope.sg/)" 184 | msgstr "" 185 | 186 | -------------------------------------------------------------------------------- /locale/it/LC_MESSAGES/contributors.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 15:22+0000\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: it\n" 15 | "Language-Team: it \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.14.0\n" 21 | 22 | #: ../../contributors.md:1 23 | msgid "Contributing to this guide" 24 | msgstr "" 25 | 26 | #: ../../contributors.md:3 27 | msgid "Contributors" 28 | msgstr "" 29 | 30 | #: ../../contributors.md:5 31 | msgid "" 32 | "The original material for this book was created as part of the paper " 33 | "\"[**_A biologist’s guide to planning and performing quantitative " 34 | "bioimaging " 35 | "experiments_**](https://doi.org/10.1371/journal.pbio.3002167)\" " 36 | "{cite}`Senft2023-zy`. by Rebecca A. Senft*, Barbara Diaz-Rohrer*, Pina " 37 | "Colarusso, Lucy Swift, Nasim Jamali, Helena Jambor, Thomas Pengo, Craig " 38 | "Brideau, Paula Montero Llopis, Virginie Uhlmann, Jason Kirk, Kevin Andrew" 39 | " Gonzales, Peter Bankhead, Edward L. Evans III, Kevin W Eliceiri and Beth" 40 | " A. Cimini." 41 | msgstr "" 42 | 43 | #: ../../contributors.md:7 44 | msgid "" 45 | "This project was initiated by the [Center for Open Bioimage " 46 | "Analysis](https://openbioimageanalysis.org/) .We are grateful to " 47 | "[Bioimaging North America](https://www.bioimagingnorthamerica.org/) " 48 | "(especially its [Image " 49 | "Informatics](https://www.bioimagingnorthamerica.org/image-informatics-" 50 | "wg/) and [Training and Education](https://www.bioimagingnorthamerica.org" 51 | "/te-wg/) Working Groups) for both initial and ongoing support of this " 52 | "project." 53 | msgstr "" 54 | 55 | #: ../../contributors.md:9 56 | msgid "" 57 | "Since this guide has become available, we gratefully acknowledge " 58 | "contributions from the following members of the microscopy and bioimage " 59 | "analysis community!" 60 | msgstr "" 61 | 62 | #: ../../contributors.md:10 63 | msgid "William Giang" 64 | msgstr "" 65 | 66 | #: ../../contributors.md:11 67 | msgid "Robert Haase" 68 | msgstr "" 69 | 70 | #: ../../contributors.md:13 71 | msgid "" 72 | "Improvements to the build and maintenance system for this book have come " 73 | "from" 74 | msgstr "" 75 | 76 | #: ../../contributors.md:14 77 | msgid "Pete Bankhead" 78 | msgstr "" 79 | 80 | #: ../../contributors.md:16 81 | msgid "How can I become a contributor?" 82 | msgstr "" 83 | 84 | #: ../../contributors.md:18 85 | msgid "" 86 | "Please feel free to open an " 87 | "[issue](https://github.com/broadinstitute/MicroscopyForBeginnersReferenceGuide/issues)" 88 | " or pull request to contribute! We hope for this to be a living document " 89 | "reflecting the best practices and resources available." 90 | msgstr "" 91 | 92 | #: ../../contributors.md:20 93 | msgid "" 94 | "We currently also offer a [Google " 95 | "Form](https://docs.google.com/forms/d/e/1FAIpQLScWQbemviI2OkvVkeTKUOozAzKNndcZpXIB_nE0qFMl72lqvQ/viewform)" 96 | " for contributions, though note these may be responded to more slowly " 97 | "than direct contributions to the GitHub repository." 98 | msgstr "" 99 | 100 | #: ../../contributors.md:23 101 | msgid "Translation" 102 | msgstr "" 103 | 104 | #: ../../contributors.md:25 105 | msgid "" 106 | "This guide is available in [English](https://www.bioimagingguide.org) as " 107 | "well as [Czech](https://cs.bioimagingguide.org), " 108 | "[Portuguese](https://pt.bioimagingguide.org), and " 109 | "[Spanish](https://es.bioimagingguide.org)." 110 | msgstr "" 111 | 112 | #: ../../contributors.md:27 113 | msgid "" 114 | "Work is underway to translate this guide into other languages - " 115 | "translation is planned or has begun in French, German, Finnish, Italian, " 116 | "Japanese, Polish, and Farsi. To help translate into one of these " 117 | "languages, or another language not listed here, please contact bcimini AT" 118 | " broadinstitute DOT org." 119 | msgstr "" 120 | 121 | #: ../../contributors.md:29 122 | msgid "Translations are gratefully acknowledged from:" 123 | msgstr "" 124 | 125 | #: ../../contributors.md:31 126 | msgid "Czech : Martin Schätz" 127 | msgstr "" 128 | 129 | #: ../../contributors.md:32 130 | msgid "Portuguese: Mario Costa Cruz" 131 | msgstr "" 132 | 133 | #: ../../contributors.md:33 134 | msgid "Spanish: Mariana De Niz" 135 | msgstr "" 136 | 137 | #~ msgid "" 138 | #~ "This guide is available in " 139 | #~ "[English](https://www.bioimagingguide.org) as well " 140 | #~ "as [Czech](https://cs.bioimagingguide.org)." 141 | #~ msgstr "" 142 | 143 | #~ msgid "" 144 | #~ "Work is underway to translate this " 145 | #~ "guide into other languages - translation" 146 | #~ " is planned or has begun in " 147 | #~ "French, Spanish, Portuguese, German, Finnish," 148 | #~ " and Polish. To help translate into" 149 | #~ " one of these languages, or another" 150 | #~ " language not listed here, please " 151 | #~ "contact bcimini AT broadinstitute DOT " 152 | #~ "org." 153 | #~ msgstr "" 154 | 155 | -------------------------------------------------------------------------------- /locale/it/LC_MESSAGES/genindex.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: it\n" 15 | "Language-Team: it \n" 16 | "Plural-Forms: nplurals=2; plural=(n != 1);\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.12.1\n" 21 | 22 | #: ../../genindex.md:1 23 | msgid "Index" 24 | msgstr "" 25 | 26 | -------------------------------------------------------------------------------- /locale/ja/LC_MESSAGES/QuantitativeBioimaging.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-06-28 07:29-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: ja\n" 15 | "Language-Team: ja \n" 16 | "Plural-Forms: nplurals=1; plural=0;\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.12.1\n" 21 | 22 | #: ../../QuantitativeBioimaging.md:1 23 | msgid "Quantitative Bioimaging" 24 | msgstr "" 25 | 26 | #: ../../QuantitativeBioimaging.md:3 27 | msgid "What do we mean by quantitative bioimaging?" 28 | msgstr "" 29 | 30 | #: ../../QuantitativeBioimaging.md:5 31 | msgid "" 32 | "While microscopy was by necessity a qualitative science for most of its " 33 | "history, we now live in an era where microscope images can be used to " 34 | "precisely quantify observable phenotypes." 