├── .gitignore ├── LICENSE ├── README.md ├── figure-plotting ├── Figure_plotting.ipynb └── images │ └── neuron.tif ├── find-maxima ├── guide │ ├── .DS_Store │ ├── images │ │ ├── 002eggs.png │ │ ├── C1-img_stk_x_-12099.4y_1489.2-1.tif │ │ ├── C2-img_stk_x_-12099.4y_1489.2-1.tif │ │ └── cell_fluorescent.tif │ └── live-coding-find-maxima.ipynb ├── images │ ├── 002eggs.png │ ├── C1-img_stk_x_-12099.4y_1489.2-1.tif │ ├── C2-img_stk_x_-12099.4y_1489.2-1.tif │ └── cell_fluorescent.tif └── live-coding-find-maxima.ipynb ├── how-to-solve-a-maze ├── Circularmazeexample.jpeg ├── How-to-solve-a-maze.ipynb └── MAZE_40x20_DFS_no_deadends.png └── object-colocalization └── object_coloc.ipynb /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | build/ 12 | develop-eggs/ 13 | dist/ 14 | downloads/ 15 | eggs/ 16 | .eggs/ 17 | lib/ 18 | lib64/ 19 | parts/ 20 | sdist/ 21 | var/ 22 | wheels/ 23 | pip-wheel-metadata/ 24 | share/python-wheels/ 25 | *.egg-info/ 26 | .installed.cfg 27 | *.egg 28 | MANIFEST 29 | 30 | # PyInstaller 31 | # Usually these files are written by a python script from a template 32 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 33 | *.manifest 34 | *.spec 35 | 36 | # Installer logs 37 | pip-log.txt 38 | pip-delete-this-directory.txt 39 | 40 | # Unit test / coverage reports 41 | htmlcov/ 42 | .tox/ 43 | .nox/ 44 | .coverage 45 | .coverage.* 46 | .cache 47 | nosetests.xml 48 | coverage.xml 49 | *.cover 50 | *.py,cover 51 | .hypothesis/ 52 | .pytest_cache/ 53 | 54 | # Translations 55 | *.mo 56 | *.pot 57 | 58 | # Django stuff: 59 | *.log 60 | local_settings.py 61 | db.sqlite3 62 | db.sqlite3-journal 63 | 64 | # Flask stuff: 65 | instance/ 66 | .webassets-cache 67 | 68 | # Scrapy stuff: 69 | .scrapy 70 | 71 | # Sphinx documentation 72 | docs/_build/ 73 | 74 | # PyBuilder 75 | target/ 76 | 77 | # Jupyter Notebook 78 | .ipynb_checkpoints 79 | 80 | # IPython 81 | profile_default/ 82 | ipython_config.py 83 | 84 | # pyenv 85 | .python-version 86 | 87 | # pipenv 88 | # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. 89 | # However, in case of collaboration, if having platform-specific dependencies or dependencies 90 | # having no cross-platform support, pipenv may install dependencies that don't work, or not 91 | # install all needed dependencies. 92 | #Pipfile.lock 93 | 94 | # PEP 582; used by e.g. github.com/David-OConnor/pyflow 95 | __pypackages__/ 96 | 97 | # Celery stuff 98 | celerybeat-schedule 99 | celerybeat.pid 100 | 101 | # SageMath parsed files 102 | *.sage.py 103 | 104 | # Environments 105 | .env 106 | .venv 107 | env/ 108 | venv/ 109 | ENV/ 110 | env.bak/ 111 | venv.bak/ 112 | 113 | # Spyder project settings 114 | .spyderproject 115 | .spyproject 116 | 117 | # Rope project settings 118 | .ropeproject 119 | 120 | # mkdocs documentation 121 | /site 122 | 123 | # mypy 124 | .mypy_cache/ 125 | .dmypy.json 126 | dmypy.json 127 | 128 | # Pyre type checker 129 | .pyre/ 130 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2020 Dominic Waithe 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # live-coding 2 | This is a repository containing Jupyter lab notebooks demonstrating how to code in Python and are associated with corresponding live-coding YouTube videos. The goal of this work is to show you how to approach image analysis in Python in a very practical sense. You will learn about image structure and formats and about the various libraries which can support image analysis. 3 | 4 | ## How to Solve a Maze: 5 | 6 | In this notebook and associated video I do some live-coding in Python to describe and demonstrate how to solve a maze rendered in graphical form. In this video I implement a simple breadth-first graph searching algorithm to find the shortest route through a maze, as well as show simple thresholding and image plotting. The notebook can be found in the directory 'how-to-solve-a-maze', or through this link: 7 | [How to Solve a Maze - notebook](https://github.com/dwaithe/live-coding/blob/main/how-to-solve-a-maze/How-to-solve-a-maze.ipynb). 8 | [![How to Solve a Maze - live coding - Python Video](http://img.youtube.com/vi/1KHgCRs-x1M/0.jpg)](https://www.youtube.com/watch?v=GFt2XhUZQy0 "How to Solve a Maze - live coding - Python - image analysis"). 9 | 10 | ## Object colocalization: 11 | 12 | In this notebook and assoicated video I demonstrate how to go about performing an object-based colocalization analysis procedure, using fluorescence microscopy derived images. I showcase histogram-based thresholding and also Find-maxima methods of segmentation. Finally I show how to compare the distances between foci in two different channels and how to organise the data using pandas. The notebook can be found in the directory 'how-to-solve-a-maze', or through this link: 13 | [Object Colocalization - notebook](https://github.com/dwaithe/live-coding/blob/main/object-colocalization/object_coloc.ipynb). 14 | [![Object Colocalization](http://img.youtube.com/vi/GFt2XhUZQy0/0.jpg)](http://www.youtube.com/watch?v=GFt2XhUZQy0 "Object Colocalization - live coding - bioimage analysis"). 