├── .gitignore ├── JUMP_production ├── JUMP_QC_Drag-and-Drop_Notes.docx ├── JUMP_QC_Drag-and-Drop_v1.cppipe ├── JUMP_QC_LoadData_v1.cppipe ├── JUMP_QC_Plate-CV_v1.knwf ├── JUMP_analysis_v3.cppipe ├── JUMP_illum_LoadData_v1.cppipe ├── JUMP_segment_LoadData_v1.cppipe └── readme.md ├── README.md ├── bbbc021_mcf7_20x_imagexpress ├── README.md ├── analysis.cppipe ├── analysis_without_batchfile.cppipe ├── illum.cppipe ├── illum_without_batchfile.cppipe ├── segmentation.cppipe └── segmentation_without_batchfile.cppipe ├── cellpainting_KP4_20x_phenix_bin1 ├── analysis.cppipe ├── analysis_without_batchfile.cppipe ├── illum_without_batchfile.cppipe └── qc_without_batchfile.cppipe ├── cellpainting_UMUC9_20x_phenix_bin2 ├── README.md ├── analysis.cppipe ├── analysis_without_batchfile.cppipe ├── assaydev.cppipe ├── assaydev_without_batchfile.cppipe ├── illum.cppipe └── illum_without_batchfile.cppipe ├── cellpainting_a549_20x_imagexpress ├── README.md ├── analysis.cppipe ├── analysis_without_batchfile.cppipe ├── illum.cppipe ├── illum_without_batchfile.cppipe └── qc.cppipe ├── cellpainting_a549_20x_phenix_bin1 ├── README.md ├── analysis.cppipe ├── analysis_with_mito_radial.cppipe ├── analysis_with_mito_radial_without_batchfile.cppipe ├── analysis_without_batchfile.cppipe ├── illum.cppipe ├── illum_without_batchfile.cppipe ├── qc.cppipe └── qc_without_batchfile.cppipe ├── cellpainting_a549_20x_with_bf_phenix_bin1 ├── README.md ├── analysis.cppipe ├── analysis_without_batchfile.cppipe ├── illum.cppipe ├── illum_without_batchfile.cppipe ├── qc.cppipe └── qc_without_batchfile.cppipe ├── cellpainting_a549_20x_with_bf_with_qc_phenix_bin1 ├── README.md ├── analysis.cppipe ├── analysis_without_batchfile.cppipe ├── illum.cppipe ├── illum_without_batchfile.cppipe ├── qc.cppipe └── qc_without_batchfile.cppipe ├── cellpainting_adipocytes_20x_phenix_bin2 ├── NJ_DavidTest_Analysis_Bin2_prelim_COBLL1.cpproj ├── README.md ├── Update_2021 │ ├── README.md │ ├── analysis.cpproj │ ├── analysis_without_batchfile.cppipe │ ├── assayDev_v7.cppipe │ └── illum_without_batchfile.cppipe ├── analysis.cppipe ├── analysis_with_batchfile.cppipe ├── analysis_without_batchfile.cppipe ├── analysisr2.cppipe ├── illum.cppipe ├── illum_without_batchfile.cppipe ├── qc.cppipe └── qc_without_batchfile.cppipe ├── cellpainting_astrocyte_20x_phenix ├── ProjectionPipeline.cppipe ├── README.md ├── analysis_with_branching.cppipe ├── assaydev.cppipe └── illum_without_batchfile.cppipe ├── cellpainting_ipsc_20x_phenix_with_bf_bin1 ├── README.md ├── analysis.cppipe ├── analysis_without_batchfile.cppipe ├── illum.cppipe └── illum_without_batchfile.cppipe ├── cellpainting_ipsc_20x_phenix_with_bf_bin1_cp3 ├── README.md ├── analysis.cppipe ├── analysis_without_batchfile.cppipe ├── illum.cppipe └── illum_without_batchfile.cppipe ├── cellpainting_ipsc_20x_phenix_with_bf_bin1_cp4 ├── Zproj.cppipe ├── analysis.cppipe ├── assaydev.cppipe └── illum.cppipe ├── cellpainting_min6_63x_phenix_bin2 ├── analysis.cppipe ├── illum.cppipe ├── illum_without_batchfile.cppipe ├── qc.cppipe └── qc_without_batchfile.cppipe ├── cellpainting_neuralprogenitor_20x_phenix ├── README.md ├── analysis_with_branching.cppipe ├── analysis_without_batchfile.cppipe ├── assaydev.cppipe ├── branch_analysis_without_batchfile.cppipe └── illum_without_batchfile.cppipe ├── cellpainting_neuron_20x_phenix ├── ProjectionPipeline.cppipe ├── README.md ├── analysis_with_branching.cppipe ├── assaydev.cppipe └── illum_without_batchfile.cppipe ├── cellpainting_neuron_63x_phenix ├── ProjectionPipeline.cppipe ├── README.md ├── analysis_with_branching.cppipe ├── assaydev.cppipe └── illum_without_batchfile.cppipe ├── cellpainting_snu761_20x_phenix_bin1 ├── analysis.cppipe ├── analysis_without_batchfile.cppipe ├── assaydev.cpproj ├── illum.cppipe ├── illum_without_batchfile.cppipe ├── qc.cppipe └── qc_without_batchfile.cppipe ├── cellpainting_u2os_20x_imagexpress ├── README.md ├── analysis.cppipe ├── analysis_without_batchfile.cppipe ├── illum.cppipe ├── illum_without_batchfile.cppipe ├── qc.cppipe └── save_illum_corrected_files_without_batchfile.cppipe ├── cellpainting_u2os_20x_imagexpress_cdrp ├── README.md ├── analysis.cppipe ├── analysis_without_batchfile.cppipe ├── illum_8x.cppipe ├── illum_8x_without_batchfile.cppipe ├── segmentation.cppipe └── segmentation_without_batchfile.cppipe ├── cellpainting_u2os_63x_phenix_bin2 ├── analysis.cppipe ├── analysis_without_batchfile.cppipe ├── illum.cppipe ├── illum_without_batchfile.cppipe ├── maxproj.cppipe ├── qc.cppipe └── qc_without_batchfile.cppipe ├── segmentation_paramorama └── segmentation_paramorama.cppipe └── tracking_neutrophiles_matrix_comparison ├── readme.md ├── tracking_neutrophiles_4CP22.cppipe └── tracking_neutrophiles_4CP3.cppipe /.gitignore: -------------------------------------------------------------------------------- 1 | .cpproj 2 | -------------------------------------------------------------------------------- /JUMP_production/JUMP_QC_Drag-and-Drop_Notes.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/broadinstitute/imaging-platform-pipelines/7b107db5b54cbe3f0cce4e6488dc24e374d235a0/JUMP_production/JUMP_QC_Drag-and-Drop_Notes.docx -------------------------------------------------------------------------------- /JUMP_production/JUMP_QC_Plate-CV_v1.knwf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/broadinstitute/imaging-platform-pipelines/7b107db5b54cbe3f0cce4e6488dc24e374d235a0/JUMP_production/JUMP_QC_Plate-CV_v1.knwf -------------------------------------------------------------------------------- /JUMP_production/readme.md: -------------------------------------------------------------------------------- 1 | ## JUMP Production 2 | For the [cpg0016-jump](https://github.com/broadinstitute/cellpainting-gallery?tab=readme-ov-file) [JUMP](https://github.com/jump-cellpainting/datasets) production data: 3 | `JUMP_illum_LoadData_v1.cppipe` was used to make the flat-field illumination correction files 4 | `JUMP_analysis_v3.cppipe` was used to apply the illumination correction and perform feature extraction 5 | 6 | ## Pipeline descriptions 7 | 8 | ### Image processing 9 | - `JUMP_illum_LoadData_v1.cppipe`: This is for making flat-field illumination correction files. 10 | - `JUMP_segment_LoadData_v1.cppipe` : This is not necessary for data generation. It is useful for testing segmentation parameters across your dataset prior to running the analysis pipeline. It outputs an overlay image of the Nuclei and Cells objects identified using the segmentation parameters set in the pipeline overlaid on the input image. A previous version of this file accidentally had the ExportToSpreadsheet module enabled, but this module is not needed for downstream usage so has now been disabled in the copy of the pipeline archived here. 11 | - `JUMP_analysis_v2.cppipe` : Second version of the analysis pipeline with additional modules for special mitochondrial features, including EnhanceOrSuppressFeatures, Threshold, MorphologicalSkeleton, MeasureObjectSkeleton, MeasureObjectIntensityDistribution. Mito special features will contain either mito_skel or mito_tubeness in their name. 12 | - `JUMP_analysis_v3.cppipe` : Third version of the analysis pipeline, turning off the exporting of measurements starting with the word `Location` for Cells and Cytoplasm as well as `Number_Object_Number` from Cells only, because a) those measurements are not useful on their own (only relative to one another, which is not an analysis we currently ever perform) and b) the added measurements added in v2 resulted in >2000 measurements for those compartments, which would complicate using SQLite if not manually compiled. If you wish to use those measurements, you may do so, but you must use something besides SQLite (MySQL, Parquet, etc) to store your per-plate databases OR you must [manually compile SQLite](https://gist.github.com/bethac07/1888995cebd3723eb47d04020d65dc7e). If you wish to remove these columns from data that has been processed via the v2 pipeline to avoid the need to reprocess, you may find [this gist](https://gist.github.com/bethac07/c907850982e5ba8164a14f963504edc9) helpful in doing so. 13 | 14 | ### QC pipeline/workflow 15 | 16 | These pipelines/workflow were provided for quickly measuring QC metrics during image acquisition. 17 | 18 | - `JUMP_QC_Drag-and-Drop_v1.cppipe`: QC feature extraction pipeline with drag-and-drop functionality to load images in a quick way 19 | - `JUMP_QC_LoadData_v1.cppipe`: QC feature extraction pipeline using LoadData module to load images in a systematic way 20 | - `JUMP_QC_Plate-CV_v1.knwf`: Knime pipeline to visualize plate QC results 21 | - `JUMP_QC_Drag-and-Drop_Notes.docx`: Notes on how to run the complete on-the-fly QC. Also explained below and in a [demo](https://jjcloud.box.com/s/qlxp7o3bbp02yejvl318udd4ap5gotf1) (starting on minute 3:45) 22 | 23 | To run the QC on-the-fly workflow: 24 | 25 | - Prerequisites: 26 | - Download and install CellProfiler version 4.1.3 desktop client 27 | - Download Knime [current version](https://www.knime.com/downloads) 28 | - Within Knime client, Install HCS Tools 29 | - Download the CellProfiler pipeline `JUMP_QC_Drag-and-Drop_v1.cppipe` from this repo 30 | - Download the Knime workflow `JUMP_QC_Plate-CV_v1.knwf` from this repo 31 | - Run CellProfiler QC on-the-fly pipeline. Notes for most modules are documented within the pipeline notes, but in brief: 32 | - Drag your exported images folder(s) onto the Images module 33 | - Set Output Folder 34 | - Check segmentation settings 35 | - Enter Test Mode 36 | - Run pipeline through the Identify* modules 37 | - Adjust threshold settings as necessary 38 | - Run full set of images 39 | - Ensure to turn off window display for faster processing (Window -> Turn off…) 40 | - Run Knime and load Knime workflow 41 | - Open the CSV Reader “Top Line Per-Image” and set the File path 42 | 43 | ![Screenshot 2021-07-01 at 12 49 31](https://user-images.githubusercontent.com/57905348/124112665-cfa4ba80-da6a-11eb-84cd-87d4a103bea0.png) 44 | - Open the CSV Reader “Top Line Per-Object” and set the File path 45 | 46 | ![Screenshot 2021-07-01 at 12 51 03](https://user-images.githubusercontent.com/57905348/124112851-08dd2a80-da6b-11eb-874c-51c18a488ab7.png) 47 | - Run the workflow 48 | 49 | ![Screenshot 2021-07-01 at 12 51 47](https://user-images.githubusercontent.com/57905348/124113003-375b0580-da6b-11eb-8e2f-9551d43487a1.png) 50 | - Inspect the plots 51 | - Right-click the final nodes and select “View …” 52 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Broad Imaging Platform pipelines 2 | 3 | Cell Painting and other pipelines from the Imaging Platform. 4 | 5 | ## Guidelines for creating pipelines 6 | 7 | **Note**: 8 | 9 | 1. Each pipeline has two versions – one with `CreateBatchFiles` module enabled (named e.g. `analysis.cppipe`), and the other with the moduled disabled (named e.g. `analysis_without_batchfile.cppipe`). When updating the pipeline, ensure that these two versions are always in sync. 10 | The former is required by a [script](https://github.com/broadinstitute/cellpainting_scripts/blob/master/create_batch_files.sh) for creating CellProfiler batch files, which in turn are used to create a list of groups of images to be processed together, as well as Distributed-CellProfiler configuration files. The latter is used to run the pipeline using [Distributed-CellProfiler](https://github.com/CellProfiler/Distributed-CellProfiler/wiki). 11 | 12 | 2. The `ExportToSpreadsheet` module should always be configured with these values in order that the files are saved in a standard format and location 13 | ``` 14 | Select the column delimiter:Comma (",") 15 | Add image metadata columns to your object data file?:No 16 | Limit output to a size that is allowed in Excel?:No 17 | Select the measurements to export:No 18 | Output file location:Default Output Folder\x7C 19 | Select source of sample row name:Metadata 20 | Select the image to use as the identifier:None 21 | Select the metadata to use as the identifier:None 22 | Export all measurement types?:Yes 23 | : 24 | Representation of Nan/Inf:NaN 25 | Add a prefix to file names?:No 26 | Filename prefix: 27 | Overwrite existing files without warning?:Yes 28 | Data to export:Do not use 29 | Combine these object measurements with those of the previous object?:No 30 | File name: 31 | Use the object name for the file name?:Yes 32 | ``` 33 | 34 | 3. The `SaveImages` module should always be configured with these values in order that the files are saved in a standard format and location. The values shown for `Select image name for file prefix` and `Enter single file name` are specific for this example and should be adapted appropriately. 35 | 36 | ``` 37 | Select image name for file prefix:OrigDNA 38 | Enter single file name:\\\\g_s\\\\g--nuclei_outlines 39 | Output file location:Default Output Folder sub-folder\x7Coutlines 40 | Overwrite existing files without warning?:Yes 41 | ``` 42 | -------------------------------------------------------------------------------- /bbbc021_mcf7_20x_imagexpress/README.md: -------------------------------------------------------------------------------- 1 | Pipelines for "Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment", Ljosa et al. 2013 2 | (https://doi.org/10.1177/1087057113503553) 3 | 4 | - The segmentation pipeline is customized for MCF7 cells imaged using a ×20 PanFluor ELWD Ph1 DM objective and a 16-bit camera binning resolution of 1. 5 | -------------------------------------------------------------------------------- /bbbc021_mcf7_20x_imagexpress/illum.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20171031144938 4 | GitHash:478e2fe17 5 | ModuleCount:8 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Elsewhere...\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C. 13 | Process just a range of rows?:No 14 | Rows to process:1,240 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate 17 | Rescale intensities?:Yes 18 | 19 | CorrectIlluminationCalculate:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Select the input image:OrigDAPI 21 | Name the output image:IllumDAPI 22 | Select how the illumination function is calculated:Regular 23 | Dilate objects in the final averaged image?:No 24 | Dilation radius:1 25 | Block size:60 26 | Rescale the illumination function?:Yes 27 | Calculate function for each image individually, or based on all images?:All\x3A Across cycles 28 | Smoothing method:Median Filter 29 | Method to calculate smoothing filter size:Manually 30 | Approximate object size:10 31 | Smoothing filter size:500 32 | Retain the averaged image?:No 33 | Name the averaged image: 34 | Retain the dilated image?:No 35 | Name the dilated image:IllumDAPIDilated 36 | Automatically calculate spline parameters?:Yes 37 | Background mode:auto 38 | Number of spline points:5 39 | Background threshold:2 40 | Image resampling factor:2 41 | Maximum number of iterations:40 42 | Residual value for convergence:0.001 43 | 44 | CorrectIlluminationCalculate:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 45 | Select the input image:OrigActin 46 | Name the output image:IllumActin 47 | Select how the illumination function is calculated:Regular 48 | Dilate objects in the final averaged image?:No 49 | Dilation radius:1 50 | Block size:60 51 | Rescale the illumination function?:Yes 52 | Calculate function for each image individually, or based on all images?:All\x3A Across cycles 53 | Smoothing method:Median Filter 54 | Method to calculate smoothing filter size:Manually 55 | Approximate object size:10 56 | Smoothing filter size:500 57 | Retain the averaged image?:No 58 | Name the averaged image: 59 | Retain the dilated image?:No 60 | Name the dilated image:IllumBlueDilated 61 | Automatically calculate spline parameters?:Yes 62 | Background mode:auto 63 | Number of spline points:5 64 | Background threshold:2 65 | Image resampling factor:2 66 | Maximum number of iterations:40 67 | Residual value for convergence:0.001 68 | 69 | CorrectIlluminationCalculate:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 70 | Select the input image:OrigTubulin 71 | Name the output image:IllumTubulin 72 | Select how the illumination function is calculated:Regular 73 | Dilate objects in the final averaged image?:No 74 | Dilation radius:1 75 | Block size:60 76 | Rescale the illumination function?:Yes 77 | Calculate function for each image individually, or based on all images?:All\x3A Across cycles 78 | Smoothing method:Median Filter 79 | Method to calculate smoothing filter size:Manually 80 | Approximate object size:10 81 | Smoothing filter size:500 82 | Retain the averaged image?:No 83 | Name the averaged image: 84 | Retain the dilated image?:No 85 | Name the dilated image:IllumBlueDilated 86 | Automatically calculate spline parameters?:Yes 87 | Background mode:auto 88 | Number of spline points:5 89 | Background threshold:2 90 | Image resampling factor:2 91 | Maximum number of iterations:40 92 | Residual value for convergence:0.001 93 | 94 | SaveImages:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 95 | Select the type of image to save:Image 96 | Select the image to save:IllumActin 97 | Select the objects to save:None 98 | Select the module display window to save:CorrActin 99 | Select method for constructing file names:Single name 100 | Select image name for file prefix:Actin 101 | Enter single file name:\\\\g_IllumActin 102 | Number of digits:4 103 | Append a suffix to the image file name?:Yes 104 | Text to append to the image name:Actin 105 | Saved file format:mat 106 | Output file location:Default Output Folder\x7CNone 107 | Image bit depth:8-bit integer 108 | Overwrite existing files without warning?:Yes 109 | When to save:Last cycle 110 | Rescale the images? :No 111 | Save as grayscale or color image?:Grayscale 112 | Select colormap:gray 113 | Record the file and path information to the saved image?:No 114 | Create subfolders in the output folder?:No 115 | Base image folder:Default Input Folder 116 | Saved movie format:avi 117 | 118 | SaveImages:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 119 | Select the type of image to save:Image 120 | Select the image to save:IllumDAPI 121 | Select the objects to save:None 122 | Select the module display window to save:CorrActin 123 | Select method for constructing file names:Single name 124 | Select image name for file prefix:Actin 125 | Enter single file name:\\\\g_IllumDAPI 126 | Number of digits:4 127 | Append a suffix to the image file name?:Yes 128 | Text to append to the image name:Actin 129 | Saved file format:mat 130 | Output file location:Default Output Folder\x7CNone 131 | Image bit depth:8-bit integer 132 | Overwrite existing files without warning?:Yes 133 | When to save:Last cycle 134 | Rescale the images? :No 135 | Save as grayscale or color image?:Grayscale 136 | Select colormap:gray 137 | Record the file and path information to the saved image?:No 138 | Create subfolders in the output folder?:No 139 | Base image folder:Default Input Folder 140 | Saved movie format:avi 141 | 142 | SaveImages:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 143 | Select the type of image to save:Image 144 | Select the image to save:IllumTubulin 145 | Select the objects to save:None 146 | Select the module display window to save:CorrActin 147 | Select method for constructing file names:Single name 148 | Select image name for file prefix:Actin 149 | Enter single file name:\\\\g_IllumTubulin 150 | Number of digits:4 151 | Append a suffix to the image file name?:Yes 152 | Text to append to the image name:Actin 153 | Saved file format:mat 154 | Output file location:Default Output Folder\x7CNone 155 | Image bit depth:8-bit integer 156 | Overwrite existing files without warning?:Yes 157 | When to save:Last cycle 158 | Rescale the images? :No 159 | Save as grayscale or color image?:Grayscale 160 | Select colormap:gray 161 | Record the file and path information to the saved image?:No 162 | Create subfolders in the output folder?:No 163 | Base image folder:Default Input Folder 164 | Saved movie format:avi 165 | 166 | CreateBatchFiles:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 167 | Store batch files in default output folder?:Yes 168 | Output folder path:C\x3A\\\\\\\\Users\\\\\\\\mbray\\\\\\\\Desktop 169 | Are the cluster computers running Windows?:No 170 | Hidden\x3A in batch mode:No 171 | Hidden\x3A in distributed mode:No 172 | Hidden\x3A default input folder at time of save:C\x3A\\\\Users\\\\mbray\\\\Desktop 173 | Hidden\x3A revision number:11710 174 | Hidden\x3A from old matlab:No 175 | Launch BatchProfiler:No 176 | -------------------------------------------------------------------------------- /bbbc021_mcf7_20x_imagexpress/illum_without_batchfile.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20171031144938 4 | GitHash:478e2fe17 5 | ModuleCount:8 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Elsewhere...