35 | msgstr "" 36 | 37 | #: ../../QuantitativeBioimaging.md:7 38 | msgid "" 39 | "The ability to draw accurate quantitative answers from these experiments " 40 | "relies on certain best practices being followed. If one can confidently " 41 | "say \"Yes\" to each of the following 4 questions, one is likely to be " 42 | "able to quantify their sample." 43 | msgstr "" 44 | 45 | #: ../../QuantitativeBioimaging.md:9 46 | msgid "" 47 | "Have I prepared my sample in a way that minimizes technical artifacts and" 48 | " lets me understand exactly which molecule(s) I am observing?" 49 | msgstr "" 50 | 51 | #: ../../QuantitativeBioimaging.md:10 52 | msgid "" 53 | "Have I conducted my microscopy so that I minimize technical artifacts and" 54 | " am in the quantitative range of the detector attached to my microscope?" 55 | msgstr "" 56 | 57 | #: ../../QuantitativeBioimaging.md:11 58 | msgid "" 59 | "Have I selected analysis metric(s) that truly answer my biological " 60 | "question and measured them in a way that minimizes technical artifacts?" 61 | msgstr "" 62 | 63 | #: ../../QuantitativeBioimaging.md:12 64 | msgid "" 65 | "Have I chosen appropriate statistical comparisons and data presentation " 66 | "approaches so that the distribution of my metric(s) can be fairly " 67 | "compared across samples, answering my biolgical question?" 68 | msgstr "" 69 | 70 | #: ../../QuantitativeBioimaging.md:14 71 | msgid "" 72 | "Answering each of these questions requires thought, expertise, and often " 73 | "a fair amount of trial and error; it can feel overwhelming to grapple " 74 | "with all the technical aspects and caveats present in a bioimaging " 75 | "experiment. These questions **_can_** be answered, however, though often " 76 | "not in a single pass - [continuous optimization through multiple rounds " 77 | "of answering these questions](qb-decision-cycle) is typically needed for " 78 | "best results." 79 | msgstr "" 80 | 81 | #: ../../QuantitativeBioimaging.md:16 82 | msgid "" 83 | "The resources linked in this guide are designed to help a reader develop " 84 | "skills in each or all of these areas, helping them get the most from " 85 | "their microscopy data." 86 | msgstr "" 87 | 88 | #: ../../QuantitativeBioimaging.md:25 89 | msgid "cycle" 90 | msgstr "" 91 | 92 | #: ../../QuantitativeBioimaging.md:25 93 | msgid "" 94 | "**The decision cycle of quantitative bioimaging {cite}`Senft2023-zy`** " 95 | "Reproduced from Senft and Diaz-Rohrer et al, [**_A biologist’s guide to " 96 | "planning and performing quantitative bioimaging " 97 | "experiments_**](https://doi.org/10.1371/journal.pbio.3002167)." 98 | msgstr "" 99 | 100 | -------------------------------------------------------------------------------- /locale/ja/LC_MESSAGES/README.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: ja\n" 15 | "Language-Team: ja \n" 16 | "Plural-Forms: nplurals=1; plural=0;\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.13.1\n" 21 | 22 | #: ../../README.md:1 23 | msgid "[![DOI](https://zenodo.org/badge/568954740.svg)](https://zenodo.org/doi/10.5281/zenodo.10675608)" 24 | msgstr "" 25 | 26 | #: ../../README.md:1 27 | msgid "DOI" 28 | msgstr "" 29 | 30 | #: ../../README.md:3 31 | msgid "Microscopy For Beginners Reference Guide" 32 | msgstr "" 33 | 34 | #: ../../README.md:4 35 | msgid "Website :link: :arrow_right: [CLICK HERE](https://bioimagingguide.org)" 36 | msgstr "" 37 | 38 | #: ../../README.md:6 39 | msgid "" 40 | "A Beginner's guide to microscopy, from sample prep to acquisition, image " 41 | "analysis, and data interpretation. See the paper " 42 | "[here](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167)" 43 | " (original preprint [here](https://doi.org/10.5281/zenodo.7439283))" 44 | msgstr "" 45 | 46 | -------------------------------------------------------------------------------- /locale/ja/LC_MESSAGES/bibliography.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: ja\n" 15 | "Language-Team: ja \n" 16 | "Plural-Forms: nplurals=1; plural=0;\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.12.1\n" 21 | 22 | #: ../../bibliography.md:1 23 | msgid "Bibliography" 24 | msgstr "" 25 | 26 | -------------------------------------------------------------------------------- /locale/ja/LC_MESSAGES/community_resources.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: ja\n" 15 | "Language-Team: ja \n" 16 | "Plural-Forms: nplurals=1; plural=0;\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.13.1\n" 21 | 22 | #: ../../community_resources.md:1 23 | msgid "Community resources" 24 | msgstr "" 25 | 26 | #: ../../community_resources.md:3 27 | msgid "Below are globally and locally available community resources" 28 | msgstr "" 29 | 30 | #: ../../community_resources.md:5 31 | msgid "Global and online resources" 32 | msgstr "" 33 | 34 | #: ../../community_resources.md:12 ../../community_resources.md:38 35 | msgid "**Resource Name**" 36 | msgstr "" 37 | 38 | #: ../../community_resources.md:13 ../../community_resources.md:39 39 | msgid "**Link**" 40 | msgstr "" 41 | 42 | #: ../../community_resources.md:14 43 | msgid "**Brief description**" 44 | msgstr "" 45 | 46 | #: ../../community_resources.md:15 47 | msgid "Global BioImaging" 48 | msgstr "" 49 | 50 | #: ../../community_resources.md:16 51 | msgid "[link](https://globalbioimaging.org/)" 52 | msgstr "" 53 | 54 | #: ../../community_resources.md:17 55 | msgid "" 56 | "Training resources, working groups, recommendations for standardization " 57 | "and research reproducibility for global bioimaging efforts" 58 | msgstr "" 59 | 60 | #: ../../community_resources.md:18 61 | msgid "GloBIAS" 62 | msgstr "" 63 | 64 | #: ../../community_resources.md:19 65 | msgid "[link](https://www.globias.org/home)" 66 | msgstr "" 67 | 68 | #: ../../community_resources.md:20 69 | msgid "Connections, training, and more for bioimage analysts across the world" 70 | msgstr "" 71 | 72 | #: ../../community_resources.md:21 73 | msgid "Microforum" 74 | msgstr "" 75 | 76 | #: ../../community_resources.md:22 77 | msgid "[link](https://forum.microlist.org/)" 78 | msgstr "" 79 | 80 | #: ../../community_resources.md:23 81 | msgid "Discussion forum for bioimaging sample preparation and acquisition" 82 | msgstr "" 83 | 84 | #: ../../community_resources.md:24 85 | msgid "Scientific