15 | 16 | ## Find Maxima 2-D: 17 | 18 | In this notebook and associated video I demonstrate how to go about applying a 2-D maxima algorithm to wide-field and fluorescence microscopy derived images. axima finding (or peak finding) is a technique for finding the locations of intensity maxima within a data signal. To understand more about theory, please visit the associated video tutorial which goes through the theory and functioning of the algorithmic approach also: https://youtu.be/8YEPRf2C8Dw 19 | The code created from this practical is here: 20 | [Find Maxima - notebook](https://github.com/dwaithe/live-coding/blob/main/find-maxima/live-coding-find-maxima.ipynb). 21 | [![Find Maxima 2D](http://img.youtube.com/vi/9wvPsEzRWzI/0.jpg)](https://youtu.be/9wvPsEzRWzI "Find Maxima 2D - live coding - bioimage analysis"). 22 | 23 | 24 | ## Microscopy Figures - Creating linear LUT and merging microscopy images in Python 25 | 26 | Python and the Matplotlib library are great for creating figures. In microscopy however we frequently use linear LUT with a single colour tone, which Matplotlib doesn't support very well. In this notebook I show you how to produce nice linear LUT and also how to merge these images to create multi-channel comparisons. To see a video explaining this notebook, please see:https://youtu.be/dBXUqeXW18c 27 | The code created from this practical is here: 28 | [Microscopy Figures - notebook](https://github.com/dwaithe/live-coding/blob/main/figure-plotting/Figure_plotting.ipynb) 29 | [![Microscopy Figures](http://img.youtube.com/vi/dBXUqeXW18c/0.jpg)](https://youtu.be/dBXUqeXW18c "Microscopy Figures - live coding - Python - bioimage analysis"). 30 | -------------------------------------------------------------------------------- /figure-plotting/images/neuron.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwaithe/live-coding/34c15d763350a19d7d74d8f28c7853f1b13cd2a4/figure-plotting/images/neuron.tif -------------------------------------------------------------------------------- /find-maxima/guide/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwaithe/live-coding/34c15d763350a19d7d74d8f28c7853f1b13cd2a4/find-maxima/guide/.DS_Store -------------------------------------------------------------------------------- /find-maxima/guide/images/002eggs.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwaithe/live-coding/34c15d763350a19d7d74d8f28c7853f1b13cd2a4/find-maxima/guide/images/002eggs.png -------------------------------------------------------------------------------- /find-maxima/guide/images/C1-img_stk_x_-12099.4y_1489.2-1.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwaithe/live-coding/34c15d763350a19d7d74d8f28c7853f1b13cd2a4/find-maxima/guide/images/C1-img_stk_x_-12099.4y_1489.2-1.tif -------------------------------------------------------------------------------- /find-maxima/guide/images/C2-img_stk_x_-12099.4y_1489.2-1.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwaithe/live-coding/34c15d763350a19d7d74d8f28c7853f1b13cd2a4/find-maxima/guide/images/C2-img_stk_x_-12099.4y_1489.2-1.tif -------------------------------------------------------------------------------- /find-maxima/guide/images/cell_fluorescent.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwaithe/live-coding/34c15d763350a19d7d74d8f28c7853f1b13cd2a4/find-maxima/guide/images/cell_fluorescent.tif -------------------------------------------------------------------------------- /find-maxima/images/002eggs.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwaithe/live-coding/34c15d763350a19d7d74d8f28c7853f1b13cd2a4/find-maxima/images/002eggs.png -------------------------------------------------------------------------------- /find-maxima/images/C1-img_stk_x_-12099.4y_1489.2-1.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwaithe/live-coding/34c15d763350a19d7d74d8f28c7853f1b13cd2a4/find-maxima/images/C1-img_stk_x_-12099.4y_1489.2-1.tif -------------------------------------------------------------------------------- /find-maxima/images/C2-img_stk_x_-12099.4y_1489.2-1.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwaithe/live-coding/34c15d763350a19d7d74d8f28c7853f1b13cd2a4/find-maxima/images/C2-img_stk_x_-12099.4y_1489.2-1.tif -------------------------------------------------------------------------------- /find-maxima/images/cell_fluorescent.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwaithe/live-coding/34c15d763350a19d7d74d8f28c7853f1b13cd2a4/find-maxima/images/cell_fluorescent.tif -------------------------------------------------------------------------------- /how-to-solve-a-maze/Circularmazeexample.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwaithe/live-coding/34c15d763350a19d7d74d8f28c7853f1b13cd2a4/how-to-solve-a-maze/Circularmazeexample.jpeg -------------------------------------------------------------------------------- /how-to-solve-a-maze/MAZE_40x20_DFS_no_deadends.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dwaithe/live-coding/34c15d763350a19d7d74d8f28c7853f1b13cd2a4/how-to-solve-a-maze/MAZE_40x20_DFS_no_deadends.png --------------------------------------------------------------------------------