\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C. 13 | Process just a range of rows?:No 14 | Rows to process:1,240 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate 17 | Rescale intensities?:Yes 18 | 19 | CorrectIlluminationCalculate:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Select the input image:OrigDAPI 21 | Name the output image:IllumDAPI 22 | Select how the illumination function is calculated:Regular 23 | Dilate objects in the final averaged image?:No 24 | Dilation radius:1 25 | Block size:60 26 | Rescale the illumination function?:Yes 27 | Calculate function for each image individually, or based on all images?:All\x3A Across cycles 28 | Smoothing method:Median Filter 29 | Method to calculate smoothing filter size:Manually 30 | Approximate object size:10 31 | Smoothing filter size:500 32 | Retain the averaged image?:No 33 | Name the averaged image: 34 | Retain the dilated image?:No 35 | Name the dilated image:IllumDAPIDilated 36 | Automatically calculate spline parameters?:Yes 37 | Background mode:auto 38 | Number of spline points:5 39 | Background threshold:2 40 | Image resampling factor:2 41 | Maximum number of iterations:40 42 | Residual value for convergence:0.001 43 | 44 | CorrectIlluminationCalculate:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 45 | Select the input image:OrigActin 46 | Name the output image:IllumActin 47 | Select how the illumination function is calculated:Regular 48 | Dilate objects in the final averaged image?:No 49 | Dilation radius:1 50 | Block size:60 51 | Rescale the illumination function?:Yes 52 | Calculate function for each image individually, or based on all images?:All\x3A Across cycles 53 | Smoothing method:Median Filter 54 | Method to calculate smoothing filter size:Manually 55 | Approximate object size:10 56 | Smoothing filter size:500 57 | Retain the averaged image?:No 58 | Name the averaged image: 59 | Retain the dilated image?:No 60 | Name the dilated image:IllumBlueDilated 61 | Automatically calculate spline parameters?:Yes 62 | Background mode:auto 63 | Number of spline points:5 64 | Background threshold:2 65 | Image resampling factor:2 66 | Maximum number of iterations:40 67 | Residual value for convergence:0.001 68 | 69 | CorrectIlluminationCalculate:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 70 | Select the input image:OrigTubulin 71 | Name the output image:IllumTubulin 72 | Select how the illumination function is calculated:Regular 73 | Dilate objects in the final averaged image?:No 74 | Dilation radius:1 75 | Block size:60 76 | Rescale the illumination function?:Yes 77 | Calculate function for each image individually, or based on all images?:All\x3A Across cycles 78 | Smoothing method:Median Filter 79 | Method to calculate smoothing filter size:Manually 80 | Approximate object size:10 81 | Smoothing filter size:500 82 | Retain the averaged image?:No 83 | Name the averaged image: 84 | Retain the dilated image?:No 85 | Name the dilated image:IllumBlueDilated 86 | Automatically calculate spline parameters?:Yes 87 | Background mode:auto 88 | Number of spline points:5 89 | Background threshold:2 90 | Image resampling factor:2 91 | Maximum number of iterations:40 92 | Residual value for convergence:0.001 93 | 94 | SaveImages:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 95 | Select the type of image to save:Image 96 | Select the image to save:IllumActin 97 | Select the objects to save:None 98 | Select the module display window to save:CorrActin 99 | Select method for constructing file names:Single name 100 | Select image name for file prefix:Actin 101 | Enter single file name:\\\\g_IllumActin 102 | Number of digits:4 103 | Append a suffix to the image file name?:Yes 104 | Text to append to the image name:Actin 105 | Saved file format:mat 106 | Output file location:Default Output Folder\x7CNone 107 | Image bit depth:8-bit integer 108 | Overwrite existing files without warning?:Yes 109 | When to save:Last cycle 110 | Rescale the images? :No 111 | Save as grayscale or color image?:Grayscale 112 | Select colormap:gray 113 | Record the file and path information to the saved image?:No 114 | Create subfolders in the output folder?:No 115 | Base image folder:Default Input Folder 116 | Saved movie format:avi 117 | 118 | SaveImages:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 119 | Select the type of image to save:Image 120 | Select the image to save:IllumDAPI 121 | Select the objects to save:None 122 | Select the module display window to save:CorrActin 123 | Select method for constructing file names:Single name 124 | Select image name for file prefix:Actin 125 | Enter single file name:\\\\g_IllumDAPI 126 | Number of digits:4 127 | Append a suffix to the image file name?:Yes 128 | Text to append to the image name:Actin 129 | Saved file format:mat 130 | Output file location:Default Output Folder\x7CNone 131 | Image bit depth:8-bit integer 132 | Overwrite existing files without warning?:Yes 133 | When to save:Last cycle 134 | Rescale the images? :No 135 | Save as grayscale or color image?:Grayscale 136 | Select colormap:gray 137 | Record the file and path information to the saved image?:No 138 | Create subfolders in the output folder?:No 139 | Base image folder:Default Input Folder 140 | Saved movie format:avi 141 | 142 | SaveImages:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 143 | Select the type of image to save:Image 144 | Select the image to save:IllumTubulin 145 | Select the objects to save:None 146 | Select the module display window to save:CorrActin 147 | Select method for constructing file names:Single name 148 | Select image name for file prefix:Actin 149 | Enter single file name:\\\\g_IllumTubulin 150 | Number of digits:4 151 | Append a suffix to the image file name?:Yes 152 | Text to append to the image name:Actin 153 | Saved file format:mat 154 | Output file location:Default Output Folder\x7CNone 155 | Image bit depth:8-bit integer 156 | Overwrite existing files without warning?:Yes 157 | When to save:Last cycle 158 | Rescale the images? :No 159 | Save as grayscale or color image?:Grayscale 160 | Select colormap:gray 161 | Record the file and path information to the saved image?:No 162 | Create subfolders in the output folder?:No 163 | Base image folder:Default Input Folder 164 | Saved movie format:avi 165 | 166 | CreateBatchFiles:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:False|wants_pause:False] 167 | Store batch files in default output folder?:Yes 168 | Output folder path:C\x3A\\\\\\\\Users\\\\\\\\mbray\\\\\\\\Desktop 169 | Are the cluster computers running Windows?:No 170 | Hidden\x3A in batch mode:No 171 | Hidden\x3A in distributed mode:No 172 | Hidden\x3A default input folder at time of save:C\x3A\\\\Users\\\\mbray\\\\Desktop 173 | Hidden\x3A revision number:11710 174 | Hidden\x3A from old matlab:No 175 | Launch BatchProfiler:No 176 | -------------------------------------------------------------------------------- /cellpainting_KP4_20x_phenix_bin1/qc_without_batchfile.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160418141927 4 | GitHash:9969f42 5 | ModuleCount:5 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Elsewhere...\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well,Site 17 | Rescale intensities?:Yes 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:All loaded images 21 | Image count:1 22 | Scale count:4 23 | Threshold count:1 24 | Select the images to measure: 25 | Include the image rescaling value?:Yes 26 | Calculate blur metrics?:Yes 27 | Spatial scale for blur measurements:5 28 | Spatial scale for blur measurements:10 29 | Spatial scale for blur measurements:20 30 | Spatial scale for blur measurements:50 31 | Calculate saturation metrics?:Yes 32 | Calculate intensity metrics?:Yes 33 | Calculate thresholds?:No 34 | Use all thresholding methods?:Yes 35 | Select a thresholding method:Otsu 36 | Typical fraction of the image covered by objects:0.1 37 | Two-class or three-class thresholding?:Two classes 38 | Minimize the weighted variance or the entropy?:Weighted variance 39 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:Select... 43 | Image count:2 44 | Scale count:1 45 | Threshold count:1 46 | Scale count:1 47 | Threshold count:1 48 | Select the images to measure:OrigDNA 49 | Include the image rescaling value?:No 50 | Calculate blur metrics?:No 51 | Spatial scale for blur measurements:20 52 | Calculate saturation metrics?:No 53 | Calculate intensity metrics?:No 54 | Calculate thresholds?:Yes 55 | Use all thresholding methods?:No 56 | Select a thresholding method:Otsu 57 | Typical fraction of the image covered by objects:0.1 58 | Two-class or three-class thresholding?:Two classes 59 | Minimize the weighted variance or the entropy?:Weighted variance 60 | Assign pixels in the middle intensity class to the foreground or the background?:Background 61 | Select the images to measure:OrigRNA 62 | Include the image rescaling value?:No 63 | Calculate blur metrics?:No 64 | Spatial scale for blur measurements:20 65 | Calculate saturation metrics?:No 66 | Calculate intensity metrics?:No 67 | Calculate thresholds?:Yes 68 | Use all thresholding methods?:No 69 | Select a thresholding method:Otsu 70 | Typical fraction of the image covered by objects:0.1 71 | Two-class or three-class thresholding?:Three classes 72 | Minimize the weighted variance or the entropy?:Weighted variance 73 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:Comma (",") 77 | Add image metadata columns to your object data file?:No 78 | Limit output to a size that is allowed in Excel?:No 79 | Select the measurements to export:No 80 | Calculate the per-image mean values for object measurements?:No 81 | Calculate the per-image median values for object measurements?:No 82 | Calculate the per-image standard deviation values for object measurements?:No 83 | Output file location:Default Output Folder sub-folder\x7C 84 | Create a GenePattern GCT file?:No 85 | Select source of sample row name:Metadata 86 | Select the image to use as the identifier:None 87 | Select the metadata to use as the identifier:None 88 | Export all measurement types?:Yes 89 | : 90 | Representation of Nan/Inf:NaN 91 | Add a prefix to file names?:Yes 92 | Filename prefix:QC_ 93 | Overwrite existing files without warning?:No 94 | Data to export:Do not use 95 | Combine these object measurements with those of the previous object?:No 96 | File name:DATA.csv 97 | Use the object name for the file name?:Yes 98 | 99 | CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:False|wants_pause:False] 100 | Store batch files in default output folder?:Yes 101 | Output folder path:/imaging/analysis/2008_12_04_Imaging_CDRP_for_MLPCN/HDAC_inhibitors/20100803 102 | Are the cluster computers running Windows?:No 103 | Hidden\x3A in batch mode:No 104 | Hidden\x3A in distributed mode:No 105 | Hidden\x3A default input folder at time of save:/cbnt/cbimage/HCS 106 | Hidden\x3A revision number:10346 107 | Hidden\x3A from old matlab:No 108 | Launch BatchProfiler:No 109 | -------------------------------------------------------------------------------- /cellpainting_UMUC9_20x_phenix_bin2/README.md: -------------------------------------------------------------------------------- 1 | * CP4 pipelines for analyzing UMUC9 cells with 20x magnification and binning of 2. 2 | * Made as part of 2021_07_23_PPARG_agonist_Target_ID Batch 1 3 | * Very similar to standard JUMP CP4 production pipelines 4 | -------------------------------------------------------------------------------- /cellpainting_a549_20x_imagexpress/README.md: -------------------------------------------------------------------------------- 1 | - The analysis pipeline is customized for A549 cells imaged at 20x on ImageXpress, with binning. 2 | - The illumination pipeline requires that the image dimensions are a multiple of 10 because it downsamples and upsamples by a factor of 10. -------------------------------------------------------------------------------- /cellpainting_a549_20x_imagexpress/qc.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160503183100 4 | GitHash:ac0529e 5 | ModuleCount:4 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Elsewhere...\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well 17 | Rescale intensities?:Yes 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:All loaded images 21 | Image count:1 22 | Scale count:4 23 | Threshold count:1 24 | Select the images to measure: 25 | Include the image rescaling value?:Yes 26 | Calculate blur metrics?:Yes 27 | Spatial scale for blur measurements:2 28 | Spatial scale for blur measurements:5 29 | Spatial scale for blur measurements:10 30 | Spatial scale for blur measurements:20 31 | Calculate saturation metrics?:Yes 32 | Calculate intensity metrics?:Yes 33 | Calculate thresholds?:No 34 | Use all thresholding methods?:Yes 35 | Select a thresholding method:Otsu 36 | Typical fraction of the image covered by objects:0.1 37 | Two-class or three-class thresholding?:Two classes 38 | Minimize the weighted variance or the entropy?:Weighted variance 39 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:Select... 43 | Image count:2 44 | Scale count:1 45 | Threshold count:1 46 | Scale count:1 47 | Threshold count:1 48 | Select the images to measure:OrigDNA 49 | Include the image rescaling value?:No 50 | Calculate blur metrics?:No 51 | Spatial scale for blur measurements:20 52 | Calculate saturation metrics?:No 53 | Calculate intensity metrics?:No 54 | Calculate thresholds?:Yes 55 | Use all thresholding methods?:No 56 | Select a thresholding method:Otsu 57 | Typical fraction of the image covered by objects:0.1 58 | Two-class or three-class thresholding?:Two classes 59 | Minimize the weighted variance or the entropy?:Weighted variance 60 | Assign pixels in the middle intensity class to the foreground or the background?:Background 61 | Select the images to measure:OrigRNA 62 | Include the image rescaling value?:No 63 | Calculate blur metrics?:No 64 | Spatial scale for blur measurements:20 65 | Calculate saturation metrics?:No 66 | Calculate intensity metrics?:No 67 | Calculate thresholds?:Yes 68 | Use all thresholding methods?:No 69 | Select a thresholding method:Otsu 70 | Typical fraction of the image covered by objects:0.1 71 | Two-class or three-class thresholding?:Three classes 72 | Minimize the weighted variance or the entropy?:Weighted variance 73 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:Comma (",") 77 | Add image metadata columns to your object data file?:No 78 | Limit output to a size that is allowed in Excel?:No 79 | Select the measurements to export:No 80 | Calculate the per-image mean values for object measurements?:No 81 | Calculate the per-image median values for object measurements?:No 82 | Calculate the per-image standard deviation values for object measurements?:No 83 | Output file location:Default Output Folder\x7C 84 | Create a GenePattern GCT file?:No 85 | Select source of sample row name:Metadata 86 | Select the image to use as the identifier:None 87 | Select the metadata to use as the identifier:None 88 | Export all measurement types?:Yes 89 | : 90 | Representation of Nan/Inf:NaN 91 | Add a prefix to file names?:Yes 92 | Filename prefix:QC_ 93 | Overwrite existing files without warning?:No 94 | Data to export:Do not use 95 | Combine these object measurements with those of the previous object?:No 96 | File name:DATA.csv 97 | Use the object name for the file name?:Yes 98 | -------------------------------------------------------------------------------- /cellpainting_a549_20x_phenix_bin1/README.md: -------------------------------------------------------------------------------- 1 | - The analysis pipeline is customized for A549 cells imaged at 20x on Opera Phenix, without binning. 2 | - The illumination pipeline requires that the image dimensions are a multiple of 10 because it downsamples and upsamples by a factor of 10. 3 | -------------------------------------------------------------------------------- /cellpainting_a549_20x_phenix_bin1/qc.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160503183100 4 | GitHash:ac0529e 5 | ModuleCount:5 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Elsewhere...\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well,Site 17 | Rescale intensities?:Yes 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:All loaded images 21 | Image count:1 22 | Scale count:4 23 | Threshold count:1 24 | Select the images to measure: 25 | Include the image rescaling value?:Yes 26 | Calculate blur metrics?:Yes 27 | Spatial scale for blur measurements:5 28 | Spatial scale for blur measurements:10 29 | Spatial scale for blur measurements:20 30 | Spatial scale for blur measurements:50 31 | Calculate saturation metrics?:Yes 32 | Calculate intensity metrics?:Yes 33 | Calculate thresholds?:No 34 | Use all thresholding methods?:Yes 35 | Select a thresholding method:Otsu 36 | Typical fraction of the image covered by objects:0.1 37 | Two-class or three-class thresholding?:Two classes 38 | Minimize the weighted variance or the entropy?:Weighted variance 39 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:Select... 43 | Image count:2 44 | Scale count:1 45 | Threshold count:1 46 | Scale count:1 47 | Threshold count:1 48 | Select the images to measure:OrigDNA 49 | Include the image rescaling value?:No 50 | Calculate blur metrics?:No 51 | Spatial scale for blur measurements:20 52 | Calculate saturation metrics?:No 53 | Calculate intensity metrics?:No 54 | Calculate thresholds?:Yes 55 | Use all thresholding methods?:No 56 | Select a thresholding method:Otsu 57 | Typical fraction of the image covered by objects:0.1 58 | Two-class or three-class thresholding?:Two classes 59 | Minimize the weighted variance or the entropy?:Weighted variance 60 | Assign pixels in the middle intensity class to the foreground or the background?:Background 61 | Select the images to measure:OrigRNA 62 | Include the image rescaling value?:No 63 | Calculate blur metrics?:No 64 | Spatial scale for blur measurements:20 65 | Calculate saturation metrics?:No 66 | Calculate intensity metrics?:No 67 | Calculate thresholds?:Yes 68 | Use all thresholding methods?:No 69 | Select a thresholding method:Otsu 70 | Typical fraction of the image covered by objects:0.1 71 | Two-class or three-class thresholding?:Three classes 72 | Minimize the weighted variance or the entropy?:Weighted variance 73 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:Comma (",") 77 | Add image metadata columns to your object data file?:No 78 | Limit output to a size that is allowed in Excel?:No 79 | Select the measurements to export:No 80 | Calculate the per-image mean values for object measurements?:No 81 | Calculate the per-image median values for object measurements?:No 82 | Calculate the per-image standard deviation values for object measurements?:No 83 | Output file location:Default Output Folder sub-folder\x7C 84 | Create a GenePattern GCT file?:No 85 | Select source of sample row name:Metadata 86 | Select the image to use as the identifier:None 87 | Select the metadata to use as the identifier:None 88 | Export all measurement types?:Yes 89 | : 90 | Representation of Nan/Inf:NaN 91 | Add a prefix to file names?:Yes 92 | Filename prefix:QC_ 93 | Overwrite existing files without warning?:No 94 | Data to export:Do not use 95 | Combine these object measurements with those of the previous object?:No 96 | File name:DATA.csv 97 | Use the object name for the file name?:Yes 98 | 99 | CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 100 | Store batch files in default output folder?:Yes 101 | Output folder path:/imaging/analysis/2008_12_04_Imaging_CDRP_for_MLPCN/HDAC_inhibitors/20100803 102 | Are the cluster computers running Windows?:No 103 | Hidden\x3A in batch mode:No 104 | Hidden\x3A in distributed mode:No 105 | Hidden\x3A default input folder at time of save:/cbnt/cbimage/HCS 106 | Hidden\x3A revision number:10346 107 | Hidden\x3A from old matlab:No 108 | Launch BatchProfiler:No 109 | -------------------------------------------------------------------------------- /cellpainting_a549_20x_phenix_bin1/qc_without_batchfile.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160503183100 4 | GitHash:ac0529e 5 | ModuleCount:5 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Elsewhere...\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well,Site 17 | Rescale intensities?:Yes 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:All loaded images 21 | Image count:1 22 | Scale count:4 23 | Threshold count:1 24 | Select the images to measure: 25 | Include the image rescaling value?:Yes 26 | Calculate blur metrics?:Yes 27 | Spatial scale for blur measurements:5 28 | Spatial scale for blur measurements:10 29 | Spatial scale for blur measurements:20 30 | Spatial scale for blur measurements:50 31 | Calculate saturation metrics?:Yes 32 | Calculate intensity metrics?:Yes 33 | Calculate thresholds?:No 34 | Use all thresholding methods?:Yes 35 | Select a thresholding method:Otsu 36 | Typical fraction of the image covered by objects:0.1 37 | Two-class or three-class thresholding?:Two classes 38 | Minimize the weighted variance or the entropy?:Weighted variance 39 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:Select... 