Community Image Forum (Image . sc)" 86 | msgstr "" 87 | 88 | #: ../../community_resources.md:25 89 | msgid "[link](https://forum.image.sc/)" 90 | msgstr "" 91 | 92 | #: ../../community_resources.md:26 93 | msgid "Discussion forum for bioimage analysis software {cite}`Rueden2019-qp`" 94 | msgstr "" 95 | 96 | #: ../../community_resources.md:27 97 | msgid "HMS Nikon Imaging Center \"Favorite References\"" 98 | msgstr "" 99 | 100 | #: ../../community_resources.md:28 101 | msgid "[link](https://nic.med.harvard.edu/fav_references/)" 102 | msgstr "" 103 | 104 | #: ../../community_resources.md:29 105 | msgid "" 106 | "A curated list of references related to many aspects of microscopy and " 107 | "image analysis" 108 | msgstr "" 109 | 110 | #: ../../community_resources.md:32 111 | msgid "Local resources" 112 | msgstr "" 113 | 114 | #: ../../community_resources.md:40 115 | msgid "BioImaging North America (BINA)" 116 | msgstr "" 117 | 118 | #: ../../community_resources.md:41 119 | msgid "[link](https://www.bioimagingnorthamerica.org/)" 120 | msgstr "" 121 | 122 | #: ../../community_resources.md:42 123 | msgid "Latin America BioImaging" 124 | msgstr "" 125 | 126 | #: ../../community_resources.md:43 127 | msgid "[link](https://www.latambioimaging.org/ )" 128 | msgstr "" 129 | 130 | #: ../../community_resources.md:44 131 | msgid "African BioImaging Consortium" 132 | msgstr "" 133 | 134 | #: ../../community_resources.md:45 135 | msgid "[link](https://www.africanbioimaging.org/)" 136 | msgstr "" 137 | 138 | #: ../../community_resources.md:46 139 | msgid "South Africa BioImaging" 140 | msgstr "" 141 | 142 | #: ../../community_resources.md:47 143 | msgid "[link](https://www.sabioimaging.org/)" 144 | msgstr "" 145 | 146 | #: ../../community_resources.md:48 147 | msgid "Euro-bioimaging" 148 | msgstr "" 149 | 150 | #: ../../community_resources.md:49 151 | msgid "[link](https://www.eurobioimaging.eu/)" 152 | msgstr "" 153 | 154 | #: ../../community_resources.md:50 155 | msgid "Advanced BioImaging support (Japan)" 156 | msgstr "" 157 | 158 | #: ../../community_resources.md:51 159 | msgid "[link](https://www.nibb.ac.jp/abis/)" 160 | msgstr "" 161 | 162 | #: ../../community_resources.md:52 163 | msgid "Microscopy Australia" 164 | msgstr "" 165 | 166 | #: ../../community_resources.md:53 167 | msgid "[link](https://micro.org.au/)" 168 | msgstr "" 169 | 170 | #: ../../community_resources.md:54 171 | msgid "Canada BioImaging" 172 | msgstr "" 173 | 174 | #: ../../community_resources.md:55 175 | msgid "[link](https://www.canadabioimaging.org/)" 176 | msgstr "" 177 | 178 | #: ../../community_resources.md:56 179 | msgid "Singapore Microscopy Infrastructure Network" 180 | msgstr "" 181 | 182 | #: ../../community_resources.md:57 183 | msgid "[link](https://www.singascope.sg/)" 184 | msgstr "" 185 | 186 | -------------------------------------------------------------------------------- /locale/ja/LC_MESSAGES/contributors.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 15:22+0000\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: ja\n" 15 | "Language-Team: ja \n" 16 | "Plural-Forms: nplurals=1; plural=0;\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.14.0\n" 21 | 22 | #: ../../contributors.md:1 23 | msgid "Contributing to this guide" 24 | msgstr "" 25 | 26 | #: ../../contributors.md:3 27 | msgid "Contributors" 28 | msgstr "" 29 | 30 | #: ../../contributors.md:5 31 | msgid "" 32 | "The original material for this book was created as part of the paper " 33 | "\"[**_A biologist’s guide to planning and performing quantitative " 34 | "bioimaging " 35 | "experiments_**](https://doi.org/10.1371/journal.pbio.3002167)\" " 36 | "{cite}`Senft2023-zy`. by Rebecca A. Senft*, Barbara Diaz-Rohrer*, Pina " 37 | "Colarusso, Lucy Swift, Nasim Jamali, Helena Jambor, Thomas Pengo, Craig " 38 | "Brideau, Paula Montero Llopis, Virginie Uhlmann, Jason Kirk, Kevin Andrew" 39 | " Gonzales, Peter Bankhead, Edward L. Evans III, Kevin W Eliceiri and Beth" 40 | " A. Cimini." 41 | msgstr "" 42 | 43 | #: ../../contributors.md:7 44 | msgid "" 45 | "This project was initiated by the [Center for Open Bioimage " 46 | "Analysis](https://openbioimageanalysis.org/) .We are grateful to " 47 | "[Bioimaging North America](https://www.bioimagingnorthamerica.org/) " 48 | "(especially its [Image " 49 | "Informatics](https://www.bioimagingnorthamerica.org/image-informatics-" 50 | "wg/) and [Training and Education](https://www.bioimagingnorthamerica.org" 51 | "/te-wg/) Working Groups) for both initial and ongoing support of this " 52 | "project." 53 | msgstr "" 54 | 55 | #: ../../contributors.md:9 56 | msgid "" 57 | "Since this guide has become available, we gratefully acknowledge " 58 | "contributions from the following members of the microscopy and bioimage " 59 | "analysis community!" 60 | msgstr "" 61 | 62 | #: ../../contributors.md:10 63 | msgid "William Giang" 64 | msgstr "" 65 | 66 | #: ../../contributors.md:11 67 | msgid "Robert Haase" 68 | msgstr "" 69 | 70 | #: ../../contributors.md:13 71 | msgid "" 72 | "Improvements to the build and maintenance system for this book have come " 73 | "from" 74 | msgstr "" 75 | 76 | #: ../../contributors.md:14 77 | msgid "Pete Bankhead" 78 | msgstr "" 79 | 80 | #: ../../contributors.md:16 81 | msgid "How can I become a contributor?" 82 | msgstr "" 83 | 84 | #: ../../contributors.md:18 85 | msgid "" 86 | "Please feel free to open an " 87 | "[issue](https://github.com/broadinstitute/MicroscopyForBeginnersReferenceGuide/issues)" 88 | " or pull request to contribute! We hope for this to be a living document " 89 | "reflecting the best practices and resources available." 90 | msgstr "" 91 | 92 | #: ../../contributors.md:20 93 | msgid "" 94 | "We currently also offer a [Google " 95 | "Form](https://docs.google.com/forms/d/e/1FAIpQLScWQbemviI2OkvVkeTKUOozAzKNndcZpXIB_nE0qFMl72lqvQ/viewform)" 96 | " for contributions, though note these may be responded to more slowly " 97 | "than direct contributions to the GitHub repository." 98 | msgstr "" 99 | 100 | #: ../../contributors.md:23 101 | msgid "Translation" 102 | msgstr "" 103 | 104 | #: ../../contributors.md:25 105 | msgid "" 106 | "This guide is available in [English](https://www.bioimagingguide.org) as " 107 | "well as [Czech](https://cs.bioimagingguide.org), " 108 | "[Portuguese](https://pt.bioimagingguide.org), and " 109 | "[Spanish](https://es.bioimagingguide.org)." 