43 | Image count:2 44 | Scale count:1 45 | Threshold count:1 46 | Scale count:1 47 | Threshold count:1 48 | Select the images to measure:OrigDNA 49 | Include the image rescaling value?:No 50 | Calculate blur metrics?:No 51 | Spatial scale for blur measurements:20 52 | Calculate saturation metrics?:No 53 | Calculate intensity metrics?:No 54 | Calculate thresholds?:Yes 55 | Use all thresholding methods?:No 56 | Select a thresholding method:Otsu 57 | Typical fraction of the image covered by objects:0.1 58 | Two-class or three-class thresholding?:Two classes 59 | Minimize the weighted variance or the entropy?:Weighted variance 60 | Assign pixels in the middle intensity class to the foreground or the background?:Background 61 | Select the images to measure:OrigRNA 62 | Include the image rescaling value?:No 63 | Calculate blur metrics?:No 64 | Spatial scale for blur measurements:20 65 | Calculate saturation metrics?:No 66 | Calculate intensity metrics?:No 67 | Calculate thresholds?:Yes 68 | Use all thresholding methods?:No 69 | Select a thresholding method:Otsu 70 | Typical fraction of the image covered by objects:0.1 71 | Two-class or three-class thresholding?:Three classes 72 | Minimize the weighted variance or the entropy?:Weighted variance 73 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:Comma (",") 77 | Add image metadata columns to your object data file?:No 78 | Limit output to a size that is allowed in Excel?:No 79 | Select the measurements to export:No 80 | Calculate the per-image mean values for object measurements?:No 81 | Calculate the per-image median values for object measurements?:No 82 | Calculate the per-image standard deviation values for object measurements?:No 83 | Output file location:Default Output Folder sub-folder\x7C 84 | Create a GenePattern GCT file?:No 85 | Select source of sample row name:Metadata 86 | Select the image to use as the identifier:None 87 | Select the metadata to use as the identifier:None 88 | Export all measurement types?:Yes 89 | : 90 | Representation of Nan/Inf:NaN 91 | Add a prefix to file names?:Yes 92 | Filename prefix:QC_ 93 | Overwrite existing files without warning?:No 94 | Data to export:Do not use 95 | Combine these object measurements with those of the previous object?:No 96 | File name:DATA.csv 97 | Use the object name for the file name?:Yes 98 | 99 | CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:False|wants_pause:False] 100 | Store batch files in default output folder?:Yes 101 | Output folder path:/imaging/analysis/2008_12_04_Imaging_CDRP_for_MLPCN/HDAC_inhibitors/20100803 102 | Are the cluster computers running Windows?:No 103 | Hidden\x3A in batch mode:No 104 | Hidden\x3A in distributed mode:No 105 | Hidden\x3A default input folder at time of save:/cbnt/cbimage/HCS 106 | Hidden\x3A revision number:10346 107 | Hidden\x3A from old matlab:No 108 | Launch BatchProfiler:No 109 | -------------------------------------------------------------------------------- /cellpainting_a549_20x_with_bf_phenix_bin1/README.md: -------------------------------------------------------------------------------- 1 | - The analysis pipeline is customized for A549 cells imaged at 20x on Opera Phenix, without binning. 2 | - The illumination pipeline requires that the image dimensions are a multiple of 10 because it downsamples and upsamples by a factor of 10. 3 | 4 | Update 02-2018 5 | -Added support for six channel images / including bright field channels 6 | -------------------------------------------------------------------------------- /cellpainting_a549_20x_with_bf_phenix_bin1/qc.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160418141927 4 | GitHash:9969f42 5 | ModuleCount:5 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Elsewhere...\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well,Site 17 | Rescale intensities?:Yes 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:All loaded images 21 | Image count:1 22 | Scale count:4 23 | Threshold count:1 24 | Select the images to measure: 25 | Include the image rescaling value?:Yes 26 | Calculate blur metrics?:Yes 27 | Spatial scale for blur measurements:5 28 | Spatial scale for blur measurements:10 29 | Spatial scale for blur measurements:20 30 | Spatial scale for blur measurements:50 31 | Calculate saturation metrics?:Yes 32 | Calculate intensity metrics?:Yes 33 | Calculate thresholds?:No 34 | Use all thresholding methods?:Yes 35 | Select a thresholding method:Otsu 36 | Typical fraction of the image covered by objects:0.1 37 | Two-class or three-class thresholding?:Two classes 38 | Minimize the weighted variance or the entropy?:Weighted variance 39 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:Select... 43 | Image count:2 44 | Scale count:1 45 | Threshold count:1 46 | Scale count:1 47 | Threshold count:1 48 | Select the images to measure:OrigDNA 49 | Include the image rescaling value?:No 50 | Calculate blur metrics?:No 51 | Spatial scale for blur measurements:20 52 | Calculate saturation metrics?:No 53 | Calculate intensity metrics?:No 54 | Calculate thresholds?:Yes 55 | Use all thresholding methods?:No 56 | Select a thresholding method:Otsu 57 | Typical fraction of the image covered by objects:0.1 58 | Two-class or three-class thresholding?:Two classes 59 | Minimize the weighted variance or the entropy?:Weighted variance 60 | Assign pixels in the middle intensity class to the foreground or the background?:Background 61 | Select the images to measure:OrigRNA 62 | Include the image rescaling value?:No 63 | Calculate blur metrics?:No 64 | Spatial scale for blur measurements:20 65 | Calculate saturation metrics?:No 66 | Calculate intensity metrics?:No 67 | Calculate thresholds?:Yes 68 | Use all thresholding methods?:No 69 | Select a thresholding method:Otsu 70 | Typical fraction of the image covered by objects:0.1 71 | Two-class or three-class thresholding?:Three classes 72 | Minimize the weighted variance or the entropy?:Weighted variance 73 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:Comma (",") 77 | Add image metadata columns to your object data file?:No 78 | Limit output to a size that is allowed in Excel?:No 79 | Select the measurements to export:No 80 | Calculate the per-image mean values for object measurements?:No 81 | Calculate the per-image median values for object measurements?:No 82 | Calculate the per-image standard deviation values for object measurements?:No 83 | Output file location:Default Output Folder sub-folder\x7C 84 | Create a GenePattern GCT file?:No 85 | Select source of sample row name:Metadata 86 | Select the image to use as the identifier:None 87 | Select the metadata to use as the identifier:None 88 | Export all measurement types?:Yes 89 | : 90 | Representation of Nan/Inf:NaN 91 | Add a prefix to file names?:Yes 92 | Filename prefix:QC_ 93 | Overwrite existing files without warning?:No 94 | Data to export:Do not use 95 | Combine these object measurements with those of the previous object?:No 96 | File name:DATA.csv 97 | Use the object name for the file name?:Yes 98 | 99 | CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 100 | Store batch files in default output folder?:Yes 101 | Output folder path:/imaging/analysis/2008_12_04_Imaging_CDRP_for_MLPCN/HDAC_inhibitors/20100803 102 | Are the cluster computers running Windows?:No 103 | Hidden\x3A in batch mode:No 104 | Hidden\x3A in distributed mode:No 105 | Hidden\x3A default input folder at time of save:/cbnt/cbimage/HCS 106 | Hidden\x3A revision number:10346 107 | Hidden\x3A from old matlab:No 108 | Launch BatchProfiler:No 109 | -------------------------------------------------------------------------------- /cellpainting_a549_20x_with_bf_phenix_bin1/qc_without_batchfile.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160418141927 4 | GitHash:9969f42 5 | ModuleCount:5 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Elsewhere...\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well,Site 17 | Rescale intensities?:Yes 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:All loaded images 21 | Image count:1 22 | Scale count:4 23 | Threshold count:1 24 | Select the images to measure: 25 | Include the image rescaling value?:Yes 26 | Calculate blur metrics?:Yes 27 | Spatial scale for blur measurements:5 28 | Spatial scale for blur measurements:10 29 | Spatial scale for blur measurements:20 30 | Spatial scale for blur measurements:50 31 | Calculate saturation metrics?:Yes 32 | Calculate intensity metrics?:Yes 33 | Calculate thresholds?:No 34 | Use all thresholding methods?:Yes 35 | Select a thresholding method:Otsu 36 | Typical fraction of the image covered by objects:0.1 37 | Two-class or three-class thresholding?:Two classes 38 | Minimize the weighted variance or the entropy?:Weighted variance 39 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:Select... 43 | Image count:2 44 | Scale count:1 45 | Threshold count:1 46 | Scale count:1 47 | Threshold count:1 48 | Select the images to measure:OrigDNA 49 | Include the image rescaling value?:No 50 | Calculate blur metrics?:No 51 | Spatial scale for blur measurements:20 52 | Calculate saturation metrics?:No 53 | Calculate intensity metrics?:No 54 | Calculate thresholds?:Yes 55 | Use all thresholding methods?:No 56 | Select a thresholding method:Otsu 57 | Typical fraction of the image covered by objects:0.1 58 | Two-class or three-class thresholding?:Two classes 59 | Minimize the weighted variance or the entropy?:Weighted variance 60 | Assign pixels in the middle intensity class to the foreground or the background?:Background 61 | Select the images to measure:OrigRNA 62 | Include the image rescaling value?:No 63 | Calculate blur metrics?:No 64 | Spatial scale for blur measurements:20 65 | Calculate saturation metrics?:No 66 | Calculate intensity metrics?:No 67 | Calculate thresholds?:Yes 68 | Use all thresholding methods?:No 69 | Select a thresholding method:Otsu 70 | Typical fraction of the image covered by objects:0.1 71 | Two-class or three-class thresholding?:Three classes 72 | Minimize the weighted variance or the entropy?:Weighted variance 73 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:Comma (",") 77 | Add image metadata columns to your object data file?:No 78 | Limit output to a size that is allowed in Excel?:No 79 | Select the measurements to export:No 80 | Calculate the per-image mean values for object measurements?:No 81 | Calculate the per-image median values for object measurements?:No 82 | Calculate the per-image standard deviation values for object measurements?:No 83 | Output file location:Default Output Folder sub-folder\x7C 84 | Create a GenePattern GCT file?:No 85 | Select source of sample row name:Metadata 86 | Select the image to use as the identifier:None 87 | Select the metadata to use as the identifier:None 88 | Export all measurement types?:Yes 89 | : 90 | Representation of Nan/Inf:NaN 91 | Add a prefix to file names?:Yes 92 | Filename prefix:QC_ 93 | Overwrite existing files without warning?:No 94 | Data to export:Do not use 95 | Combine these object measurements with those of the previous object?:No 96 | File name:DATA.csv 97 | Use the object name for the file name?:Yes 98 | 99 | CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:False|wants_pause:False] 100 | Store batch files in default output folder?:Yes 101 | Output folder path:/imaging/analysis/2008_12_04_Imaging_CDRP_for_MLPCN/HDAC_inhibitors/20100803 102 | Are the cluster computers running Windows?:No 103 | Hidden\x3A in batch mode:No 104 | Hidden\x3A in distributed mode:No 105 | Hidden\x3A default input folder at time of save:/cbnt/cbimage/HCS 106 | Hidden\x3A revision number:10346 107 | Hidden\x3A from old matlab:No 108 | Launch BatchProfiler:No 109 | -------------------------------------------------------------------------------- /cellpainting_a549_20x_with_bf_with_qc_phenix_bin1/README.md: -------------------------------------------------------------------------------- 1 | - The analysis pipeline is customized for A549 cells imaged at 20x on Opera Phenix, without binning. 2 | - The illumination pipeline requires that the image dimensions are a multiple of 10 because it downsamples and upsamples by a factor of 10. 3 | - The analysis pipeline was derived from cellpainting_a549_20x_with_bf_phenix_bin1, and the QC was added. The pipeline was used to process plates from the project 2018_02_07_Image_based_Profiling_Pilot -------------------------------------------------------------------------------- /cellpainting_a549_20x_with_bf_with_qc_phenix_bin1/qc.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160418141927 4 | GitHash:9969f42 5 | ModuleCount:5 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Elsewhere...\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well,Site 17 | Rescale intensities?:Yes 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:All loaded images 21 | Image count:1 22 | Scale count:4 23 | Threshold count:1 24 | Select the images to measure: 25 | Include the image rescaling value?:Yes 26 | Calculate blur metrics?:Yes 27 | Spatial scale for blur measurements:5 28 | Spatial scale for blur measurements:10 29 | Spatial scale for blur measurements:20 30 | Spatial scale for blur measurements:50 31 | Calculate saturation metrics?:Yes 32 | Calculate intensity metrics?:Yes 33 | Calculate thresholds?:No 34 | Use all thresholding methods?:Yes 35 | Select a thresholding method:Otsu 36 | Typical fraction of the image covered by objects:0.1 37 | Two-class or three-class thresholding?:Two classes 38 | Minimize the weighted variance or the entropy?:Weighted variance 39 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:Select... 43 | Image count:2 44 | Scale count:1 45 | Threshold count:1 46 | Scale count:1 47 | Threshold count:1 48 | Select the images to measure:OrigDNA 49 | Include the image rescaling value?:No 50 | Calculate blur metrics?:No 51 | Spatial scale for blur measurements:20 52 | Calculate saturation metrics?:No 53 | Calculate intensity metrics?:No 54 | Calculate thresholds?:Yes 55 | Use all thresholding methods?:No 56 | Select a thresholding method:Otsu 57 | Typical fraction of the image covered by objects:0.1 58 | Two-class or three-class thresholding?:Two classes 59 | Minimize the weighted variance or the entropy?:Weighted variance 60 | Assign pixels in the middle intensity class to the foreground or the background?:Background 61 | Select the images to measure:OrigRNA 62 | Include the image rescaling value?:No 63 | Calculate blur metrics?:No 64 | Spatial scale for blur measurements:20 65 | Calculate saturation metrics?:No 66 | Calculate intensity metrics?:No 67 | Calculate thresholds?:Yes 68 | Use all thresholding methods?:No 69 | Select a thresholding method:Otsu 70 | Typical fraction of the image covered by objects:0.1 71 | Two-class or three-class thresholding?:Three classes 72 | Minimize the weighted variance or the entropy?:Weighted variance 73 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:Comma (",") 77 | Add image metadata columns to your object data file?:No 78 | Limit output to a size that is allowed in Excel?:No 79 | Select the measurements to export:No 80 | Calculate the per-image mean values for object measurements?:No 81 | Calculate the per-image median values for object measurements?:No 82 | Calculate the per-image standard deviation values for object measurements?:No 83 | Output file location:Default Output Folder sub-folder\x7C 84 | Create a GenePattern GCT file?:No 85 | Select source of sample row name:Metadata 86 | Select the image to use as the identifier:None 87 | Select the metadata to use as the identifier:None 88 | Export all measurement types?:Yes 89 | : 90 | Representation of Nan/Inf:NaN 91 | Add a prefix to file names?:Yes 92 | Filename prefix:QC_ 93 | Overwrite existing files without warning?:No 94 | Data to export:Do not use 95 | Combine these object measurements with those of the previous object?:No 96 | File name:DATA.csv 97 | Use the object name for the file name?:Yes 98 | 99 | CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 100 | Store batch files in default output folder?:Yes 101 | Output folder path:/imaging/analysis/2008_12_04_Imaging_CDRP_for_MLPCN/HDAC_inhibitors/20100803 102 | Are the cluster computers running Windows?:No 103 | Hidden\x3A in batch mode:No 104 | Hidden\x3A in distributed mode:No 105 | Hidden\x3A default input folder at time of save:/cbnt/cbimage/HCS 106 | Hidden\x3A revision number:10346 107 | Hidden\x3A from old matlab:No 108 | Launch BatchProfiler:No 109 | -------------------------------------------------------------------------------- /cellpainting_a549_20x_with_bf_with_qc_phenix_bin1/qc_without_batchfile.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160418141927 4 | GitHash:9969f42 5 | ModuleCount:5 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Elsewhere...\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well,Site 17 | Rescale intensities?:Yes 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:All loaded images 21 | Image count:1 22 | Scale count:4 23 | Threshold count:1 24 | Select the images to measure: 25 | Include the image rescaling value?:Yes 26 | Calculate blur metrics?:Yes 27 | Spatial scale for blur measurements:5 28 | Spatial scale for blur measurements:10 29 | Spatial scale for blur measurements:20 30 | Spatial scale for blur measurements:50 31 | Calculate saturation metrics?:Yes 32 | Calculate intensity metrics?:Yes 33 | Calculate thresholds?:No 34 | Use all thresholding methods?:Yes 35 | Select a thresholding method:Otsu 36 | Typical fraction of the image covered by objects:0.1 37 | Two-class or three-class thresholding?:Two classes 38 | Minimize the weighted variance or the entropy?:Weighted variance 39 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:Select... 43 | Image count:2 44 | Scale count:1 45 | Threshold count:1 46 | Scale count:1 47 | Threshold count:1 48 | Select the images to measure:OrigDNA 49 | Include the image rescaling value?:No 50 | Calculate blur metrics?:No 51 | Spatial scale for blur measurements:20 52 | Calculate saturation metrics?:No 53 | Calculate intensity metrics?:No 54 | Calculate thresholds?:Yes 55 | Use all thresholding methods?:No 56 | Select a thresholding method:Otsu 57 | Typical fraction of the image covered by objects:0.1 58 | Two-class or three-class thresholding?:Two classes 59 | Minimize the weighted variance or the entropy?:Weighted variance 60 | Assign pixels in the middle intensity class to the foreground or the background?:Background 61 | Select the images to measure:OrigRNA 62 | Include the image rescaling value?:No 63 | Calculate blur metrics?:No 64 | Spatial scale for blur measurements:20 65 | Calculate saturation metrics?:No 66 | Calculate intensity metrics?:No 67 | Calculate thresholds?:Yes 68 | Use all thresholding methods?:No 69 | Select a thresholding method:Otsu 70 | Typical fraction of the image covered by objects:0.1 71 | Two-class or three-class thresholding?:Three classes 72 | Minimize the weighted variance or the entropy?:Weighted variance 73 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:Comma (",") 77 | Add image metadata columns to your object data file?:No 78 | Limit output to a size that is allowed in Excel?:No 79 | Select the measurements to export:No 80 | Calculate the per-image mean values for object measurements?:No 81 | Calculate the per-image median values for object measurements?:No 82 | Calculate the per-image standard deviation values for object measurements?:No 83 | Output file location:Default Output Folder sub-folder\x7C 84 | Create a GenePattern GCT file?:No 85 | Select source of sample row name:Metadata 86 | Select the image to use as the identifier:None 87 | Select the metadata to use as the identifier:None 88 | Export all measurement types?:Yes 89 | : 90 | Representation of Nan/Inf:NaN 91 | Add a prefix to file names?:Yes 92 | Filename prefix:QC_ 93 | Overwrite existing files without warning?:No 94 | Data to export:Do not use 95 | Combine these object measurements with those of the previous object?:No 96 | File name:DATA.csv 97 | Use the object name for the file name?:Yes 98 | 99 | CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:False|wants_pause:False] 100 | Store batch files in default output folder?:Yes 101 | Output folder path:/imaging/analysis/2008_12_04_Imaging_CDRP_for_MLPCN/HDAC_inhibitors/20100803 102 | Are the cluster computers running Windows?:No 103 | Hidden\x3A in batch mode:No 104 | Hidden\x3A in distributed mode:No 105 | Hidden\x3A default input folder at time of save:/cbnt/cbimage/HCS 106 | Hidden\x3A revision number:10346 107 | Hidden\x3A from old matlab:No 108 | Launch BatchProfiler:No 109 | -------------------------------------------------------------------------------- /cellpainting_adipocytes_20x_phenix_bin2/NJ_DavidTest_Analysis_Bin2_prelim_COBLL1.cpproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/broadinstitute/imaging-platform-pipelines/7b107db5b54cbe3f0cce4e6488dc24e374d235a0/cellpainting_adipocytes_20x_phenix_bin2/NJ_DavidTest_Analysis_Bin2_prelim_COBLL1.cpproj -------------------------------------------------------------------------------- /cellpainting_adipocytes_20x_phenix_bin2/README.md: -------------------------------------------------------------------------------- 1 | The original (run) version of the analysis pipelines exported the `Object relationships.csv`; these were then removed by the command below before building the backends. The pipline versions here do not export that CSV. 2 | 3 | `aws s3 rm s3://imaging-platform/projects/2018_04_12_T2D_V2F_Saadat_Broad/workspace/analysis/2019_04_16_Batch1/ --recursive --exclude "*.