110 | msgstr "" 111 | 112 | #: ../../contributors.md:27 113 | msgid "" 114 | "Work is underway to translate this guide into other languages - " 115 | "translation is planned or has begun in French, German, Finnish, Italian, " 116 | "Japanese, Polish, and Farsi. To help translate into one of these " 117 | "languages, or another language not listed here, please contact bcimini AT" 118 | " broadinstitute DOT org." 119 | msgstr "" 120 | 121 | #: ../../contributors.md:29 122 | msgid "Translations are gratefully acknowledged from:" 123 | msgstr "" 124 | 125 | #: ../../contributors.md:31 126 | msgid "Czech : Martin Schätz" 127 | msgstr "" 128 | 129 | #: ../../contributors.md:32 130 | msgid "Portuguese: Mario Costa Cruz" 131 | msgstr "" 132 | 133 | #: ../../contributors.md:33 134 | msgid "Spanish: Mariana De Niz" 135 | msgstr "" 136 | 137 | #~ msgid "" 138 | #~ "This guide is available in " 139 | #~ "[English](https://www.bioimagingguide.org) as well " 140 | #~ "as [Czech](https://cs.bioimagingguide.org)." 141 | #~ msgstr "" 142 | 143 | #~ msgid "" 144 | #~ "Work is underway to translate this " 145 | #~ "guide into other languages - translation" 146 | #~ " is planned or has begun in " 147 | #~ "French, Spanish, Portuguese, German, Finnish," 148 | #~ " and Polish. To help translate into" 149 | #~ " one of these languages, or another" 150 | #~ " language not listed here, please " 151 | #~ "contact bcimini AT broadinstitute DOT " 152 | #~ "org." 153 | #~ msgstr "" 154 | 155 | -------------------------------------------------------------------------------- /locale/ja/LC_MESSAGES/genindex.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: ja\n" 15 | "Language-Team: ja \n" 16 | "Plural-Forms: nplurals=1; plural=0;\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.12.1\n" 21 | 22 | #: ../../genindex.md:1 23 | msgid "Index" 24 | msgstr "" 25 | 26 | -------------------------------------------------------------------------------- /locale/ja/LC_MESSAGES/welcome.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-06-28 07:29-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language: ja\n" 15 | "Language-Team: ja \n" 16 | "Plural-Forms: nplurals=1; plural=0;\n" 17 | "MIME-Version: 1.0\n" 18 | "Content-Type: text/plain; charset=utf-8\n" 19 | "Content-Transfer-Encoding: 8bit\n" 20 | "Generated-By: Babel 2.12.1\n" 21 | 22 | #: ../../welcome.md:1 23 | msgid "Sample Preparation" 24 | msgstr "" 25 | 26 | #: ../../welcome.md:1 27 | msgid "Sample Acquisition" 28 | msgstr "" 29 | 30 | #: ../../welcome.md:1 31 | msgid "Image Analysis and Data Handling" 32 | msgstr "" 33 | 34 | #: ../../welcome.md:1 35 | msgid "Data Interpretation" 36 | msgstr "" 37 | 38 | #: ../../welcome.md:1 39 | msgid "Additional Resources" 40 | msgstr "" 41 | 42 | #: ../../welcome.md:1 43 | msgid "Welcome" 44 | msgstr "" 45 | 46 | #: ../../welcome.md:3 47 | msgid "Welcome to the world of bioimaging and bioimage analysis! 🎉" 48 | msgstr "" 49 | 50 | #: ../../welcome.md:11 51 | msgid "BBBC image montage" 52 | msgstr "" 53 | 54 | #: ../../welcome.md:11 55 | msgid "" 56 | "**Montage of fluorescence microscopy images from " 57 | "[BBBC](https://bbbc.broadinstitute.org/) {cite}`Ljosa2012-fr` (Broad " 58 | "Institute).** Images shown are from experiments BBBC007, BBBC008, " 59 | "BBBC034, BBBC038, BBBC039, and BBBC020 from left to right, top to bottom." 60 | msgstr "" 61 | 62 | #: ../../welcome.md:13 63 | msgid "What is this book?" 64 | msgstr "" 65 | 66 | #: ../../welcome.md:15 67 | msgid "" 68 | "This book is a companion website to our paper \"[**_A biologist’s guide " 69 | "to planning and performing quantitative bioimaging " 70 | "experiments_**](https://doi.org/10.1371/journal.pbio.3002167)\" " 71 | "{cite}`Senft2023-zy`. Our goal is to provide recommendations and a " 72 | "curated set of resources for biologists looking to understand the factors" 73 | " that impact their fluorescence microscopy experiments." 74 | msgstr "" 75 | 76 | #: ../../welcome.md:17 77 | msgid "" 78 | "This book is a collaborative effort from experts in biology, imaging, " 79 | "image analysis, and data management, interpretation, and presentation. " 80 | "Our tips and recommendations come from real experiences training and " 81 | "working with biologists who are beginners to bioimaging and bioimage " 82 | "analysis. When starting out in a new field, you often don't know what you" 83 | " don't know. Here we provide context, tips for avoiding common beginner " 84 | "errors, and a focused list of high-quality, open source resources (full " 85 | "list available [here](bibliography)). We use icons to indicate the type " 86 | "of resource:" 87 | msgstr "" 88 | 89 | #: ../../welcome.md:39 90 | msgid "What **isn't** this book?" 91 | msgstr "" 92 | 93 | #: ../../welcome.md:41 94 | msgid "" 95 | "This book is **not** meant to be an exhaustive list of all resources. " 96 | "Many others have curated excellent such resources(see " 97 | "[here](https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14451) " 98 | "{cite}`Haase2022-ad` and [here](https://www.bioimagingnorthamerica.org" 99 | "/training-education-resources/) and [here](https://biii.eu/) {cite}`Paul-" 100 | "Gilloteaux2021-vw`). Our goal is to create a more streamlined, beginner-" 101 | "accessible guide." 102 | msgstr "" 103 | 104 | #: ../../welcome.md:42 105 | msgid "" 106 | "This book is **not** a protocol or step by step guide, though certain " 107 | "resources we link to might be. Each subsection from sample prep to data " 108 | "interpretation are massive topics that we can't exhaustively cover in a " 109 | "guide for beginners." 110 | msgstr "" 111 | 112 | #: ../../welcome.md:45 113 | msgid "How to use this book:" 114 | msgstr "" 115 | 116 | #: ../../welcome.md:46 117 | msgid "" 118 | "Please select a section using the navigation panel on the left to get " 119 | "started or begin with sample preparation by clicking the \"Next\" button " 120 | "below ↘️." 121 | msgstr "" 122 | 123 | #: ../../welcome.md:48 124 | msgid "" 125 | "Most sections will guide you through individual subtopics using some or " 126 | "all of the following list of questions:" 127 | msgstr "" 128 | 129 | #: ../../welcome.md:49 130 | msgid "What is it?" 131 | msgstr "" 132 | 133 | #: ../../welcome.md:50 134 | msgid "What are my options?" 