*" --include "*/analysis/*/Object relationships.csv"` 4 | -------------------------------------------------------------------------------- /cellpainting_adipocytes_20x_phenix_bin2/Update_2021/README.md: -------------------------------------------------------------------------------- 1 | RS updated the pipeline to better detect cells and lipid droplets for lipocyte painting project 2019_08_03_Adipocyte_CellPainting_Claussnitzer Batch11. 2 | -------------------------------------------------------------------------------- /cellpainting_adipocytes_20x_phenix_bin2/Update_2021/analysis.cpproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/broadinstitute/imaging-platform-pipelines/7b107db5b54cbe3f0cce4e6488dc24e374d235a0/cellpainting_adipocytes_20x_phenix_bin2/Update_2021/analysis.cpproj -------------------------------------------------------------------------------- /cellpainting_adipocytes_20x_phenix_bin2/Update_2021/illum_without_batchfile.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:5 3 | DateRevision:413 4 | GitHash: 5 | ModuleCount:18 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:'Unknown'|variable_revision_number:6|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Default Input Folder sub-folder|Desktop\Load_data_CSV\BR00124353 10 | Name of the file:load_data.csv 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder| 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate 17 | Rescale intensities?:Yes 18 | 19 | Resize:[module_num:2|svn_version:'Unknown'|variable_revision_number:4|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 20 | Select the input image:OrigDNA 21 | Name the output image:DownsampledDNA 22 | Resizing method:Resize by a fraction or multiple of the original size 23 | Resizing factor:0.2 24 | Width of the final image:100 25 | Height of the final image:100 26 | Interpolation method:Bilinear 27 | Method to specify the dimensions:Manual 28 | Select the image with the desired dimensions:None 29 | Additional image count:0 30 | 31 | CorrectIlluminationCalculate:[module_num:3|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 32 | Select the input image:DownsampledDNA 33 | Name the output image:IllumDNA 34 | Select how the illumination function is calculated:Regular 35 | Dilate objects in the final averaged image?:No 36 | Dilation radius:1 37 | Block size:60 38 | Rescale the illumination function?:Yes 39 | Calculate function for each image individually, or based on all images?:All: Across cycles 40 | Smoothing method:Median Filter 41 | Method to calculate smoothing filter size:Manually 42 | Approximate object diameter:10 43 | Smoothing filter size:20 44 | Retain the averaged image?:No 45 | Name the averaged image:IllumBlueAvg 46 | Retain the dilated image?:No 47 | Name the dilated image:IllumBlueDilated 48 | Automatically calculate spline parameters?:Yes 49 | Background mode:auto 50 | Number of spline points:5 51 | Background threshold:2 52 | Image resampling factor:2 53 | Maximum number of iterations:40 54 | Residual value for convergence:0.001 55 | 56 | Resize:[module_num:4|svn_version:'Unknown'|variable_revision_number:4|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 57 | Select the input image:IllumDNA 58 | Name the output image:UpsampledIllumDNA 59 | Resizing method:Resize by a fraction or multiple of the original size 60 | Resizing factor:5 61 | Width of the final image:100 62 | Height of the final image:100 63 | Interpolation method:Bilinear 64 | Method to specify the dimensions:Manual 65 | Select the image with the desired dimensions:None 66 | Additional image count:0 67 | 68 | Resize:[module_num:5|svn_version:'Unknown'|variable_revision_number:4|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 69 | Select the input image:OrigBODIPY 70 | Name the output image:DownsampledBODIPY 71 | Resizing method:Resize by a fraction or multiple of the original size 72 | Resizing factor:0.2 73 | Width of the final image:100 74 | Height of the final image:100 75 | Interpolation method:Bilinear 76 | Method to specify the dimensions:Manual 77 | Select the image with the desired dimensions:None 78 | Additional image count:0 79 | 80 | CorrectIlluminationCalculate:[module_num:6|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 81 | Select the input image:DownsampledBODIPY 82 | Name the output image:IllumBODIPY 83 | Select how the illumination function is calculated:Regular 84 | Dilate objects in the final averaged image?:No 85 | Dilation radius:1 86 | Block size:60 87 | Rescale the illumination function?:Yes 88 | Calculate function for each image individually, or based on all images?:All: Across cycles 89 | Smoothing method:Median Filter 90 | Method to calculate smoothing filter size:Manually 91 | Approximate object diameter:10 92 | Smoothing filter size:20 93 | Retain the averaged image?:No 94 | Name the averaged image:IllumBlueAvg 95 | Retain the dilated image?:No 96 | Name the dilated image:IllumBlueDilated 97 | Automatically calculate spline parameters?:Yes 98 | Background mode:auto 99 | Number of spline points:5 100 | Background threshold:2 101 | Image resampling factor:2 102 | Maximum number of iterations:40 103 | Residual value for convergence:0.001 104 | 105 | Resize:[module_num:7|svn_version:'Unknown'|variable_revision_number:4|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 106 | Select the input image:IllumBODIPY 107 | Name the output image:UpsampledIllumBODIPY 108 | Resizing method:Resize by a fraction or multiple of the original size 109 | Resizing factor:5 110 | Width of the final image:100 111 | Height of the final image:100 112 | Interpolation method:Bilinear 113 | Method to specify the dimensions:Manual 114 | Select the image with the desired dimensions:None 115 | Additional image count:0 116 | 117 | Resize:[module_num:8|svn_version:'Unknown'|variable_revision_number:4|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 118 | Select the input image:OrigAGP 119 | Name the output image:DownsampledAGP 120 | Resizing method:Resize by a fraction or multiple of the original size 121 | Resizing factor:0.2 122 | Width of the final image:100 123 | Height of the final image:100 124 | Interpolation method:Bilinear 125 | Method to specify the dimensions:Manual 126 | Select the image with the desired dimensions:None 127 | Additional image count:0 128 | 129 | CorrectIlluminationCalculate:[module_num:9|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 130 | Select the input image:DownsampledAGP 131 | Name the output image:IllumAGP 132 | Select how the illumination function is calculated:Regular 133 | Dilate objects in the final averaged image?:No 134 | Dilation radius:1 135 | Block size:60 136 | Rescale the illumination function?:Yes 137 | Calculate function for each image individually, or based on all images?:All: Across cycles 138 | Smoothing method:Median Filter 139 | Method to calculate smoothing filter size:Manually 140 | Approximate object diameter:10 141 | Smoothing filter size:20 142 | Retain the averaged image?:No 143 | Name the averaged image:IllumBlueAvg 144 | Retain the dilated image?:No 145 | Name the dilated image:IllumBlueDilated 146 | Automatically calculate spline parameters?:Yes 147 | Background mode:auto 148 | Number of spline points:5 149 | Background threshold:2 150 | Image resampling factor:2 151 | Maximum number of iterations:40 152 | Residual value for convergence:0.001 153 | 154 | Resize:[module_num:10|svn_version:'Unknown'|variable_revision_number:4|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 155 | Select the input image:IllumAGP 156 | Name the output image:UpsampledIllumAGP 157 | Resizing method:Resize by a fraction or multiple of the original size 158 | Resizing factor:5 159 | Width of the final image:100 160 | Height of the final image:100 161 | Interpolation method:Bilinear 162 | Method to specify the dimensions:Manual 163 | Select the image with the desired dimensions:None 164 | Additional image count:0 165 | 166 | Resize:[module_num:11|svn_version:'Unknown'|variable_revision_number:4|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 167 | Select the input image:OrigMito 168 | Name the output image:DownsampledMito 169 | Resizing method:Resize by a fraction or multiple of the original size 170 | Resizing factor:0.2 171 | Width of the final image:100 172 | Height of the final image:100 173 | Interpolation method:Bilinear 174 | Method to specify the dimensions:Manual 175 | Select the image with the desired dimensions:None 176 | Additional image count:0 177 | 178 | CorrectIlluminationCalculate:[module_num:12|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 179 | Select the input image:DownsampledMito 180 | Name the output image:IllumMito 181 | Select how the illumination function is calculated:Regular 182 | Dilate objects in the final averaged image?:No 183 | Dilation radius:1 184 | Block size:60 185 | Rescale the illumination function?:Yes 186 | Calculate function for each image individually, or based on all images?:All: Across cycles 187 | Smoothing method:Median Filter 188 | Method to calculate smoothing filter size:Manually 189 | Approximate object diameter:10 190 | Smoothing filter size:20 191 | Retain the averaged image?:No 192 | Name the averaged image:IllumBlueAvg 193 | Retain the dilated image?:No 194 | Name the dilated image:IllumBlueDilated 195 | Automatically calculate spline parameters?:Yes 196 | Background mode:auto 197 | Number of spline points:5 198 | Background threshold:2 199 | Image resampling factor:2 200 | Maximum number of iterations:40 201 | Residual value for convergence:0.001 202 | 203 | Resize:[module_num:13|svn_version:'Unknown'|variable_revision_number:4|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 204 | Select the input image:IllumMito 205 | Name the output image:UpsampledIllumMito 206 | Resizing method:Resize by a fraction or multiple of the original size 207 | Resizing factor:5 208 | Width of the final image:100 209 | Height of the final image:100 210 | Interpolation method:Bilinear 211 | Method to specify the dimensions:Manual 212 | Select the image with the desired dimensions:None 213 | Additional image count:0 214 | 215 | SaveImages:[module_num:14|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 216 | Select the type of image to save:Image 217 | Select the image to save:UpsampledIllumAGP 218 | Select method for constructing file names:Single name 219 | Select image name for file prefix:None 220 | Enter single file name:\g_IllumAGP 221 | Number of digits:4 222 | Append a suffix to the image file name?:No 223 | Text to append to the image name: 224 | Saved file format:npy 225 | Output file location:Default Output Folder| 226 | Image bit depth:8-bit integer 227 | Overwrite existing files without warning?:No 228 | When to save:Last cycle 229 | Record the file and path information to the saved image?:No 230 | Create subfolders in the output folder?:No 231 | Base image folder:Elsewhere...| 232 | How to save the series:T (Time) 233 | 234 | SaveImages:[module_num:15|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 235 | Select the type of image to save:Image 236 | Select the image to save:UpsampledIllumDNA 237 | Select method for constructing file names:Single name 238 | Select image name for file prefix:None 239 | Enter single file name:\g_IllumDNA 240 | Number of digits:4 241 | Append a suffix to the image file name?:No 242 | Text to append to the image name: 243 | Saved file format:npy 244 | Output file location:Default Output Folder| 245 | Image bit depth:8-bit integer 246 | Overwrite existing files without warning?:No 247 | When to save:Last cycle 248 | Record the file and path information to the saved image?:No 249 | Create subfolders in the output folder?:No 250 | Base image folder:Elsewhere...| 251 | How to save the series:T (Time) 252 | 253 | SaveImages:[module_num:16|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 254 | Select the type of image to save:Image 255 | Select the image to save:UpsampledIllumBODIPY 256 | Select method for constructing file names:Single name 257 | Select image name for file prefix:None 258 | Enter single file name:\g_IllumBODIPY 259 | Number of digits:4 260 | Append a suffix to the image file name?:No 261 | Text to append to the image name: 262 | Saved file format:npy 263 | Output file location:Default Output Folder| 264 | Image bit depth:8-bit integer 265 | Overwrite existing files without warning?:No 266 | When to save:Last cycle 267 | Record the file and path information to the saved image?:No 268 | Create subfolders in the output folder?:No 269 | Base image folder:Elsewhere...| 270 | How to save the series:T (Time) 271 | 272 | SaveImages:[module_num:17|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 273 | Select the type of image to save:Image 274 | Select the image to save:UpsampledIllumMito 275 | Select method for constructing file names:Single name 276 | Select image name for file prefix:None 277 | Enter single file name:\g_IllumMito 278 | Number of digits:4 279 | Append a suffix to the image file name?:No 280 | Text to append to the image name: 281 | Saved file format:npy 282 | Output file location:Default Output Folder| 283 | Image bit depth:8-bit integer 284 | Overwrite existing files without warning?:No 285 | When to save:Last cycle 286 | Record the file and path information to the saved image?:No 287 | Create subfolders in the output folder?:No 288 | Base image folder:Elsewhere...| 289 | How to save the series:T (Time) 290 | 291 | CreateBatchFiles:[module_num:18|svn_version:'Unknown'|variable_revision_number:8|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:False|wants_pause:False] 292 | Store batch files in default output folder?:Yes 293 | Output folder path:/Users/bcimini/Desktop/Nanostring 294 | Are the cluster computers running Windows?:No 295 | Hidden- in batch mode:No 296 | Hidden- in distributed mode:No 297 | Hidden- default input folder at time of save:/Users/bcimini/Desktop/2018_08_14_Lysosomes_RyanTyler_Amathus 298 | Hidden- revision number:0 299 | Hidden- from old matlab:No 300 | -------------------------------------------------------------------------------- /cellpainting_adipocytes_20x_phenix_bin2/qc.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:4 3 | DateRevision:318 4 | GitHash: 5 | ModuleCount:5 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00/\x00U\x00s\x00e\x00r\x00s\x00/\x00b\x00c\x00i\x00m\x00i\x00n\x00i\x00/\x00D\x00o\x00w\x00n\x00l\x00o\x00a\x00d\x00s\x00 10 | Name of the file:\xff\xfel\x00o\x00a\x00d\x00_\x00d\x00a\x00t\x00a\x00.\x00c\x00s\x00v\x00 11 | Load images based on this data?:\xff\xfeY\x00e\x00s\x00 12 | Base image location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00I\x00n\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 13 | Process just a range of rows?:\xff\xfeN\x00o\x00 14 | Rows to process:\xff\xfe1\x00,\x001\x000\x000\x000\x000\x000\x00 15 | Group images by metadata?:\xff\xfeY\x00e\x00s\x00 16 | Select metadata tags for grouping:\xff\xfeP\x00l\x00a\x00t\x00e\x00,\x00W\x00e\x00l\x00l\x00,\x00S\x00i\x00t\x00e\x00 17 | Rescale intensities?:\xff\xfeY\x00e\x00s\x00 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:\xff\xfeA\x00l\x00l\x00 \x00l\x00o\x00a\x00d\x00e\x00d\x00 \x00i\x00m\x00a\x00g\x00e\x00s\x00 21 | Image count:\xff\xfe1\x00 22 | Scale count:\xff\xfe4\x00 23 | Threshold count:\xff\xfe1\x00 24 | Select the images to measure:\xff\xfe 25 | Include the image rescaling value?:\xff\xfeY\x00e\x00s\x00 26 | Calculate blur metrics?:\xff\xfeY\x00e\x00s\x00 27 | Spatial scale for blur measurements:\xff\xfe2\x00 28 | Spatial scale for blur measurements:\xff\xfe5\x00 29 | Spatial scale for blur measurements:\xff\xfe1\x000\x00 30 | Spatial scale for blur measurements:\xff\xfe2\x005\x00 31 | Calculate saturation metrics?:\xff\xfeY\x00e\x00s\x00 32 | Calculate intensity metrics?:\xff\xfeY\x00e\x00s\x00 33 | Calculate thresholds?:\xff\xfeN\x00o\x00 34 | Use all thresholding methods?:\xff\xfeY\x00e\x00s\x00 35 | Select a thresholding method:\xff\xfeO\x00t\x00s\x00u\x00 36 | Typical fraction of the image covered by objects:\xff\xfe0\x00.\x001\x00 37 | Two-class or three-class thresholding?:\xff\xfeT\x00w\x00o\x00 \x00c\x00l\x00a\x00s\x00s\x00e\x00s\x00 38 | Minimize the weighted variance or the entropy?:\xff\xfeW\x00e\x00i\x00g\x00h\x00t\x00e\x00d\x00 \x00v\x00a\x00r\x00i\x00a\x00n\x00c\x00e\x00 39 | Assign pixels in the middle intensity class to the foreground or the background?:\xff\xfeF\x00o\x00r\x00e\x00g\x00r\x00o\x00u\x00n\x00d\x00 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:\xff\xfeS\x00e\x00l\x00e\x00c\x00t\x00.\x00.\x00.\x00 43 | Image count:\xff\xfe2\x00 44 | Scale count:\xff\xfe1\x00 45 | Threshold count:\xff\xfe1\x00 46 | Scale count:\xff\xfe1\x00 47 | Threshold count:\xff\xfe1\x00 48 | Select the images to measure:\xff\xfeO\x00r\x00i\x00g\x00D\x00N\x00A\x00 49 | Include the image rescaling value?:\xff\xfeN\x00o\x00 50 | Calculate blur metrics?:\xff\xfeN\x00o\x00 51 | Spatial scale for blur measurements:\xff\xfe2\x000\x00 52 | Calculate saturation metrics?:\xff\xfeN\x00o\x00 53 | Calculate intensity metrics?:\xff\xfeN\x00o\x00 54 | Calculate thresholds?:\xff\xfeY\x00e\x00s\x00 55 | Use all thresholding methods?:\xff\xfeN\x00o\x00 56 | Select a thresholding method:\xff\xfeO\x00t\x00s\x00u\x00 57 | Typical fraction of the image covered by objects:\xff\xfe0\x00.\x001\x00 58 | Two-class or three-class thresholding?:\xff\xfeT\x00w\x00o\x00 \x00c\x00l\x00a\x00s\x00s\x00e\x00s\x00 59 | Minimize the weighted variance or the entropy?:\xff\xfeW\x00e\x00i\x00g\x00h\x00t\x00e\x00d\x00 \x00v\x00a\x00r\x00i\x00a\x00n\x00c\x00e\x00 60 | Assign pixels in the middle intensity class to the foreground or the background?:\xff\xfeB\x00a\x00c\x00k\x00g\x00r\x00o\x00u\x00n\x00d\x00 61 | Select the images to measure:\xff\xfeO\x00r\x00i\x00g\x00A\x00G\x00P\x00 62 | Include the image rescaling value?:\xff\xfeN\x00o\x00 63 | Calculate blur metrics?:\xff\xfeN\x00o\x00 64 | Spatial scale for blur measurements:\xff\xfe2\x000\x00 65 | Calculate saturation metrics?:\xff\xfeN\x00o\x00 66 | Calculate intensity metrics?:\xff\xfeN\x00o\x00 67 | Calculate thresholds?:\xff\xfeY\x00e\x00s\x00 68 | Use all thresholding methods?:\xff\xfeN\x00o\x00 69 | Select a thresholding method:\xff\xfeO\x00t\x00s\x00u\x00 70 | Typical fraction of the image covered by objects:\xff\xfe0\x00.\x001\x00 71 | Two-class or three-class thresholding?:\xff\xfeT\x00h\x00r\x00e\x00e\x00 \x00c\x00l\x00a\x00s\x00s\x00e\x00s\x00 72 | Minimize the weighted variance or the entropy?:\xff\xfeW\x00e\x00i\x00g\x00h\x00t\x00e\x00d\x00 \x00v\x00a\x00r\x00i\x00a\x00n\x00c\x00e\x00 73 | Assign pixels in the middle intensity class to the foreground or the background?:\xff\xfeF\x00o\x00r\x00e\x00g\x00r\x00o\x00u\x00n\x00d\x00 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:12|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:\xff\xfeC\x00o\x00m\x00m\x00a\x00 \x00(\x00"\x00,\x00"\x00)\x00 77 | Add image metadata columns to your object data file?:\xff\xfeN\x00o\x00 78 | Select the measurements to export:\xff\xfeN\x00o\x00 79 | Calculate the per-image mean values for object measurements?:\xff\xfeN\x00o\x00 80 | Calculate the per-image median values for object measurements?:\xff\xfeN\x00o\x00 81 | Calculate the per-image standard deviation values for object measurements?:\xff\xfeN\x00o\x00 82 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00 \x00s\x00u\x00b\x00-\x00f\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 83 | Create a GenePattern GCT file?:\xff\xfeN\x00o\x00 84 | Select source of sample row name:\xff\xfeM\x00e\x00t\x00a\x00d\x00a\x00t\x00a\x00 85 | Select the image to use as the identifier:\xff\xfeN\x00o\x00n\x00e\x00 86 | Select the metadata to use as the identifier:\xff\xfeN\x00o\x00n\x00e\x00 87 | Export all measurement types?:\xff\xfeY\x00e\x00s\x00 88 | Press button to select measurements:\xff\xfe 89 | Representation of Nan/Inf:\xff\xfeN\x00a\x00N\x00 90 | Add a prefix to file names?:\xff\xfeY\x00e\x00s\x00 91 | Filename prefix:\xff\xfeQ\x00C\x00_\x00 92 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 93 | Data to export:\xff\xfeD\x00o\x00 \x00n\x00o\x00t\x00 \x00u\x00s\x00e\x00 94 | Combine these object measurements with those of the previous object?:\xff\xfeN\x00o\x00 95 | File name:\xff\xfeD\x00A\x00T\x00A\x00.