135 | msgstr "" 136 | 137 | #: ../../welcome.md:51 138 | msgid "How do I do it?" 139 | msgstr "" 140 | 141 | #: ../../welcome.md:52 142 | msgid "Where can things go wrong?" 143 | msgstr "" 144 | 145 | #: ../../welcome.md:53 146 | msgid "Where can I learn more? (links to resources)" 147 | msgstr "" 148 | 149 | #: ../../welcome.md:55 150 | msgid "" 151 | "Which questions are used and the exact phrasing may vary by section, but " 152 | "we hope this structure helps guide users to a deeper understanding of " 153 | "each subtopic." 154 | msgstr "" 155 | 156 | #: ../../welcome.md:57 157 | msgid "What if my resource/topic is not included?" 158 | msgstr "" 159 | 160 | #: ../../welcome.md:58 161 | msgid "" 162 | "Please feel free to open an " 163 | "[issue](https://github.com/broadinstitute/MicroscopyForBeginnersReferenceGuide/issues)" 164 | " or pull request to contribute! We hope for this to be a living document " 165 | "reflecting the best practices and resources available." 166 | msgstr "" 167 | 168 | -------------------------------------------------------------------------------- /locale/pl/LC_MESSAGES/QuantitativeBioimaging.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-06-28 07:29-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=utf-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | "Generated-By: Babel 2.10.3\n" 19 | 20 | #: ../../QuantitativeBioimaging.md:1 21 | msgid "Quantitative Bioimaging" 22 | msgstr "" 23 | 24 | #: ../../QuantitativeBioimaging.md:3 25 | msgid "What do we mean by quantitative bioimaging?" 26 | msgstr "" 27 | 28 | #: ../../QuantitativeBioimaging.md:5 29 | msgid "" 30 | "While microscopy was by necessity a qualitative science for most of its " 31 | "history, we now live in an era where microscope images can be used to " 32 | "precisely quantify observable phenotypes." 33 | msgstr "" 34 | 35 | #: ../../QuantitativeBioimaging.md:7 36 | msgid "" 37 | "The ability to draw accurate quantitative answers from these experiments " 38 | "relies on certain best practices being followed. If one can confidently " 39 | "say \"Yes\" to each of the following 4 questions, one is likely to be " 40 | "able to quantify their sample." 41 | msgstr "" 42 | 43 | #: ../../QuantitativeBioimaging.md:9 44 | msgid "" 45 | "Have I prepared my sample in a way that minimizes technical artifacts and" 46 | " lets me understand exactly which molecule(s) I am observing?" 47 | msgstr "" 48 | 49 | #: ../../QuantitativeBioimaging.md:10 50 | msgid "" 51 | "Have I conducted my microscopy so that I minimize technical artifacts and" 52 | " am in the quantitative range of the detector attached to my microscope?" 53 | msgstr "" 54 | 55 | #: ../../QuantitativeBioimaging.md:11 56 | msgid "" 57 | "Have I selected analysis metric(s) that truly answer my biological " 58 | "question and measured them in a way that minimizes technical artifacts?" 59 | msgstr "" 60 | 61 | #: ../../QuantitativeBioimaging.md:12 62 | msgid "" 63 | "Have I chosen appropriate statistical comparisons and data presentation " 64 | "approaches so that the distribution of my metric(s) can be fairly " 65 | "compared across samples, answering my biolgical question?" 66 | msgstr "" 67 | 68 | #: ../../QuantitativeBioimaging.md:14 69 | msgid "" 70 | "Answering each of these questions requires thought, expertise, and often " 71 | "a fair amount of trial and error; it can feel overwhelming to grapple " 72 | "with all the technical aspects and caveats present in a bioimaging " 73 | "experiment. These questions **_can_** be answered, however, though often " 74 | "not in a single pass - [continuous optimization through multiple rounds " 75 | "of answering these questions](qb-decision-cycle) is typically needed for " 76 | "best results." 77 | msgstr "" 78 | 79 | #: ../../QuantitativeBioimaging.md:16 80 | msgid "" 81 | "The resources linked in this guide are designed to help a reader develop " 82 | "skills in each or all of these areas, helping them get the most from " 83 | "their microscopy data." 84 | msgstr "" 85 | 86 | #: ../../QuantitativeBioimaging.md:25 87 | msgid "cycle" 88 | msgstr "" 89 | 90 | #: ../../QuantitativeBioimaging.md:25 91 | msgid "" 92 | "**The decision cycle of quantitative bioimaging {cite}`Senft2023-zy`** " 93 | "Reproduced from Senft and Diaz-Rohrer et al, [**_A biologist’s guide to " 94 | "planning and performing quantitative bioimaging " 95 | "experiments_**](https://doi.org/10.1371/journal.pbio.3002167)." 96 | msgstr "" 97 | 98 | -------------------------------------------------------------------------------- /locale/pl/LC_MESSAGES/README.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=utf-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | "Generated-By: Babel 2.13.1\n" 19 | 20 | #: ../../README.md:1 21 | msgid "[![DOI](https://zenodo.org/badge/568954740.svg)](https://zenodo.org/doi/10.5281/zenodo.10675608)" 22 | msgstr "" 23 | 24 | #: ../../README.md:1 25 | msgid "DOI" 26 | msgstr "" 27 | 28 | #: ../../README.md:3 29 | msgid "Microscopy For Beginners Reference Guide" 30 | msgstr "" 31 | 32 | #: ../../README.md:4 33 | msgid "Website :link: :arrow_right: [CLICK HERE](https://bioimagingguide.org)" 34 | msgstr "" 35 | 36 | #: ../../README.md:6 37 | msgid "" 38 | "A Beginner's guide to microscopy, from sample prep to acquisition, image " 39 | "analysis, and data interpretation. See the paper " 40 | "[here](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167)" 41 | " (original preprint [here](https://doi.org/10.5281/zenodo.7439283))" 42 | msgstr "" 43 | 44 | #~ msgid "" 45 | #~ "A Beginner's guide to microscopy, from" 46 | #~ " sample prep to acquisition, image " 47 | #~ "analysis, and data interpretation. See " 48 | #~ "the related preprint " 49 | #~ "[here](https://doi.org/10.5281/zenodo.7439283)" 50 | #~ msgstr "" 51 | 52 | -------------------------------------------------------------------------------- /locale/pl/LC_MESSAGES/bibliography.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=utf-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | "Generated-By: Babel 2.10.3\n" 19 | 20 | #: ../../bibliography.md:1 21 | msgid "Bibliography" 22 | msgstr "" 23 | 24 | -------------------------------------------------------------------------------- /locale/pl/LC_MESSAGES/community_resources.