\x00c\x00s\x00v\x00 96 | Use the object name for the file name?:\xff\xfeY\x00e\x00s\x00 97 | 98 | CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:8|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 99 | Store batch files in default output folder?:\xff\xfeY\x00e\x00s\x00 100 | Output folder path:\xff\xfe/\x00i\x00m\x00a\x00g\x00i\x00n\x00g\x00/\x00a\x00n\x00a\x00l\x00y\x00s\x00i\x00s\x00/\x002\x000\x000\x008\x00_\x001\x002\x00_\x000\x004\x00_\x00I\x00m\x00a\x00g\x00i\x00n\x00g\x00_\x00C\x00D\x00R\x00P\x00_\x00f\x00o\x00r\x00_\x00M\x00L\x00P\x00C\x00N\x00/\x00H\x00D\x00A\x00C\x00_\x00i\x00n\x00h\x00i\x00b\x00i\x00t\x00o\x00r\x00s\x00/\x002\x000\x001\x000\x000\x008\x000\x003\x00 101 | Are the cluster computers running Windows?:\xff\xfeN\x00o\x00 102 | Hidden\x3A in batch mode:\xff\xfeN\x00o\x00 103 | Hidden\x3A in distributed mode:\xff\xfeN\x00o\x00 104 | Hidden\x3A default input folder at time of save:\xff\xfe/\x00c\x00b\x00n\x00t\x00/\x00c\x00b\x00i\x00m\x00a\x00g\x00e\x00/\x00H\x00C\x00S\x00 105 | Hidden\x3A revision number:\xff\xfe1\x000\x003\x004\x006\x00 106 | Hidden\x3A from old matlab:\xff\xfeN\x00o\x00 107 | -------------------------------------------------------------------------------- /cellpainting_adipocytes_20x_phenix_bin2/qc_without_batchfile.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:4 3 | DateRevision:318 4 | GitHash: 5 | ModuleCount:5 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00/\x00U\x00s\x00e\x00r\x00s\x00/\x00b\x00c\x00i\x00m\x00i\x00n\x00i\x00/\x00D\x00o\x00w\x00n\x00l\x00o\x00a\x00d\x00s\x00 10 | Name of the file:\xff\xfel\x00o\x00a\x00d\x00_\x00d\x00a\x00t\x00a\x00.\x00c\x00s\x00v\x00 11 | Load images based on this data?:\xff\xfeY\x00e\x00s\x00 12 | Base image location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00I\x00n\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 13 | Process just a range of rows?:\xff\xfeN\x00o\x00 14 | Rows to process:\xff\xfe1\x00,\x001\x000\x000\x000\x000\x000\x00 15 | Group images by metadata?:\xff\xfeY\x00e\x00s\x00 16 | Select metadata tags for grouping:\xff\xfeP\x00l\x00a\x00t\x00e\x00,\x00W\x00e\x00l\x00l\x00,\x00S\x00i\x00t\x00e\x00 17 | Rescale intensities?:\xff\xfeY\x00e\x00s\x00 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:\xff\xfeA\x00l\x00l\x00 \x00l\x00o\x00a\x00d\x00e\x00d\x00 \x00i\x00m\x00a\x00g\x00e\x00s\x00 21 | Image count:\xff\xfe1\x00 22 | Scale count:\xff\xfe4\x00 23 | Threshold count:\xff\xfe1\x00 24 | Select the images to measure:\xff\xfe 25 | Include the image rescaling value?:\xff\xfeY\x00e\x00s\x00 26 | Calculate blur metrics?:\xff\xfeY\x00e\x00s\x00 27 | Spatial scale for blur measurements:\xff\xfe2\x00 28 | Spatial scale for blur measurements:\xff\xfe5\x00 29 | Spatial scale for blur measurements:\xff\xfe1\x000\x00 30 | Spatial scale for blur measurements:\xff\xfe2\x005\x00 31 | Calculate saturation metrics?:\xff\xfeY\x00e\x00s\x00 32 | Calculate intensity metrics?:\xff\xfeY\x00e\x00s\x00 33 | Calculate thresholds?:\xff\xfeN\x00o\x00 34 | Use all thresholding methods?:\xff\xfeY\x00e\x00s\x00 35 | Select a thresholding method:\xff\xfeO\x00t\x00s\x00u\x00 36 | Typical fraction of the image covered by objects:\xff\xfe0\x00.\x001\x00 37 | Two-class or three-class thresholding?:\xff\xfeT\x00w\x00o\x00 \x00c\x00l\x00a\x00s\x00s\x00e\x00s\x00 38 | Minimize the weighted variance or the entropy?:\xff\xfeW\x00e\x00i\x00g\x00h\x00t\x00e\x00d\x00 \x00v\x00a\x00r\x00i\x00a\x00n\x00c\x00e\x00 39 | Assign pixels in the middle intensity class to the foreground or the background?:\xff\xfeF\x00o\x00r\x00e\x00g\x00r\x00o\x00u\x00n\x00d\x00 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:\xff\xfeS\x00e\x00l\x00e\x00c\x00t\x00.\x00.\x00.\x00 43 | Image count:\xff\xfe2\x00 44 | Scale count:\xff\xfe1\x00 45 | Threshold count:\xff\xfe1\x00 46 | Scale count:\xff\xfe1\x00 47 | Threshold count:\xff\xfe1\x00 48 | Select the images to measure:\xff\xfeO\x00r\x00i\x00g\x00D\x00N\x00A\x00 49 | Include the image rescaling value?:\xff\xfeN\x00o\x00 50 | Calculate blur metrics?:\xff\xfeN\x00o\x00 51 | Spatial scale for blur measurements:\xff\xfe2\x000\x00 52 | Calculate saturation metrics?:\xff\xfeN\x00o\x00 53 | Calculate intensity metrics?:\xff\xfeN\x00o\x00 54 | Calculate thresholds?:\xff\xfeY\x00e\x00s\x00 55 | Use all thresholding methods?:\xff\xfeN\x00o\x00 56 | Select a thresholding method:\xff\xfeO\x00t\x00s\x00u\x00 57 | Typical fraction of the image covered by objects:\xff\xfe0\x00.\x001\x00 58 | Two-class or three-class thresholding?:\xff\xfeT\x00w\x00o\x00 \x00c\x00l\x00a\x00s\x00s\x00e\x00s\x00 59 | Minimize the weighted variance or the entropy?:\xff\xfeW\x00e\x00i\x00g\x00h\x00t\x00e\x00d\x00 \x00v\x00a\x00r\x00i\x00a\x00n\x00c\x00e\x00 60 | Assign pixels in the middle intensity class to the foreground or the background?:\xff\xfeB\x00a\x00c\x00k\x00g\x00r\x00o\x00u\x00n\x00d\x00 61 | Select the images to measure:\xff\xfeO\x00r\x00i\x00g\x00A\x00G\x00P\x00 62 | Include the image rescaling value?:\xff\xfeN\x00o\x00 63 | Calculate blur metrics?:\xff\xfeN\x00o\x00 64 | Spatial scale for blur measurements:\xff\xfe2\x000\x00 65 | Calculate saturation metrics?:\xff\xfeN\x00o\x00 66 | Calculate intensity metrics?:\xff\xfeN\x00o\x00 67 | Calculate thresholds?:\xff\xfeY\x00e\x00s\x00 68 | Use all thresholding methods?:\xff\xfeN\x00o\x00 69 | Select a thresholding method:\xff\xfeO\x00t\x00s\x00u\x00 70 | Typical fraction of the image covered by objects:\xff\xfe0\x00.\x001\x00 71 | Two-class or three-class thresholding?:\xff\xfeT\x00h\x00r\x00e\x00e\x00 \x00c\x00l\x00a\x00s\x00s\x00e\x00s\x00 72 | Minimize the weighted variance or the entropy?:\xff\xfeW\x00e\x00i\x00g\x00h\x00t\x00e\x00d\x00 \x00v\x00a\x00r\x00i\x00a\x00n\x00c\x00e\x00 73 | Assign pixels in the middle intensity class to the foreground or the background?:\xff\xfeF\x00o\x00r\x00e\x00g\x00r\x00o\x00u\x00n\x00d\x00 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:12|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:\xff\xfeC\x00o\x00m\x00m\x00a\x00 \x00(\x00"\x00,\x00"\x00)\x00 77 | Add image metadata columns to your object data file?:\xff\xfeN\x00o\x00 78 | Select the measurements to export:\xff\xfeN\x00o\x00 79 | Calculate the per-image mean values for object measurements?:\xff\xfeN\x00o\x00 80 | Calculate the per-image median values for object measurements?:\xff\xfeN\x00o\x00 81 | Calculate the per-image standard deviation values for object measurements?:\xff\xfeN\x00o\x00 82 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00 \x00s\x00u\x00b\x00-\x00f\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 83 | Create a GenePattern GCT file?:\xff\xfeN\x00o\x00 84 | Select source of sample row name:\xff\xfeM\x00e\x00t\x00a\x00d\x00a\x00t\x00a\x00 85 | Select the image to use as the identifier:\xff\xfeN\x00o\x00n\x00e\x00 86 | Select the metadata to use as the identifier:\xff\xfeN\x00o\x00n\x00e\x00 87 | Export all measurement types?:\xff\xfeY\x00e\x00s\x00 88 | Press button to select measurements:\xff\xfe 89 | Representation of Nan/Inf:\xff\xfeN\x00a\x00N\x00 90 | Add a prefix to file names?:\xff\xfeY\x00e\x00s\x00 91 | Filename prefix:\xff\xfeQ\x00C\x00_\x00 92 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 93 | Data to export:\xff\xfeD\x00o\x00 \x00n\x00o\x00t\x00 \x00u\x00s\x00e\x00 94 | Combine these object measurements with those of the previous object?:\xff\xfeN\x00o\x00 95 | File name:\xff\xfeD\x00A\x00T\x00A\x00.\x00c\x00s\x00v\x00 96 | Use the object name for the file name?:\xff\xfeY\x00e\x00s\x00 97 | 98 | CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:8|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:False|wants_pause:False] 99 | Store batch files in default output folder?:\xff\xfeY\x00e\x00s\x00 100 | Output folder path:\xff\xfe/\x00i\x00m\x00a\x00g\x00i\x00n\x00g\x00/\x00a\x00n\x00a\x00l\x00y\x00s\x00i\x00s\x00/\x002\x000\x000\x008\x00_\x001\x002\x00_\x000\x004\x00_\x00I\x00m\x00a\x00g\x00i\x00n\x00g\x00_\x00C\x00D\x00R\x00P\x00_\x00f\x00o\x00r\x00_\x00M\x00L\x00P\x00C\x00N\x00/\x00H\x00D\x00A\x00C\x00_\x00i\x00n\x00h\x00i\x00b\x00i\x00t\x00o\x00r\x00s\x00/\x002\x000\x001\x000\x000\x008\x000\x003\x00 101 | Are the cluster computers running Windows?:\xff\xfeN\x00o\x00 102 | Hidden\x3A in batch mode:\xff\xfeN\x00o\x00 103 | Hidden\x3A in distributed mode:\xff\xfeN\x00o\x00 104 | Hidden\x3A default input folder at time of save:\xff\xfe/\x00c\x00b\x00n\x00t\x00/\x00c\x00b\x00i\x00m\x00a\x00g\x00e\x00/\x00H\x00C\x00S\x00 105 | Hidden\x3A revision number:\xff\xfe1\x000\x003\x004\x006\x00 106 | Hidden\x3A from old matlab:\xff\xfeN\x00o\x00 107 | -------------------------------------------------------------------------------- /cellpainting_astrocyte_20x_phenix/ProjectionPipeline.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:4 3 | DateRevision:319 4 | GitHash: 5 | ModuleCount:13 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00/\x00U\x00s\x00e\x00r\x00s\x00/\x00n\x00j\x00a\x00m\x00a\x00l\x00i\x00/\x00D\x00o\x00c\x00u\x00m\x00e\x00n\x00t\x00s\x00 10 | Name of the file:\xff\xfel\x00o\x00a\x00d\x00_\x00d\x00a\x00t\x00a\x00.\x00c\x00s\x00v\x00 11 | Load images based on this data?:\xff\xfeY\x00e\x00s\x00 12 | Base image location:\xff\xfeN\x00o\x00n\x00e\x00\x7C\x00 13 | Process just a range of rows?:\xff\xfeN\x00o\x00 14 | Rows to process:\xff\xfe1\x00,\x001\x000\x000\x000\x000\x000\x00 15 | Group images by metadata?:\xff\xfeY\x00e\x00s\x00 16 | Select metadata tags for grouping:\xff\xfeP\x00l\x00a\x00t\x00e\x00,\x00W\x00e\x00l\x00l\x00,\x00S\x00i\x00t\x00e\x00 17 | Rescale intensities?:\xff\xfeY\x00e\x00s\x00 18 | 19 | MakeProjection:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00E\x00R\x00 21 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 22 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x004\x008\x008\x00 23 | Frequency:\xff\xfe6\x00.\x000\x00 24 | 25 | MakeProjection:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 26 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00A\x00G\x00P\x00 27 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 28 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x005\x006\x008\x00 29 | Frequency:\xff\xfe6\x00.\x000\x00 30 | 31 | MakeProjection:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 32 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00M\x00i\x00t\x00o\x00 33 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 34 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x006\x004\x007\x00 35 | Frequency:\xff\xfe6\x00.\x000\x00 36 | 37 | MakeProjection:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 38 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00D\x00N\x00A\x00 39 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 40 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00D\x00A\x00P\x00I\x00 41 | Frequency:\xff\xfe6\x00.\x000\x00 42 | 43 | MakeProjection:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 44 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00B\x00r\x00i\x00g\x00h\x00t\x00f\x00i\x00e\x00l\x00d\x00 45 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 46 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00B\x00r\x00i\x00g\x00h\x00t\x00f\x00i\x00e\x00l\x00d\x00 47 | Frequency:\xff\xfe6\x00.\x000\x00 48 | 49 | MakeProjection:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 50 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00R\x00N\x00A\x00 51 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 52 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00R\x00N\x00A\x00 53 | Frequency:\xff\xfe6\x00.\x000\x00 54 | 55 | SaveImages:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 56 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 57 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x004\x008\x008\x00 58 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 59 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00E\x00R\x00 60 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 61 | Number of digits:\xff\xfe4\x00 62 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 63 | Text to append to the image name:\xff\xfe 64 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 65 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 66 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 67 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 68 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 69 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 70 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 71 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 72 | 73 | SaveImages:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 74 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 75 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x005\x006\x008\x00 76 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 77 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00A\x00G\x00P\x00 78 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 79 | Number of digits:\xff\xfe4\x00 80 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 81 | Text to append to the image name:\xff\xfe 82 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 83 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 84 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 85 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 86 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 87 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 88 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 89 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 90 | 91 | SaveImages:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 92 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 93 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x006\x004\x007\x00 94 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 95 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00M\x00i\x00t\x00o\x00 96 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 97 | Number of digits:\xff\xfe4\x00 98 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 99 | Text to append to the image name:\xff\xfe 100 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 101 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 102 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 103 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 104 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 105 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 106 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 107 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 108 | 109 | SaveImages:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 110 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 111 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00D\x00A\x00P\x00I\x00 112 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 113 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00D\x00N\x00A\x00 114 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 115 | Number of digits:\xff\xfe4\x00 116 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 117 | Text to append to the image name:\xff\xfe 118 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 119 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 120 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 121 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 122 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 123 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 124 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 125 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 126 | 127 | SaveImages:[module_num:12|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 128 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 129 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00B\x00r\x00i\x00g\x00h\x00t\x00f\x00i\x00e\x00l\x00d\x00 130 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 131 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00B\x00r\x00i\x00g\x00h\x00t\x00f\x00i\x00e\x00l\x00d\x00 132 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 133 | Number of digits:\xff\xfe4\x00 134 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 135 | Text to append to the image name:\xff\xfe 136 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 137 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 138 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 139 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 140 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 141 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 142 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 143 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 144 | 145 | SaveImages:[module_num:13|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 146 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 147 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00R\x00N\x00A\x00 148 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 149 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00R\x00N\x00A\x00 150 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 151 | Number of digits:\xff\xfe4\x00 152 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 153 | Text to append to the image name:\xff\xfe 154 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 155 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 156 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 157 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 158 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 159 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 160 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 161 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 162 | -------------------------------------------------------------------------------- /cellpainting_astrocyte_20x_phenix/README.md: -------------------------------------------------------------------------------- 1 | source: https://github.com/broadinstitute/NeuroPainting/tree/v0.0.1/1.run-workflows/pipeline/2022_03_03_NCP_NEURONS_2_20x 2 | 3 | -------------------------------------------------------------------------------- /cellpainting_ipsc_20x_phenix_with_bf_bin1/README.md: -------------------------------------------------------------------------------- 1 | - The analysis pipeline is customized for iPSCs cells imaged at 20x on Opera Phenix, without binning. 2 | - The illumination pipeline requires that the image dimensions are a multiple of 10 because it downsamples and upsamples by a factor of 10. 3 | - Both pipelines were set up to process 2 brightfield channels (which are used for digital phase contrast imaging). There are 7 channels in all: 5 Cell Painting channels + 2 brightfield channels. 4 | -------------------------------------------------------------------------------- /cellpainting_ipsc_20x_phenix_with_bf_bin1_cp3/README.md: -------------------------------------------------------------------------------- 1 | Same as [cellpainting_ipsc_20x_phenix_with_bf_bin1](https://github.com/broadinstitute/imaging-platform-pipelines/blob/master/cellpainting_ipsc_20x_phenix_with_bf_bin1/README.md) but using CellProfiler 3. 2 | -------------------------------------------------------------------------------- /cellpainting_ipsc_20x_phenix_with_bf_bin1_cp4/Zproj.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:5 3 | DateRevision:424 4 | GitHash: 5 | ModuleCount:13 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:'Unknown'|variable_revision_number:6|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Default Input Folder sub-folder|Downloads 10 | Name of the file:load_data_unprojected (1).csv 11 | Load images based on this data?:Yes 12 | Base image location:None| 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well,Site 17 | Rescale intensities?:Yes 18 | 19 | MakeProjection:[module_num:2|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 20 | Select the input image:OrigDNA 21 | Type of projection:Maximum 22 | Name the output image:MaximumDNA 23 | Frequency:6.0 24 | 25 | SaveImages:[module_num:3|svn_version:'Unknown'|variable_revision_number:16|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 26 | Select the type of image to save:Image 27 | Select the image to save:MaximumDNA 28 | Select method for constructing file names:From image filename 29 | Select image name for file prefix:OrigDNA 30 | Enter single file name:OrigBlue 31 | Number of digits:4 32 | Append a suffix to the image file name?:No 33 | Text to append to the image name: 34 | Saved file format:tiff 35 | Output file location:Default Output Folder| 36 | Image bit depth:16-bit integer 37 | Overwrite existing files without warning?:No 38 | When to save:Last cycle 39 | Record the file and path information to the saved image?:No 40 | Create subfolders in the output folder?:No 41 | Base image folder:Elsewhere...