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=utf-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | "Generated-By: Babel 2.13.1\n" 19 | 20 | #: ../../community_resources.md:1 21 | msgid "Community resources" 22 | msgstr "" 23 | 24 | #: ../../community_resources.md:3 25 | msgid "Below are globally and locally available community resources" 26 | msgstr "" 27 | 28 | #: ../../community_resources.md:5 29 | msgid "Global and online resources" 30 | msgstr "" 31 | 32 | #: ../../community_resources.md:12 ../../community_resources.md:38 33 | msgid "**Resource Name**" 34 | msgstr "" 35 | 36 | #: ../../community_resources.md:13 ../../community_resources.md:39 37 | msgid "**Link**" 38 | msgstr "" 39 | 40 | #: ../../community_resources.md:14 41 | msgid "**Brief description**" 42 | msgstr "" 43 | 44 | #: ../../community_resources.md:15 45 | msgid "Global BioImaging" 46 | msgstr "" 47 | 48 | #: ../../community_resources.md:16 49 | msgid "[link](https://globalbioimaging.org/)" 50 | msgstr "" 51 | 52 | #: ../../community_resources.md:17 53 | msgid "" 54 | "Training resources, working groups, recommendations for standardization " 55 | "and research reproducibility for global bioimaging efforts" 56 | msgstr "" 57 | 58 | #: ../../community_resources.md:18 59 | msgid "GloBIAS" 60 | msgstr "" 61 | 62 | #: ../../community_resources.md:19 63 | msgid "[link](https://www.globias.org/home)" 64 | msgstr "" 65 | 66 | #: ../../community_resources.md:20 67 | msgid "Connections, training, and more for bioimage analysts across the world" 68 | msgstr "" 69 | 70 | #: ../../community_resources.md:21 71 | msgid "Microforum" 72 | msgstr "" 73 | 74 | #: ../../community_resources.md:22 75 | msgid "[link](https://forum.microlist.org/)" 76 | msgstr "" 77 | 78 | #: ../../community_resources.md:23 79 | msgid "Discussion forum for bioimaging sample preparation and acquisition" 80 | msgstr "" 81 | 82 | #: ../../community_resources.md:24 83 | msgid "Scientific Community Image Forum (Image . sc)" 84 | msgstr "" 85 | 86 | #: ../../community_resources.md:25 87 | msgid "[link](https://forum.image.sc/)" 88 | msgstr "" 89 | 90 | #: ../../community_resources.md:26 91 | msgid "Discussion forum for bioimage analysis software {cite}`Rueden2019-qp`" 92 | msgstr "" 93 | 94 | #: ../../community_resources.md:27 95 | msgid "HMS Nikon Imaging Center \"Favorite References\"" 96 | msgstr "" 97 | 98 | #: ../../community_resources.md:28 99 | msgid "[link](https://nic.med.harvard.edu/fav_references/)" 100 | msgstr "" 101 | 102 | #: ../../community_resources.md:29 103 | msgid "" 104 | "A curated list of references related to many aspects of microscopy and " 105 | "image analysis" 106 | msgstr "" 107 | 108 | #: ../../community_resources.md:32 109 | msgid "Local resources" 110 | msgstr "" 111 | 112 | #: ../../community_resources.md:40 113 | msgid "BioImaging North America (BINA)" 114 | msgstr "" 115 | 116 | #: ../../community_resources.md:41 117 | msgid "[link](https://www.bioimagingnorthamerica.org/)" 118 | msgstr "" 119 | 120 | #: ../../community_resources.md:42 121 | msgid "Latin America BioImaging" 122 | msgstr "" 123 | 124 | #: ../../community_resources.md:43 125 | msgid "[link](https://www.latambioimaging.org/ )" 126 | msgstr "" 127 | 128 | #: ../../community_resources.md:44 129 | msgid "African BioImaging Consortium" 130 | msgstr "" 131 | 132 | #: ../../community_resources.md:45 133 | msgid "[link](https://www.africanbioimaging.org/)" 134 | msgstr "" 135 | 136 | #: ../../community_resources.md:46 137 | msgid "South Africa BioImaging" 138 | msgstr "" 139 | 140 | #: ../../community_resources.md:47 141 | msgid "[link](https://www.sabioimaging.org/)" 142 | msgstr "" 143 | 144 | #: ../../community_resources.md:48 145 | msgid "Euro-bioimaging" 146 | msgstr "" 147 | 148 | #: ../../community_resources.md:49 149 | msgid "[link](https://www.eurobioimaging.eu/)" 150 | msgstr "" 151 | 152 | #: ../../community_resources.md:50 153 | msgid "Advanced BioImaging support (Japan)" 154 | msgstr "" 155 | 156 | #: ../../community_resources.md:51 157 | msgid "[link](https://www.nibb.ac.jp/abis/)" 158 | msgstr "" 159 | 160 | #: ../../community_resources.md:52 161 | msgid "Microscopy Australia" 162 | msgstr "" 163 | 164 | #: ../../community_resources.md:53 165 | msgid "[link](https://micro.org.au/)" 166 | msgstr "" 167 | 168 | #: ../../community_resources.md:54 169 | msgid "Canada BioImaging" 170 | msgstr "" 171 | 172 | #: ../../community_resources.md:55 173 | msgid "[link](https://www.canadabioimaging.org/)" 174 | msgstr "" 175 | 176 | #: ../../community_resources.md:56 177 | msgid "Singapore Microscopy Infrastructure Network" 178 | msgstr "" 179 | 180 | #: ../../community_resources.md:57 181 | msgid "[link](https://www.singascope.sg/)" 182 | msgstr "" 183 | 184 | -------------------------------------------------------------------------------- /locale/pl/LC_MESSAGES/genindex.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=utf-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | "Generated-By: Babel 2.10.3\n" 19 | 20 | #: ../../genindex.md:1 21 | msgid "Index" 22 | msgstr "" 23 | 24 | -------------------------------------------------------------------------------- /locale/pl/LC_MESSAGES/welcome.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2023-06-28 07:29-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=utf-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | "Generated-By: Babel 2.10.3\n" 19 | 20 | #: ../../welcome.md:1 21 | msgid "Sample Preparation" 22 | msgstr "" 23 | 24 | #: ../../welcome.md:1 25 | msgid "Sample Acquisition" 26 | msgstr "" 27 | 28 | #: ../../welcome.md:1 29 | msgid "Image Analysis and Data Handling" 30 | msgstr "" 31 | 32 | #: ../../welcome.md:1 33 | msgid "Data Interpretation" 34 | msgstr "" 35 | 36 | #: ../../welcome.md:1 37 | msgid "Additional Resources" 38 | msgstr "" 39 | 40 | #: ../../welcome.md:1 41 | msgid "Welcome" 42 | msgstr "" 43 | 44 | #: ../../welcome.md:3 45 | msgid "Welcome to the world of bioimaging and bioimage analysis! 🎉" 46 | msgstr "" 47 | 48 | #: ../../welcome.md:11 49 | msgid "BBBC image montage" 50 | msgstr "" 51 | 52 | #: ../../welcome.md:11 53 | msgid "" 54 | "**Montage of fluorescence microscopy images from " 55 | "[BBBC](https://bbbc.broadinstitute.org/) {cite}`Ljosa2012-fr` (Broad " 56 | "Institute).