| 42 | How to save the series:T (Time) 43 | Save with lossless compression?:No 44 | 45 | MakeProjection:[module_num:4|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 46 | Select the input image:OrigER 47 | Type of projection:Maximum 48 | Name the output image:MaximumER 49 | Frequency:6.0 50 | 51 | SaveImages:[module_num:5|svn_version:'Unknown'|variable_revision_number:16|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 52 | Select the type of image to save:Image 53 | Select the image to save:MaximumER 54 | Select method for constructing file names:From image filename 55 | Select image name for file prefix:OrigER 56 | Enter single file name:OrigBlue 57 | Number of digits:4 58 | Append a suffix to the image file name?:No 59 | Text to append to the image name: 60 | Saved file format:tiff 61 | Output file location:Default Output Folder| 62 | Image bit depth:16-bit integer 63 | Overwrite existing files without warning?:No 64 | When to save:Last cycle 65 | Record the file and path information to the saved image?:No 66 | Create subfolders in the output folder?:No 67 | Base image folder:Elsewhere...| 68 | How to save the series:T (Time) 69 | Save with lossless compression?:No 70 | 71 | MakeProjection:[module_num:6|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 72 | Select the input image:OrigRNA 73 | Type of projection:Maximum 74 | Name the output image:MaximumRNA 75 | Frequency:6.0 76 | 77 | SaveImages:[module_num:7|svn_version:'Unknown'|variable_revision_number:16|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 78 | Select the type of image to save:Image 79 | Select the image to save:MaximumRNA 80 | Select method for constructing file names:From image filename 81 | Select image name for file prefix:OrigRNA 82 | Enter single file name:OrigBlue 83 | Number of digits:4 84 | Append a suffix to the image file name?:No 85 | Text to append to the image name: 86 | Saved file format:tiff 87 | Output file location:Default Output Folder| 88 | Image bit depth:16-bit integer 89 | Overwrite existing files without warning?:No 90 | When to save:Last cycle 91 | Record the file and path information to the saved image?:No 92 | Create subfolders in the output folder?:No 93 | Base image folder:Elsewhere...| 94 | How to save the series:T (Time) 95 | Save with lossless compression?:No 96 | 97 | MakeProjection:[module_num:8|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 98 | Select the input image:OrigAGP 99 | Type of projection:Maximum 100 | Name the output image:MaximumAGP 101 | Frequency:6.0 102 | 103 | SaveImages:[module_num:9|svn_version:'Unknown'|variable_revision_number:16|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 104 | Select the type of image to save:Image 105 | Select the image to save:MaximumAGP 106 | Select method for constructing file names:From image filename 107 | Select image name for file prefix:OrigAGP 108 | Enter single file name:OrigBlue 109 | Number of digits:4 110 | Append a suffix to the image file name?:No 111 | Text to append to the image name: 112 | Saved file format:tiff 113 | Output file location:Default Output Folder| 114 | Image bit depth:16-bit integer 115 | Overwrite existing files without warning?:No 116 | When to save:Last cycle 117 | Record the file and path information to the saved image?:No 118 | Create subfolders in the output folder?:No 119 | Base image folder:Elsewhere...| 120 | How to save the series:T (Time) 121 | Save with lossless compression?:No 122 | 123 | MakeProjection:[module_num:10|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 124 | Select the input image:OrigMito 125 | Type of projection:Maximum 126 | Name the output image:MaximumMito 127 | Frequency:6.0 128 | 129 | SaveImages:[module_num:11|svn_version:'Unknown'|variable_revision_number:16|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 130 | Select the type of image to save:Image 131 | Select the image to save:MaximumMito 132 | Select method for constructing file names:From image filename 133 | Select image name for file prefix:OrigMito 134 | Enter single file name:OrigBlue 135 | Number of digits:4 136 | Append a suffix to the image file name?:No 137 | Text to append to the image name: 138 | Saved file format:tiff 139 | Output file location:Default Output Folder| 140 | Image bit depth:16-bit integer 141 | Overwrite existing files without warning?:No 142 | When to save:Last cycle 143 | Record the file and path information to the saved image?:No 144 | Create subfolders in the output folder?:No 145 | Base image folder:Elsewhere...| 146 | How to save the series:T (Time) 147 | Save with lossless compression?:No 148 | 149 | MakeProjection:[module_num:12|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 150 | Select the input image:OrigBrightfield 151 | Type of projection:Maximum 152 | Name the output image:MaximumBrightfield 153 | Frequency:6.0 154 | 155 | SaveImages:[module_num:13|svn_version:'Unknown'|variable_revision_number:16|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] 156 | Select the type of image to save:Image 157 | Select the image to save:MaximumBrightfield 158 | Select method for constructing file names:From image filename 159 | Select image name for file prefix:OrigBrightfield 160 | Enter single file name:OrigBlue 161 | Number of digits:4 162 | Append a suffix to the image file name?:No 163 | Text to append to the image name: 164 | Saved file format:tiff 165 | Output file location:Default Output Folder| 166 | Image bit depth:16-bit integer 167 | Overwrite existing files without warning?:No 168 | When to save:Last cycle 169 | Record the file and path information to the saved image?:No 170 | Create subfolders in the output folder?:No 171 | Base image folder:Elsewhere...| 172 | How to save the series:T (Time) 173 | Save with lossless compression?:No 174 | -------------------------------------------------------------------------------- /cellpainting_min6_63x_phenix_bin2/qc.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160418141927 4 | GitHash:9969f42 5 | ModuleCount:5 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Default Input Folder\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well,Site 17 | Rescale intensities?:Yes 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:All loaded images 21 | Image count:1 22 | Scale count:4 23 | Threshold count:1 24 | Select the images to measure: 25 | Include the image rescaling value?:Yes 26 | Calculate blur metrics?:Yes 27 | Spatial scale for blur measurements:5 28 | Spatial scale for blur measurements:10 29 | Spatial scale for blur measurements:20 30 | Spatial scale for blur measurements:50 31 | Calculate saturation metrics?:Yes 32 | Calculate intensity metrics?:Yes 33 | Calculate thresholds?:No 34 | Use all thresholding methods?:Yes 35 | Select a thresholding method:Otsu 36 | Typical fraction of the image covered by objects:0.1 37 | Two-class or three-class thresholding?:Two classes 38 | Minimize the weighted variance or the entropy?:Weighted variance 39 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:Select... 43 | Image count:2 44 | Scale count:1 45 | Threshold count:1 46 | Scale count:1 47 | Threshold count:1 48 | Select the images to measure:OrigDNA 49 | Include the image rescaling value?:No 50 | Calculate blur metrics?:No 51 | Spatial scale for blur measurements:20 52 | Calculate saturation metrics?:No 53 | Calculate intensity metrics?:No 54 | Calculate thresholds?:Yes 55 | Use all thresholding methods?:No 56 | Select a thresholding method:Otsu 57 | Typical fraction of the image covered by objects:0.1 58 | Two-class or three-class thresholding?:Two classes 59 | Minimize the weighted variance or the entropy?:Weighted variance 60 | Assign pixels in the middle intensity class to the foreground or the background?:Background 61 | Select the images to measure:OrigAGP 62 | Include the image rescaling value?:No 63 | Calculate blur metrics?:No 64 | Spatial scale for blur measurements:20 65 | Calculate saturation metrics?:No 66 | Calculate intensity metrics?:No 67 | Calculate thresholds?:Yes 68 | Use all thresholding methods?:No 69 | Select a thresholding method:Otsu 70 | Typical fraction of the image covered by objects:0.1 71 | Two-class or three-class thresholding?:Three classes 72 | Minimize the weighted variance or the entropy?:Weighted variance 73 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:Comma (",") 77 | Add image metadata columns to your object data file?:No 78 | Limit output to a size that is allowed in Excel?:No 79 | Select the measurements to export:No 80 | Calculate the per-image mean values for object measurements?:No 81 | Calculate the per-image median values for object measurements?:No 82 | Calculate the per-image standard deviation values for object measurements?:No 83 | Output file location:Default Output Folder\x7C 84 | Create a GenePattern GCT file?:No 85 | Select source of sample row name:Metadata 86 | Select the image to use as the identifier:None 87 | Select the metadata to use as the identifier:None 88 | Export all measurement types?:Yes 89 | : 90 | Representation of Nan/Inf:NaN 91 | Add a prefix to file names?:No 92 | Filename prefix:AlzheimersQC_ 93 | Overwrite existing files without warning?:No 94 | Data to export:Do not use 95 | Combine these object measurements with those of the previous object?:No 96 | File name:DATA.csv 97 | Use the object name for the file name?:Yes 98 | 99 | CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 100 | Store batch files in default output folder?:Yes 101 | Output folder path:/Users/shsingh 102 | Are the cluster computers running Windows?:No 103 | Hidden\x3A in batch mode:No 104 | Hidden\x3A in distributed mode:No 105 | Hidden\x3A default input folder at time of save:/Users/shsingh/Desktop 106 | Hidden\x3A revision number:0 107 | Hidden\x3A from old matlab:No 108 | Launch BatchProfiler:No 109 | -------------------------------------------------------------------------------- /cellpainting_min6_63x_phenix_bin2/qc_without_batchfile.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160418141927 4 | GitHash:9969f42 5 | ModuleCount:5 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Default Input Folder\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well,Site 17 | Rescale intensities?:Yes 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:All loaded images 21 | Image count:1 22 | Scale count:4 23 | Threshold count:1 24 | Select the images to measure: 25 | Include the image rescaling value?:Yes 26 | Calculate blur metrics?:Yes 27 | Spatial scale for blur measurements:5 28 | Spatial scale for blur measurements:10 29 | Spatial scale for blur measurements:20 30 | Spatial scale for blur measurements:50 31 | Calculate saturation metrics?:Yes 32 | Calculate intensity metrics?:Yes 33 | Calculate thresholds?:No 34 | Use all thresholding methods?:Yes 35 | Select a thresholding method:Otsu 36 | Typical fraction of the image covered by objects:0.1 37 | Two-class or three-class thresholding?:Two classes 38 | Minimize the weighted variance or the entropy?:Weighted variance 39 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:Select... 43 | Image count:2 44 | Scale count:1 45 | Threshold count:1 46 | Scale count:1 47 | Threshold count:1 48 | Select the images to measure:OrigDNA 49 | Include the image rescaling value?:No 50 | Calculate blur metrics?:No 51 | Spatial scale for blur measurements:20 52 | Calculate saturation metrics?:No 53 | Calculate intensity metrics?:No 54 | Calculate thresholds?:Yes 55 | Use all thresholding methods?:No 56 | Select a thresholding method:Otsu 57 | Typical fraction of the image covered by objects:0.1 58 | Two-class or three-class thresholding?:Two classes 59 | Minimize the weighted variance or the entropy?:Weighted variance 60 | Assign pixels in the middle intensity class to the foreground or the background?:Background 61 | Select the images to measure:OrigAGP 62 | Include the image rescaling value?:No 63 | Calculate blur metrics?:No 64 | Spatial scale for blur measurements:20 65 | Calculate saturation metrics?:No 66 | Calculate intensity metrics?:No 67 | Calculate thresholds?:Yes 68 | Use all thresholding methods?:No 69 | Select a thresholding method:Otsu 70 | Typical fraction of the image covered by objects:0.1 71 | Two-class or three-class thresholding?:Three classes 72 | Minimize the weighted variance or the entropy?:Weighted variance 73 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:Comma (",") 77 | Add image metadata columns to your object data file?:No 78 | Limit output to a size that is allowed in Excel?:No 79 | Select the measurements to export:No 80 | Calculate the per-image mean values for object measurements?:No 81 | Calculate the per-image median values for object measurements?:No 82 | Calculate the per-image standard deviation values for object measurements?:No 83 | Output file location:Default Output Folder\x7C 84 | Create a GenePattern GCT file?:No 85 | Select source of sample row name:Metadata 86 | Select the image to use as the identifier:None 87 | Select the metadata to use as the identifier:None 88 | Export all measurement types?:Yes 89 | : 90 | Representation of Nan/Inf:NaN 91 | Add a prefix to file names?:No 92 | Filename prefix:AlzheimersQC_ 93 | Overwrite existing files without warning?:No 94 | Data to export:Do not use 95 | Combine these object measurements with those of the previous object?:No 96 | File name:DATA.csv 97 | Use the object name for the file name?:Yes 98 | 99 | CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:False|wants_pause:False] 100 | Store batch files in default output folder?:Yes 101 | Output folder path:/Users/shsingh 102 | Are the cluster computers running Windows?:No 103 | Hidden\x3A in batch mode:No 104 | Hidden\x3A in distributed mode:No 105 | Hidden\x3A default input folder at time of save:/Users/shsingh/Desktop 106 | Hidden\x3A revision number:0 107 | Hidden\x3A from old matlab:No 108 | Launch BatchProfiler:No 109 | -------------------------------------------------------------------------------- /cellpainting_neuralprogenitor_20x_phenix/README.md: -------------------------------------------------------------------------------- 1 | source: https://github.com/broadinstitute/NeuroPainting/tree/v0.0.1/1.run-workflows/pipeline/NCP_PROGENITORS_1 2 | -------------------------------------------------------------------------------- /cellpainting_neuron_20x_phenix/ProjectionPipeline.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:4 3 | DateRevision:319 4 | GitHash: 5 | ModuleCount:13 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00/\x00U\x00s\x00e\x00r\x00s\x00/\x00n\x00j\x00a\x00m\x00a\x00l\x00i\x00/\x00D\x00o\x00c\x00u\x00m\x00e\x00n\x00t\x00s\x00 10 | Name of the file:\xff\xfel\x00o\x00a\x00d\x00_\x00d\x00a\x00t\x00a\x00.\x00c\x00s\x00v\x00 11 | Load images based on this data?:\xff\xfeY\x00e\x00s\x00 12 | Base image location:\xff\xfeN\x00o\x00n\x00e\x00\x7C\x00 13 | Process just a range of rows?:\xff\xfeN\x00o\x00 14 | Rows to process:\xff\xfe1\x00,\x001\x000\x000\x000\x000\x000\x00 15 | Group images by metadata?:\xff\xfeY\x00e\x00s\x00 16 | Select metadata tags for grouping:\xff\xfeP\x00l\x00a\x00t\x00e\x00,\x00W\x00e\x00l\x00l\x00,\x00S\x00i\x00t\x00e\x00 17 | Rescale intensities?:\xff\xfeY\x00e\x00s\x00 18 | 19 | MakeProjection:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00E\x00R\x00 21 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 22 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x004\x008\x008\x00 23 | Frequency:\xff\xfe6\x00.\x000\x00 24 | 25 | MakeProjection:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 26 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00A\x00G\x00P\x00 27 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 28 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x005\x006\x008\x00 29 | Frequency:\xff\xfe6\x00.\x000\x00 30 | 31 | MakeProjection:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 32 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00M\x00i\x00t\x00o\x00 33 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 34 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x006\x004\x007\x00 35 | Frequency:\xff\xfe6\x00.\x000\x00 36 | 37 | MakeProjection:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 38 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00D\x00N\x00A\x00 39 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 40 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00D\x00A\x00P\x00I\x00 41 | Frequency:\xff\xfe6\x00.\x000\x00 42 | 43 | MakeProjection:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 44 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00B\x00r\x00i\x00g\x00h\x00t\x00f\x00i\x00e\x00l\x00d\x00 45 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 46 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00B\x00r\x00i\x00g\x00h\x00t\x00f\x00i\x00e\x00l\x00d\x00 47 | Frequency:\xff\xfe6\x00.\x000\x00 48 | 49 | MakeProjection:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 50 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00R\x00N\x00A\x00 51 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 52 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00R\x00N\x00A\x00 53 | Frequency:\xff\xfe6\x00.\x000\x00 54 | 55 | SaveImages:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 56 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 57 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x004\x008\x008\x00 58 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 59 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00E\x00R\x00 60 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 61 | Number of digits:\xff\xfe4\x00 62 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 63 | Text to append to the image name:\xff\xfe 64 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 65 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 66 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 67 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 68 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 69 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 70 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 71 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 72 | 73 | SaveImages:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 74 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 75 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x005\x006\x008\x00 76 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 77 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00A\x00G\x00P\x00 78 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 79 | Number of digits:\xff\xfe4\x00 80 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 81 | Text to append to the image name:\xff\xfe 82 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 83 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 84 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 85 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 86 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 87 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 88 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 89 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 90 | 91 | SaveImages:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 92 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 93 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x006\x004\x007\x00 94 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 95 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00M\x00i\x00t\x00o\x00 96 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 97 | Number of digits:\xff\xfe4\x00 98 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 99 | Text to append to the image name:\xff\xfe 100 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 101 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 102 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 103 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 104 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 105 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 106 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 107 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 108 | 109 | SaveImages:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 110 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 111 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00D\x00A\x00P\x00I\x00 112 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 113 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00D\x00N\x00A\x00 114 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 115 | Number of digits:\xff\xfe4\x00 116 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 117 | Text to append to the image name:\xff\xfe 118 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 119 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 120 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 121 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 122 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 123 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 124 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 125 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 126 | 127 | SaveImages:[module_num:12|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 128 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 129 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00B\x00r\x00i\x00g\x00h\x00t\x00f\x00i\x00e\x00l\x00d\x00 130 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 131 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00B\x00r\x00i\x00g\x00h\x00t\x00f\x00i\x00e\x00l\x00d\x00 132 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 133 | Number of digits:\xff\xfe4\x00 134 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 135 | Text to append to the image name:\xff\xfe 136 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 137 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 138 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 139 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 140 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 141 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 142 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 143 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 144 | 145 | SaveImages:[module_num:13|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 146 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 147 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00R\x00N\x00A\x00 148 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 149 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00R\x00N\x00A\x00 150 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 151 | Number of digits:\xff\xfe4\x00 152 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 153 | Text to append to the image name:\xff\xfe 154 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 155 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 156 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 157 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 158 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 159 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 160 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 161 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 162 | -------------------------------------------------------------------------------- /cellpainting_neuron_20x_phenix/README.md: -------------------------------------------------------------------------------- 1 | source: https://github.com/broadinstitute/NeuroPainting/tree/v0.0.1/1.run-workflows/pipeline/2022_03_03_NCP_NEURONS_2_20x 2 | 3 | -------------------------------------------------------------------------------- /cellpainting_neuron_63x_phenix/ProjectionPipeline.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:4 3 | DateRevision:319 4 | GitHash: 5 | ModuleCount:13 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00/\x00U\x00s\x00e\x00r\x00s\x00/\x00n\x00j\x00a\x00m\x00a\x00l\x00i\x00/\x00D\x00o\x00c\x00u\x00m\x00e\x00n\x00t\x00s\x00 10 | Name of the file:\xff\xfel\x00o\x00a\x00d\x00_\x00d\x00a\x00t\x00a\x00.\x00c\x00s\x00v\x00 11 | Load images based on this data?:\xff\xfeY\x00e\x00s\x00 12 | Base image location:\xff\xfeN\x00o\x00n\x00e\x00\x7C\x00 13 | Process just a range of rows?:\xff\xfeN\x00o\x00 14 | Rows to process:\xff\xfe1\x00,\x001\x000\x000\x000\x000\x000\x00 15 | Group images by metadata?:\xff\xfeY\x00e\x00s\x00 16 | Select metadata tags for grouping:\xff\xfeP\x00l\x00a\x00t\x00e\x00,\x00W\x00e\x00l\x00l\x00,\x00S\x00i\x00t\x00e\x00 17 | Rescale intensities?:\xff\xfeY\x00e\x00s\x00 18 | 19 | MakeProjection:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00E\x00R\x00 21 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 22 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x004\x008\x008\x00 23 | Frequency:\xff\xfe6\x00.\x000\x00 24 | 25 | MakeProjection:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 26 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00A\x00G\x00P\x00 27 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 28 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x005\x006\x008\x00 29 | Frequency:\xff\xfe6\x00.\x000\x00 30 | 31 | MakeProjection:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 32 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00M\x00i\x00t\x00o\x00 33 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 34 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x006\x004\x007\x00 35 | Frequency:\xff\xfe6\x00.\x000\x00 36 | 37 | MakeProjection:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 38 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00D\x00N\x00A\x00 39 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 40 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00D\x00A\x00P\x00I\x00 41 | Frequency:\xff\xfe6\x00.\x000\x00 42 | 43 | MakeProjection:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 44 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00B\x00r\x00i\x00g\x00h\x00t\x00f\x00i\x00e\x00l\x00d\x00 45 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 46 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00B\x00r\x00i\x00g\x00h\x00t\x00f\x00i\x00e\x00l\x00d\x00 47 | Frequency:\xff\xfe6\x00.\x000\x00 48 | 49 | MakeProjection:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 50 | Select the input image:\xff\xfeO\x00r\x00i\x00g\x00R\x00N\x00A\x00 51 | Type of projection:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00 52 | Name the output image:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00R\x00N\x00A\x00 53 | Frequency:\xff\xfe6\x00.\x000\x00 54 | 55 | SaveImages:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 56 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 57 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x004\x008\x008\x00 58 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 59 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00E\x00R\x00 60 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 61 | Number of digits:\xff\xfe4\x00 62 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 63 | Text to append to the image name:\xff\xfe 64 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 65 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 66 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 67 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 68 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 69 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 70 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 71 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 72 | 73 | SaveImages:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 74 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 75 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x005\x006\x008\x00 76 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 77 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00A\x00G\x00P\x00 78 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 79 | Number of digits:\xff\xfe4\x00 80 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 81 | Text to append to the image name:\xff\xfe 82 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 83 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 84 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 85 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 86 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 87 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 88 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 89 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 90 | 91 | SaveImages:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 92 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 93 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x006\x004\x007\x00 94 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 95 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00M\x00i\x00t\x00o\x00 96 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 97 | Number of digits:\xff\xfe4\x00 98 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 99 | Text to append to the image name:\xff\xfe 100 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 101 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 102 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 103 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 104 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 105 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 106 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 107 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 108 | 109 | SaveImages:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 110 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 111 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00D\x00A\x00P\x00I\x00 112 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 113 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00D\x00N\x00A\x00 114 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 115 | Number of digits:\xff\xfe4\x00 116 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 117 | Text to append to the image name:\xff\xfe 118 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 119 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 120 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 121 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 122 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 123 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 124 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 125 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 126 | 127 | SaveImages:[module_num:12|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 128 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 129 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00B\x00r\x00i\x00g\x00h\x00t\x00f\x00i\x00e\x00l\x00d\x00 130 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 131 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00B\x00r\x00i\x00g\x00h\x00t\x00f\x00i\x00e\x00l\x00d\x00 132 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 133 | Number of digits:\xff\xfe4\x00 134 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 135 | Text to append to the image name:\xff\xfe 136 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 137 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 138 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 139 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 140 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 141 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 142 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 143 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 144 | 145 | SaveImages:[module_num:13|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 146 | Select the type of image to save:\xff\xfeI\x00m\x00a\x00g\x00e\x00 147 | Select the image to save:\xff\xfeM\x00a\x00x\x00i\x00m\x00u\x00m\x00R\x00N\x00A\x00 148 | Select method for constructing file names:\xff\xfeF\x00r\x00o\x00m\x00 \x00i\x00m\x00a\x00g\x00e\x00 \x00f\x00i\x00l\x00e\x00n\x00a\x00m\x00e\x00 149 | Select image name for file prefix:\xff\xfeO\x00r\x00i\x00g\x00R\x00N\x00A\x00 150 | Enter single file name:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00 151 | Number of digits:\xff\xfe4\x00 152 | Append a suffix to the image file name?:\xff\xfeN\x00o\x00 153 | Text to append to the image name:\xff\xfe 154 | Saved file format:\xff\xfet\x00i\x00f\x00f\x00 155 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 156 | Image bit depth:\xff\xfe1\x006\x00-\x00b\x00i\x00t\x00 \x00i\x00n\x00t\x00e\x00g\x00e\x00r\x00 157 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 158 | When to save:\xff\xfeL\x00a\x00s\x00t\x00 \x00c\x00y\x00c\x00l\x00e\x00 159 | Record the file and path information to the saved image?:\xff\xfeN\x00o\x00 160 | Create subfolders in the output folder?:\xff\xfeN\x00o\x00 161 | Base image folder:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00 162 | -------------------------------------------------------------------------------- /cellpainting_neuron_63x_phenix/README.md: -------------------------------------------------------------------------------- 1 | source: https://github.com/broadinstitute/NeuroPainting/tree/v0.0.1/1.run-workflows/pipeline/2022_03_03_NCP_NEURONS_2_63x 2 | 3 | -------------------------------------------------------------------------------- /cellpainting_snu761_20x_phenix_bin1/assaydev.cpproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/broadinstitute/imaging-platform-pipelines/7b107db5b54cbe3f0cce4e6488dc24e374d235a0/cellpainting_snu761_20x_phenix_bin1/assaydev.cpproj -------------------------------------------------------------------------------- /cellpainting_snu761_20x_phenix_bin1/qc.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160418141927 4 | GitHash:9969f42 5 | ModuleCount:5 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Elsewhere...\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well,Site 17 | Rescale intensities?:Yes 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:All loaded images 21 | Image count:1 22 | Scale count:4 23 | Threshold count:1 24 | Select the images to measure: 25 | Include the image rescaling value?:Yes 26 | Calculate blur metrics?:Yes 27 | Spatial scale for blur measurements:5 28 | Spatial scale for blur measurements:10 29 | Spatial scale for blur measurements:20 30 | Spatial scale for blur measurements:50 31 | Calculate saturation metrics?:Yes 32 | Calculate intensity metrics?:Yes 33 | Calculate thresholds?:No 34 | Use all thresholding methods?:Yes 35 | Select a thresholding method:Otsu 36 | Typical fraction of the image covered by objects:0.1 37 | Two-class or three-class thresholding?:Two classes 38 | Minimize the weighted variance or the entropy?:Weighted variance 39 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:Select... 43 | Image count:2 44 | Scale count:1 45 | Threshold count:1 46 | Scale count:1 47 | Threshold count:1 48 | Select the images to measure:OrigDNA 49 | Include the image rescaling value?:No 50 | Calculate blur metrics?:No 51 | Spatial scale for blur measurements:20 52 | Calculate saturation metrics?:No 53 | Calculate intensity metrics?:No 54 | Calculate thresholds?:Yes 55 | Use all thresholding methods?:No 56 | Select a thresholding method:Otsu 57 | Typical fraction of the image covered by objects:0.1 58 | Two-class or three-class thresholding?:Two classes 59 | Minimize the weighted variance or the entropy?:Weighted variance 60 | Assign pixels in the middle intensity class to the foreground or the background?:Background 61 | Select the images to measure:OrigRNA 62 | Include the image rescaling value?:No 63 | Calculate blur metrics?:No 64 | Spatial scale for blur measurements:20 65 | Calculate saturation metrics?:No 66 | Calculate intensity metrics?:No 67 | Calculate thresholds?:Yes 68 | Use all thresholding methods?:No 69 | Select a thresholding method:Otsu 70 | Typical fraction of the image covered by objects:0.1 71 | Two-class or three-class thresholding?:Three classes 72 | Minimize the weighted variance or the entropy?:Weighted variance 73 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:Comma (",") 77 | Add image metadata columns to your object data file?:No 78 | Limit output to a size that is allowed in Excel?:No 79 | Select the measurements to export:No 80 | Calculate the per-image mean values for object measurements?:No 81 | Calculate the per-image median values for object measurements?:No 82 | Calculate the per-image standard deviation values for object measurements?:No 83 | Output file location:Default Output Folder sub-folder\x7C 84 | Create a GenePattern GCT file?:No 85 | Select source of sample row name:Metadata 86 | Select the image to use as the identifier:None 87 | Select the metadata to use as the identifier:None 88 | Export all measurement types?:Yes 89 | : 90 | Representation of Nan/Inf:NaN 91 | Add a prefix to file names?:Yes 92 | Filename prefix:QC_ 93 | Overwrite existing files without warning?:No 94 | Data to export:Do not use 95 | Combine these object measurements with those of the previous object?:No 96 | File name:DATA.csv 97 | Use the object name for the file name?:Yes 98 | 99 | CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 100 | Store batch files in default output folder?:Yes 101 | Output folder path:/imaging/analysis/2008_12_04_Imaging_CDRP_for_MLPCN/HDAC_inhibitors/20100803 102 | Are the cluster computers running Windows?:No 103 | Hidden\x3A in batch mode:No 104 | Hidden\x3A in distributed mode:No 105 | Hidden\x3A default input folder at time of save:/cbnt/cbimage/HCS 106 | Hidden\x3A revision number:10346 107 | Hidden\x3A from old matlab:No 108 | Launch BatchProfiler:No 109 | -------------------------------------------------------------------------------- /cellpainting_snu761_20x_phenix_bin1/qc_without_batchfile.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:4 3 | DateRevision:318 4 | GitHash: 5 | ModuleCount:5 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00/\x00U\x00s\x00e\x00r\x00s\x00/\x00b\x00c\x00i\x00m\x00i\x00n\x00i\x00/\x00D\x00o\x00w\x00n\x00l\x00o\x00a\x00d\x00s\x00 10 | Name of the file:\xff\xfel\x00o\x00a\x00d\x00_\x00d\x00a\x00t\x00a\x00.\x00c\x00s\x00v\x00 11 | Load images based on this data?:\xff\xfeY\x00e\x00s\x00 12 | Base image location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00I\x00n\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 13 | Process just a range of rows?:\xff\xfeN\x00o\x00 14 | Rows to process:\xff\xfe1\x00,\x001\x000\x000\x000\x000\x000\x00 15 | Group images by metadata?:\xff\xfeY\x00e\x00s\x00 16 | Select metadata tags for grouping:\xff\xfeP\x00l\x00a\x00t\x00e\x00,\x00W\x00e\x00l\x00l\x00,\x00S\x00i\x00t\x00e\x00 17 | Rescale intensities?:\xff\xfeY\x00e\x00s\x00 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:\xff\xfeA\x00l\x00l\x00 \x00l\x00o\x00a\x00d\x00e\x00d\x00 \x00i\x00m\x00a\x00g\x00e\x00s\x00 21 | Image count:\xff\xfe1\x00 22 | Scale count:\xff\xfe4\x00 23 | Threshold count:\xff\xfe1\x00 24 | Select the images to measure:\xff\xfe 25 | Include the image rescaling value?:\xff\xfeY\x00e\x00s\x00 26 | Calculate blur metrics?:\xff\xfeY\x00e\x00s\x00 27 | Spatial scale for blur measurements:\xff\xfe2\x00 28 | Spatial scale for blur measurements:\xff\xfe5\x00 29 | Spatial scale for blur measurements:\xff\xfe1\x000\x00 30 | Spatial scale for blur measurements:\xff\xfe2\x005\x00 31 | Calculate saturation metrics?:\xff\xfeY\x00e\x00s\x00 32 | Calculate intensity metrics?:\xff\xfeY\x00e\x00s\x00 33 | Calculate thresholds?:\xff\xfeN\x00o\x00 34 | Use all thresholding methods?:\xff\xfeY\x00e\x00s\x00 35 | Select a thresholding method:\xff\xfeO\x00t\x00s\x00u\x00 36 | Typical fraction of the image covered by objects:\xff\xfe0\x00.\x001\x00 37 | Two-class or three-class thresholding?:\xff\xfeT\x00w\x00o\x00 \x00c\x00l\x00a\x00s\x00s\x00e\x00s\x00 38 | Minimize the weighted variance or the entropy?:\xff\xfeW\x00e\x00i\x00g\x00h\x00t\x00e\x00d\x00 \x00v\x00a\x00r\x00i\x00a\x00n\x00c\x00e\x00 39 | Assign pixels in the middle intensity class to the foreground or the background?:\xff\xfeF\x00o\x00r\x00e\x00g\x00r\x00o\x00u\x00n\x00d\x00 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:\xff\xfeS\x00e\x00l\x00e\x00c\x00t\x00.\x00.\x00.\x00 43 | Image count:\xff\xfe2\x00 44 | Scale count:\xff\xfe1\x00 45 | Threshold count:\xff\xfe1\x00 46 | Scale count:\xff\xfe1\x00 47 | Threshold count:\xff\xfe1\x00 48 | Select the images to measure:\xff\xfeO\x00r\x00i\x00g\x00D\x00N\x00A\x00 49 | Include the image rescaling value?:\xff\xfeN\x00o\x00 50 | Calculate blur metrics?:\xff\xfeN\x00o\x00 51 | Spatial scale for blur measurements:\xff\xfe2\x000\x00 52 | Calculate saturation metrics?:\xff\xfeN\x00o\x00 53 | Calculate intensity metrics?:\xff\xfeN\x00o\x00 54 | Calculate thresholds?:\xff\xfeY\x00e\x00s\x00 55 | Use all thresholding methods?:\xff\xfeN\x00o\x00 56 | Select a thresholding method:\xff\xfeO\x00t\x00s\x00u\x00 57 | Typical fraction of the image covered by objects:\xff\xfe0\x00.\x001\x00 58 | Two-class or three-class thresholding?:\xff\xfeT\x00w\x00o\x00 \x00c\x00l\x00a\x00s\x00s\x00e\x00s\x00 59 | Minimize the weighted variance or the entropy?:\xff\xfeW\x00e\x00i\x00g\x00h\x00t\x00e\x00d\x00 \x00v\x00a\x00r\x00i\x00a\x00n\x00c\x00e\x00 60 | Assign pixels in the middle intensity class to the foreground or the background?:\xff\xfeB\x00a\x00c\x00k\x00g\x00r\x00o\x00u\x00n\x00d\x00 61 | Select the images to measure:\xff\xfeO\x00r\x00i\x00g\x00A\x00G\x00P\x00 62 | Include the image rescaling value?:\xff\xfeN\x00o\x00 63 | Calculate blur metrics?:\xff\xfeN\x00o\x00 64 | Spatial scale for blur measurements:\xff\xfe2\x000\x00 65 | Calculate saturation metrics?:\xff\xfeN\x00o\x00 66 | Calculate intensity metrics?:\xff\xfeN\x00o\x00 67 | Calculate thresholds?:\xff\xfeY\x00e\x00s\x00 68 | Use all thresholding methods?:\xff\xfeN\x00o\x00 69 | Select a thresholding method:\xff\xfeO\x00t\x00s\x00u\x00 70 | Typical fraction of the image covered by objects:\xff\xfe0\x00.