** Images shown are from experiments BBBC007, BBBC008, " 57 | "BBBC034, BBBC038, BBBC039, and BBBC020 from left to right, top to bottom." 58 | msgstr "" 59 | 60 | #: ../../welcome.md:13 61 | msgid "What is this book?" 62 | msgstr "" 63 | 64 | #: ../../welcome.md:15 65 | msgid "" 66 | "This book is a companion website to our paper \"[**_A biologist’s guide " 67 | "to planning and performing quantitative bioimaging " 68 | "experiments_**](https://doi.org/10.1371/journal.pbio.3002167)\" " 69 | "{cite}`Senft2023-zy`. Our goal is to provide recommendations and a " 70 | "curated set of resources for biologists looking to understand the factors" 71 | " that impact their fluorescence microscopy experiments." 72 | msgstr "" 73 | 74 | #: ../../welcome.md:17 75 | msgid "" 76 | "This book is a collaborative effort from experts in biology, imaging, " 77 | "image analysis, and data management, interpretation, and presentation. " 78 | "Our tips and recommendations come from real experiences training and " 79 | "working with biologists who are beginners to bioimaging and bioimage " 80 | "analysis. When starting out in a new field, you often don't know what you" 81 | " don't know. Here we provide context, tips for avoiding common beginner " 82 | "errors, and a focused list of high-quality, open source resources (full " 83 | "list available [here](bibliography)). We use icons to indicate the type " 84 | "of resource:" 85 | msgstr "" 86 | 87 | #: ../../welcome.md:39 88 | msgid "What **isn't** this book?" 89 | msgstr "" 90 | 91 | #: ../../welcome.md:41 92 | msgid "" 93 | "This book is **not** meant to be an exhaustive list of all resources. " 94 | "Many others have curated excellent such resources(see " 95 | "[here](https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14451) " 96 | "{cite}`Haase2022-ad` and [here](https://www.bioimagingnorthamerica.org" 97 | "/training-education-resources/) and [here](https://biii.eu/) {cite}`Paul-" 98 | "Gilloteaux2021-vw`). Our goal is to create a more streamlined, beginner-" 99 | "accessible guide." 100 | msgstr "" 101 | 102 | #: ../../welcome.md:42 103 | msgid "" 104 | "This book is **not** a protocol or step by step guide, though certain " 105 | "resources we link to might be. Each subsection from sample prep to data " 106 | "interpretation are massive topics that we can't exhaustively cover in a " 107 | "guide for beginners." 108 | msgstr "" 109 | 110 | #: ../../welcome.md:45 111 | msgid "How to use this book:" 112 | msgstr "" 113 | 114 | #: ../../welcome.md:46 115 | msgid "" 116 | "Please select a section using the navigation panel on the left to get " 117 | "started or begin with sample preparation by clicking the \"Next\" button " 118 | "below ↘️." 119 | msgstr "" 120 | 121 | #: ../../welcome.md:48 122 | msgid "" 123 | "Most sections will guide you through individual subtopics using some or " 124 | "all of the following list of questions:" 125 | msgstr "" 126 | 127 | #: ../../welcome.md:49 128 | msgid "What is it?" 129 | msgstr "" 130 | 131 | #: ../../welcome.md:50 132 | msgid "What are my options?" 133 | msgstr "" 134 | 135 | #: ../../welcome.md:51 136 | msgid "How do I do it?" 137 | msgstr "" 138 | 139 | #: ../../welcome.md:52 140 | msgid "Where can things go wrong?" 141 | msgstr "" 142 | 143 | #: ../../welcome.md:53 144 | msgid "Where can I learn more? (links to resources)" 145 | msgstr "" 146 | 147 | #: ../../welcome.md:55 148 | msgid "" 149 | "Which questions are used and the exact phrasing may vary by section, but " 150 | "we hope this structure helps guide users to a deeper understanding of " 151 | "each subtopic." 152 | msgstr "" 153 | 154 | #: ../../welcome.md:57 155 | msgid "What if my resource/topic is not included?" 156 | msgstr "" 157 | 158 | #: ../../welcome.md:58 159 | msgid "" 160 | "Please feel free to open an " 161 | "[issue](https://github.com/broadinstitute/MicroscopyForBeginnersReferenceGuide/issues)" 162 | " or pull request to contribute! We hope for this to be a living document " 163 | "reflecting the best practices and resources available." 164 | msgstr "" 165 | 166 | -------------------------------------------------------------------------------- /locale/pt/LC_MESSAGES/README.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , 2023. 5 | # 6 | #, fuzzy 7 | msgid "" 8 | msgstr "" 9 | "Project-Id-Version: Python \n" 10 | "Report-Msgid-Bugs-To: \n" 11 | "POT-Creation-Date: 2024-03-29 09:37-0400\n" 12 | "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" 13 | "Last-Translator: FULL NAME \n" 14 | "Language-Team: LANGUAGE \n" 15 | "MIME-Version: 1.0\n" 16 | "Content-Type: text/plain; charset=utf-8\n" 17 | "Content-Transfer-Encoding: 8bit\n" 18 | "Generated-By: Babel 2.13.1\n" 19 | 20 | #: ../../README.md:1 21 | msgid "[![DOI](https://zenodo.org/badge/568954740.svg)](https://zenodo.org/doi/10.5281/zenodo.10675608)" 22 | msgstr "" 23 | 24 | #: ../../README.md:1 25 | msgid "DOI" 26 | msgstr "" 27 | 28 | #: ../../README.md:3 29 | msgid "Microscopy For Beginners Reference Guide" 30 | msgstr "" 31 | 32 | #: ../../README.md:4 33 | msgid "Website :link: :arrow_right: [CLICK HERE](https://bioimagingguide.org)" 34 | msgstr "" 35 | 36 | #: ../../README.md:6 37 | msgid "" 38 | "A Beginner's guide to microscopy, from sample prep to acquisition, image " 39 | "analysis, and data interpretation. See the paper " 40 | "[here](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167)" 41 | " (original preprint [here](https://doi.org/10.5281/zenodo.7439283))" 42 | msgstr "" 43 | 44 | #~ msgid "" 45 | #~ "A Beginner's guide to microscopy, from" 46 | #~ " sample prep to acquisition, image " 47 | #~ "analysis, and data interpretation. See " 48 | #~ "the related preprint " 49 | #~ "[here](https://doi.org/10.5281/zenodo.7439283)" 50 | #~ msgstr "" 51 | 52 | -------------------------------------------------------------------------------- /locale/pt/LC_MESSAGES/bibliography.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , YEAR. 5 | # 6 | # Translators: 7 | # Beth Cimini, 2023 8 | # 9 | #, fuzzy 10 | msgid "" 11 | msgstr "" 12 | "Project-Id-Version: Python\n" 13 | "Report-Msgid-Bugs-To: \n" 14 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 15 | "PO-Revision-Date: 2023-05-02 18:49+0000\n" 16 | "Last-Translator: Beth Cimini, 2023\n" 17 | "Language-Team: Portuguese (https://app.transifex.com/center-for-open-bioimage-analysis/teams/169123/pt/)\n" 18 | "MIME-Version: 1.0\n" 19 | "Content-Type: text/plain; charset=UTF-8\n" 20 | "Content-Transfer-Encoding: 8bit\n" 21 | "Language: pt\n" 22 | "Plural-Forms: nplurals=3; plural=(n == 0 || n == 1) ? 0 : n != 0 && n % 1000000 == 0 ? 1 : 2;\n" 23 | 24 | #: ../../bibliography.md:1 25 | msgid "Bibliography" 26 | msgstr "Bibliografia" 27 | -------------------------------------------------------------------------------- /locale/pt/LC_MESSAGES/genindex.po: -------------------------------------------------------------------------------- 1 | # SOME DESCRIPTIVE TITLE. 2 | # Copyright (C) 2023 3 | # This file is distributed under the same license as the Python package. 4 | # FIRST AUTHOR , YEAR. 5 | # 6 | # Translators: 7 | # Beth Cimini, 2023 8 | # 9 | #, fuzzy 10 | msgid "" 11 | msgstr "" 12 | "Project-Id-Version: Python\n" 13 | "Report-Msgid-Bugs-To: \n" 14 | "POT-Creation-Date: 2023-05-02 14:28-0400\n" 15 | "PO-Revision-Date: 2023-05-02 18:49+0000\n" 16 | "Last-Translator: Beth Cimini, 2023\n" 17 | "Language-Team: Portuguese (https://app.transifex.com/center-for-open-bioimage-analysis/teams/169123/pt/)\n" 18 | "MIME-Version: 1.0\n" 19 | "Content-Type: text/plain; charset=UTF-8\n" 20 | "Content-Transfer-Encoding: 8bit\n" 21 | "Language: pt\n" 22 | "Plural-Forms: nplurals=3; plural=(n == 0 || n == 1) ? 0 : n != 0 && n % 1000000 == 0 ? 1 : 2;\n" 23 | 24 | #: ../../genindex.md:1 25 | msgid "Index" 26 | msgstr "Índice" 27 | -------------------------------------------------------------------------------- /logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/COBA-NIH/MicroscopyForBeginnersReferenceGuide/76e48826ded54fdd505832e7328b78c31f1c3f07/logo.png -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | jupyter-book 2 | jupytext 3 | git+https://github.com/brownsarahm/sphinxcontrib-mermaid@cdnupdate 4 | -------------------------------------------------------------------------------- /transifex.yml: -------------------------------------------------------------------------------- 1 | git: 2 | filters: 3 | - filter_type: dir 4 | file_format: PO 5 | source_file_extension: pot 6 | source_language: en 7 | source_file_dir: _build/gettext 8 | translation_files_expression: 'locale//LC_MESSAGES' 9 | ignore_files: 10 | - _build/gettext/README.pot 11 | -------------------------------------------------------------------------------- /welcome.md: -------------------------------------------------------------------------------- 1 | # Welcome 2 | 3 | Welcome to the world of bioimaging and bioimage analysis! 🎉 4 | ```{figure} ./BBBC_montage.png 5 | --- 6 | alt: BBBC image montage 7 | width: 80% 8 | align: center 9 | name: BBBC-montage 10 | --- 11 | **Montage of fluorescence microscopy images from [BBBC](https://bbbc.broadinstitute.org/) {cite}`Ljosa2012-fr` (Broad Institute).** Images shown are from experiments BBBC007, BBBC008, BBBC034, BBBC038, BBBC039, and BBBC020 from left to right, top to bottom. 12 | ``` 13 | ## What is this book? 14 | 15 | This book is a companion website to our paper "[**_A biologist’s guide to planning and performing quantitative bioimaging experiments_**](https://doi.org/10.1371/journal.pbio.3002167)" {cite}`Senft2023-zy`. Our goal is to provide recommendations and a curated set of resources for biologists looking to understand the factors that impact their fluorescence microscopy experiments. 16 | 17 | This book is a collaborative effort from experts in biology, imaging, image analysis, and data management, interpretation, and presentation. Our tips and recommendations come from real experiences training and working with biologists who are beginners to bioimaging and bioimage analysis. When starting out in a new field, you often don't know what you don't know. Here we provide context, tips for avoiding common beginner errors, and a focused list of high-quality, open source resources (full list available [here](bibliography)). We use icons to indicate the type of resource: 18 | 19 | ::::{grid} 20 | :::{grid-item} 21 | :columns: 3 22 | ::: 23 | :::{grid-item} 24 | :columns: 6 25 | 26 | | **Icon** | **Resource type** | 27 | |:--------:|----------------------------| 28 | | 📖 | Textbook (free online) | 29 | | 📄 | Scientific paper | 30 | | 💻 | Software or software notes | 31 | | 🌐 | Website | 32 | | 🎓 | Lecture notes or slides | 33 | | 🎥 | Video | 34 | | 🔢 | Math-heavy theory | 35 | 36 | ::: 37 | :::: 38 | 39 | ## What **isn't** this book? 40 | 41 | * This book is **not** meant to be an exhaustive list of all resources. Many others have curated excellent such resources(see [here](https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14451) {cite}`Haase2022-ad` and [here](https://www.bioimagingnorthamerica.org/training-education-resources/) and [here](https://biii.eu/) {cite}`Paul-Gilloteaux2021-vw`). Our goal is to create a more streamlined, beginner-accessible guide. 42 | * This book is **not** a protocol or step by step guide, though certain resources we link to might be. Each subsection from sample prep to data interpretation are massive topics that we can't exhaustively cover in a guide for beginners. 43 | 44 | 45 | ## How to use this book: 46 | Please select a section using the navigation panel on the left to get started or begin with sample preparation by clicking the "Next" button below ↘️. 47 | 48 | Most sections will guide you through individual subtopics using some or all of the following list of questions: 49 | * What is it? 50 | * What are my options? 51 | * How do I do it? 52 | * Where can things go wrong? 53 | * Where can I learn more? (links to resources) 54 | 55 | Which questions are used and the exact phrasing may vary by section, but we hope this structure helps guide users to a deeper understanding of each subtopic. 56 | 57 | ## What if my resource/topic is not included? 58 | Please feel free to open an [issue](https://github.com/broadinstitute/MicroscopyForBeginnersReferenceGuide/issues) or pull request to contribute! We hope for this to be a living document reflecting the best practices and resources available. 59 | --------------------------------------------------------------------------------