\x001\x00 71 | Two-class or three-class thresholding?:\xff\xfeT\x00h\x00r\x00e\x00e\x00 \x00c\x00l\x00a\x00s\x00s\x00e\x00s\x00 72 | Minimize the weighted variance or the entropy?:\xff\xfeW\x00e\x00i\x00g\x00h\x00t\x00e\x00d\x00 \x00v\x00a\x00r\x00i\x00a\x00n\x00c\x00e\x00 73 | Assign pixels in the middle intensity class to the foreground or the background?:\xff\xfeF\x00o\x00r\x00e\x00g\x00r\x00o\x00u\x00n\x00d\x00 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:12|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:\xff\xfeC\x00o\x00m\x00m\x00a\x00 \x00(\x00"\x00,\x00"\x00)\x00 77 | Add image metadata columns to your object data file?:\xff\xfeN\x00o\x00 78 | Select the measurements to export:\xff\xfeN\x00o\x00 79 | Calculate the per-image mean values for object measurements?:\xff\xfeN\x00o\x00 80 | Calculate the per-image median values for object measurements?:\xff\xfeN\x00o\x00 81 | Calculate the per-image standard deviation values for object measurements?:\xff\xfeN\x00o\x00 82 | Output file location:\xff\xfeD\x00e\x00f\x00a\x00u\x00l\x00t\x00 \x00O\x00u\x00t\x00p\x00u\x00t\x00 \x00F\x00o\x00l\x00d\x00e\x00r\x00 \x00s\x00u\x00b\x00-\x00f\x00o\x00l\x00d\x00e\x00r\x00\x7C\x00 83 | Create a GenePattern GCT file?:\xff\xfeN\x00o\x00 84 | Select source of sample row name:\xff\xfeM\x00e\x00t\x00a\x00d\x00a\x00t\x00a\x00 85 | Select the image to use as the identifier:\xff\xfeN\x00o\x00n\x00e\x00 86 | Select the metadata to use as the identifier:\xff\xfeN\x00o\x00n\x00e\x00 87 | Export all measurement types?:\xff\xfeY\x00e\x00s\x00 88 | Press button to select measurements:\xff\xfe 89 | Representation of Nan/Inf:\xff\xfeN\x00a\x00N\x00 90 | Add a prefix to file names?:\xff\xfeY\x00e\x00s\x00 91 | Filename prefix:\xff\xfeQ\x00C\x00_\x00 92 | Overwrite existing files without warning?:\xff\xfeN\x00o\x00 93 | Data to export:\xff\xfeD\x00o\x00 \x00n\x00o\x00t\x00 \x00u\x00s\x00e\x00 94 | Combine these object measurements with those of the previous object?:\xff\xfeN\x00o\x00 95 | File name:\xff\xfeD\x00A\x00T\x00A\x00.\x00c\x00s\x00v\x00 96 | Use the object name for the file name?:\xff\xfeY\x00e\x00s\x00 97 | 98 | CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:8|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:False|wants_pause:False] 99 | Store batch files in default output folder?:\xff\xfeY\x00e\x00s\x00 100 | Output folder path:\xff\xfe/\x00i\x00m\x00a\x00g\x00i\x00n\x00g\x00/\x00a\x00n\x00a\x00l\x00y\x00s\x00i\x00s\x00/\x002\x000\x000\x008\x00_\x001\x002\x00_\x000\x004\x00_\x00I\x00m\x00a\x00g\x00i\x00n\x00g\x00_\x00C\x00D\x00R\x00P\x00_\x00f\x00o\x00r\x00_\x00M\x00L\x00P\x00C\x00N\x00/\x00H\x00D\x00A\x00C\x00_\x00i\x00n\x00h\x00i\x00b\x00i\x00t\x00o\x00r\x00s\x00/\x002\x000\x001\x000\x000\x008\x000\x003\x00 101 | Are the cluster computers running Windows?:\xff\xfeN\x00o\x00 102 | Hidden\x3A in batch mode:\xff\xfeN\x00o\x00 103 | Hidden\x3A in distributed mode:\xff\xfeN\x00o\x00 104 | Hidden\x3A default input folder at time of save:\xff\xfe/\x00c\x00b\x00n\x00t\x00/\x00c\x00b\x00i\x00m\x00a\x00g\x00e\x00/\x00H\x00C\x00S\x00 105 | Hidden\x3A revision number:\xff\xfe1\x000\x003\x004\x006\x00 106 | Hidden\x3A from old matlab:\xff\xfeN\x00o\x00 107 | -------------------------------------------------------------------------------- /cellpainting_u2os_20x_imagexpress/README.md: -------------------------------------------------------------------------------- 1 | - The analysis pipeline is customized for U2OS cells imaged at 20x on ImageXpress, with binning. 2 | - The illumination pipeline requires that the image dimensions are a multiple of 10 because it downsamples and upsamples by a factor of 10. -------------------------------------------------------------------------------- /cellpainting_u2os_20x_imagexpress/qc.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160503183100 4 | GitHash:ac0529e 5 | ModuleCount:4 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Elsewhere...\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well 17 | Rescale intensities?:Yes 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:All loaded images 21 | Image count:1 22 | Scale count:4 23 | Threshold count:1 24 | Select the images to measure: 25 | Include the image rescaling value?:Yes 26 | Calculate blur metrics?:Yes 27 | Spatial scale for blur measurements:2 28 | Spatial scale for blur measurements:5 29 | Spatial scale for blur measurements:10 30 | Spatial scale for blur measurements:20 31 | Calculate saturation metrics?:Yes 32 | Calculate intensity metrics?:Yes 33 | Calculate thresholds?:No 34 | Use all thresholding methods?:Yes 35 | Select a thresholding method:Otsu 36 | Typical fraction of the image covered by objects:0.1 37 | Two-class or three-class thresholding?:Two classes 38 | Minimize the weighted variance or the entropy?:Weighted variance 39 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:Select... 43 | Image count:2 44 | Scale count:1 45 | Threshold count:1 46 | Scale count:1 47 | Threshold count:1 48 | Select the images to measure:OrigDNA 49 | Include the image rescaling value?:No 50 | Calculate blur metrics?:No 51 | Spatial scale for blur measurements:20 52 | Calculate saturation metrics?:No 53 | Calculate intensity metrics?:No 54 | Calculate thresholds?:Yes 55 | Use all thresholding methods?:No 56 | Select a thresholding method:Otsu 57 | Typical fraction of the image covered by objects:0.1 58 | Two-class or three-class thresholding?:Two classes 59 | Minimize the weighted variance or the entropy?:Weighted variance 60 | Assign pixels in the middle intensity class to the foreground or the background?:Background 61 | Select the images to measure:OrigRNA 62 | Include the image rescaling value?:No 63 | Calculate blur metrics?:No 64 | Spatial scale for blur measurements:20 65 | Calculate saturation metrics?:No 66 | Calculate intensity metrics?:No 67 | Calculate thresholds?:Yes 68 | Use all thresholding methods?:No 69 | Select a thresholding method:Otsu 70 | Typical fraction of the image covered by objects:0.1 71 | Two-class or three-class thresholding?:Three classes 72 | Minimize the weighted variance or the entropy?:Weighted variance 73 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:Comma (",") 77 | Add image metadata columns to your object data file?:No 78 | Limit output to a size that is allowed in Excel?:No 79 | Select the measurements to export:No 80 | Calculate the per-image mean values for object measurements?:No 81 | Calculate the per-image median values for object measurements?:No 82 | Calculate the per-image standard deviation values for object measurements?:No 83 | Output file location:Default Output Folder\x7C 84 | Create a GenePattern GCT file?:No 85 | Select source of sample row name:Metadata 86 | Select the image to use as the identifier:None 87 | Select the metadata to use as the identifier:None 88 | Export all measurement types?:Yes 89 | : 90 | Representation of Nan/Inf:NaN 91 | Add a prefix to file names?:Yes 92 | Filename prefix:QC_ 93 | Overwrite existing files without warning?:No 94 | Data to export:Do not use 95 | Combine these object measurements with those of the previous object?:No 96 | File name:DATA.csv 97 | Use the object name for the file name?:Yes 98 | -------------------------------------------------------------------------------- /cellpainting_u2os_20x_imagexpress/save_illum_corrected_files_without_batchfile.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160418141927 4 | GitHash:9969f42 5 | ModuleCount:8 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Default Input Folder\x7C 10 | Name of the file: 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,2 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well,Site 17 | Rescale intensities?:Yes 18 | 19 | CorrectIlluminationApply:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\'\', \n dtype=\'\x7CS1\')|enabled:True|wants_pause:False] 20 | Select the input image:OrigDNA 21 | Name the output image:DNA 22 | Select the illumination function:IllumDNA 23 | Select how the illumination function is applied:Divide 24 | Select the input image:OrigER 25 | Name the output image:ER 26 | Select the illumination function:IllumER 27 | Select how the illumination function is applied:Divide 28 | Select the input image:OrigAGP 29 | Name the output image:AGP 30 | Select the illumination function:IllumAGP 31 | Select how the illumination function is applied:Divide 32 | Select the input image:OrigMito 33 | Name the output image:Mito 34 | Select the illumination function:IllumMito 35 | Select how the illumination function is applied:Divide 36 | Select the input image:OrigRNA 37 | Name the output image:RNA 38 | Select the illumination function:IllumRNA 39 | Select how the illumination function is applied:Divide 40 | 41 | SaveImages:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Select the type of image to save:Image 43 | Select the image to save:AGP 44 | Select the objects to save:None 45 | Select the module display window to save:None 46 | Select method for constructing file names:From image filename 47 | Select image name for file prefix:OrigAGP 48 | Enter single file name:OrigBlue 49 | Number of digits:4 50 | Append a suffix to the image file name?:Yes 51 | Text to append to the image name:_illum_corrected 52 | Saved file format:tif 53 | Output file location:Default Output Folder sub-folder\x7Cillum_corrected 54 | Image bit depth:16-bit integer 55 | Overwrite existing files without warning?:No 56 | When to save:Every cycle 57 | Rescale the images? :No 58 | Save as grayscale or color image?:Grayscale 59 | Select colormap:gray 60 | Record the file and path information to the saved image?:No 61 | Create subfolders in the output folder?:No 62 | Base image folder:Elsewhere...\x7C 63 | Saved movie format:avi 64 | 65 | SaveImages:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 66 | Select the type of image to save:Image 67 | Select the image to save:DNA 68 | Select the objects to save:None 69 | Select the module display window to save:None 70 | Select method for constructing file names:From image filename 71 | Select image name for file prefix:OrigDNA 72 | Enter single file name:OrigBlue 73 | Number of digits:4 74 | Append a suffix to the image file name?:Yes 75 | Text to append to the image name:_illum_corrected 76 | Saved file format:tif 77 | Output file location:Default Output Folder sub-folder\x7Cillum_corrected 78 | Image bit depth:16-bit integer 79 | Overwrite existing files without warning?:No 80 | When to save:Every cycle 81 | Rescale the images? :No 82 | Save as grayscale or color image?:Grayscale 83 | Select colormap:gray 84 | Record the file and path information to the saved image?:No 85 | Create subfolders in the output folder?:No 86 | Base image folder:Elsewhere...\x7C 87 | Saved movie format:avi 88 | 89 | SaveImages:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 90 | Select the type of image to save:Image 91 | Select the image to save:ER 92 | Select the objects to save:None 93 | Select the module display window to save:None 94 | Select method for constructing file names:From image filename 95 | Select image name for file prefix:OrigER 96 | Enter single file name:OrigBlue 97 | Number of digits:4 98 | Append a suffix to the image file name?:Yes 99 | Text to append to the image name:_illum_corrected 100 | Saved file format:tif 101 | Output file location:Default Output Folder sub-folder\x7Cillum_corrected 102 | Image bit depth:16-bit integer 103 | Overwrite existing files without warning?:No 104 | When to save:Every cycle 105 | Rescale the images? :No 106 | Save as grayscale or color image?:Grayscale 107 | Select colormap:gray 108 | Record the file and path information to the saved image?:No 109 | Create subfolders in the output folder?:No 110 | Base image folder:Elsewhere...\x7C 111 | Saved movie format:avi 112 | 113 | SaveImages:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 114 | Select the type of image to save:Image 115 | Select the image to save:Mito 116 | Select the objects to save:None 117 | Select the module display window to save:None 118 | Select method for constructing file names:From image filename 119 | Select image name for file prefix:OrigMito 120 | Enter single file name:OrigBlue 121 | Number of digits:4 122 | Append a suffix to the image file name?:Yes 123 | Text to append to the image name:_illum_corrected 124 | Saved file format:tif 125 | Output file location:Default Output Folder sub-folder\x7Cillum_corrected 126 | Image bit depth:16-bit integer 127 | Overwrite existing files without warning?:No 128 | When to save:Every cycle 129 | Rescale the images? :No 130 | Save as grayscale or color image?:Grayscale 131 | Select colormap:gray 132 | Record the file and path information to the saved image?:No 133 | Create subfolders in the output folder?:No 134 | Base image folder:Elsewhere...\x7C 135 | Saved movie format:avi 136 | 137 | SaveImages:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 138 | Select the type of image to save:Image 139 | Select the image to save:RNA 140 | Select the objects to save:None 141 | Select the module display window to save:None 142 | Select method for constructing file names:From image filename 143 | Select image name for file prefix:OrigRNA 144 | Enter single file name:OrigBlue 145 | Number of digits:4 146 | Append a suffix to the image file name?:Yes 147 | Text to append to the image name:_illum_corrected 148 | Saved file format:tif 149 | Output file location:Default Output Folder sub-folder\x7Cillum_corrected 150 | Image bit depth:16-bit integer 151 | Overwrite existing files without warning?:No 152 | When to save:Every cycle 153 | Rescale the images? :No 154 | Save as grayscale or color image?:Grayscale 155 | Select colormap:gray 156 | Record the file and path information to the saved image?:No 157 | Create subfolders in the output folder?:No 158 | Base image folder:Elsewhere...\x7C 159 | Saved movie format:avi 160 | 161 | CreateBatchFiles:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:False|wants_pause:False] 162 | Store batch files in default output folder?:Yes 163 | Output folder path:/imaging/analysis/2008_12_04_Imaging_CDRP_for_MLPCN/HDAC_inhibitors/20100803 164 | Are the cluster computers running Windows?:No 165 | Hidden\x3A in batch mode:No 166 | Hidden\x3A in distributed mode:No 167 | Hidden\x3A default input folder at time of save:/cbnt/cbimage/HCS 168 | Hidden\x3A revision number:10346 169 | Hidden\x3A from old matlab:No 170 | Launch BatchProfiler:No 171 | -------------------------------------------------------------------------------- /cellpainting_u2os_20x_imagexpress_cdrp/README.md: -------------------------------------------------------------------------------- 1 | Pipelines for "A dataset of images and morphological profiles of 30,000 small-molecule treatments using the Cell Painting assay", Bray et al. 2016 (https://doi.org/10.5524/100200) 2 | 3 | Differences with (cellpainting_u2os_20x_imagexpress/analysis.cppipe)[https://github.com/broadinstitute/imaging-platform-pipelines/blob/master/cellpainting_u2os_20x_imagexpress/analysis.cppipe] are: 4 | 5 | ``` 6 | 139,140c139,140 7 | < Size of smoothing filter:8 8 | < Suppress local maxima that are closer than this minimum allowed distance:8 9 | --- 10 | > Size of smoothing filter:20 11 | > Suppress local maxima that are closer than this minimum allowed distance:20 12 | 159c159 13 | < Lower and upper bounds on threshold:0.0125,1.0 14 | --- 15 | > Lower and upper bounds on threshold:0.003,1.0 16 | 197,198c197,198 17 | < Threshold correction factor:.8 18 | < Lower and upper bounds on threshold:0.02,1.0 19 | --- 20 | > Threshold correction factor:.9 21 | > Lower and upper bounds on threshold:0.002,1.0 22 | ``` 23 | 24 | - The analysis pipeline is customized for U2OS cells imaged at 20x on ImageXpress, with binning. 25 | - The illumination pipeline requires that the image dimensions are a multiple of 8 because it downsamples and upsamples by a factor of 8. 26 | -------------------------------------------------------------------------------- /cellpainting_u2os_63x_phenix_bin2/maxproj.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160418141927 4 | GitHash:9969f42 5 | ModuleCount:9 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Default Input Folder sub-folder\x7CDesktop 10 | Name of the file:load_data.csv 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Well,Site,ChannelName 17 | Rescale intensities?:Yes 18 | 19 | MakeProjection:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Select the input image:OrigDNA 21 | Type of projection:Maximum 22 | Name the output image:OirgDNA_maxproj 23 | Frequency:6.0 24 | 25 | SaveImages:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 26 | Select the type of image to save:Image 27 | Select the image to save:OirgDNA_maxproj 28 | Select the objects to save:None 29 | Select the module display window to save:None 30 | Select method for constructing file names:Single name 31 | Select image name for file prefix:OrigDNA 32 | Enter single file name:r\\\\gc\\\\gf\\\\gp01-ch1sk1fk1fl1.tiff 33 | Number of digits:4 34 | Append a suffix to the image file name?:No 35 | Text to append to the image name:_maxproj 36 | Saved file format:tif 37 | Output file location:Default Output Folder\x7C 38 | Image bit depth:16-bit integer 39 | Overwrite existing files without warning?:No 40 | When to save:Last cycle 41 | Rescale the images? :No 42 | Save as grayscale or color image?:Grayscale 43 | Select colormap:gray 44 | Record the file and path information to the saved image?:No 45 | Create subfolders in the output folder?:No 46 | Base image folder:Elsewhere...\x7C 47 | Saved movie format:avi 48 | 49 | MakeProjection:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 50 | Select the input image:OrigProtein 51 | Type of projection:Maximum 52 | Name the output image:OrigProtein_maxproj 53 | Frequency:6.0 54 | 55 | SaveImages:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 56 | Select the type of image to save:Image 57 | Select the image to save:OrigProtein_maxproj 58 | Select the objects to save:None 59 | Select the module display window to save:None 60 | Select method for constructing file names:Single name 61 | Select image name for file prefix:OrigDNA 62 | Enter single file name:r\\\\gc\\\\gf\\\\gp01-ch2sk1fk1fl1.tiff 63 | Number of digits:4 64 | Append a suffix to the image file name?:No 65 | Text to append to the image name:_maxproj 66 | Saved file format:tif 67 | Output file location:Default Output Folder\x7C 68 | Image bit depth:16-bit integer 69 | Overwrite existing files without warning?:No 70 | When to save:Last cycle 71 | Rescale the images? :No 72 | Save as grayscale or color image?:Grayscale 73 | Select colormap:gray 74 | Record the file and path information to the saved image?:No 75 | Create subfolders in the output folder?:No 76 | Base image folder:Elsewhere...\x7C 77 | Saved movie format:avi 78 | 79 | MakeProjection:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 80 | Select the input image:OrigMito 81 | Type of projection:Maximum 82 | Name the output image:OrigMito_maxproj 83 | Frequency:6.0 84 | 85 | SaveImages:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 86 | Select the type of image to save:Image 87 | Select the image to save:OrigMito_maxproj 88 | Select the objects to save:None 89 | Select the module display window to save:None 90 | Select method for constructing file names:Single name 91 | Select image name for file prefix:OrigDNA 92 | Enter single file name:r\\\\gc\\\\gf\\\\gp01-ch3sk1fk1fl1.tiff 93 | Number of digits:4 94 | Append a suffix to the image file name?:No 95 | Text to append to the image name:_maxproj 96 | Saved file format:tif 97 | Output file location:Default Output Folder\x7C 98 | Image bit depth:16-bit integer 99 | Overwrite existing files without warning?:No 100 | When to save:Last cycle 101 | Rescale the images? :No 102 | Save as grayscale or color image?:Grayscale 103 | Select colormap:gray 104 | Record the file and path information to the saved image?:No 105 | Create subfolders in the output folder?:No 106 | Base image folder:Elsewhere...\x7C 107 | Saved movie format:avi 108 | 109 | MakeProjection:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 110 | Select the input image:OrigER 111 | Type of projection:Maximum 112 | Name the output image:OrigER_maxproj 113 | Frequency:6.0 114 | 115 | SaveImages:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 116 | Select the type of image to save:Image 117 | Select the image to save:OrigER_maxproj 118 | Select the objects to save:None 119 | Select the module display window to save:None 120 | Select method for constructing file names:Single name 121 | Select image name for file prefix:OrigDNA 122 | Enter single file name:r\\\\gc\\\\gf\\\\gp01-ch4sk1fk1fl1.tiff 123 | Number of digits:4 124 | Append a suffix to the image file name?:No 125 | Text to append to the image name:_maxproj 126 | Saved file format:tif 127 | Output file location:Default Output Folder\x7C 128 | Image bit depth:16-bit integer 129 | Overwrite existing files without warning?:No 130 | When to save:Last cycle 131 | Rescale the images? :No 132 | Save as grayscale or color image?:Grayscale 133 | Select colormap:gray 134 | Record the file and path information to the saved image?:No 135 | Create subfolders in the output folder?:No 136 | Base image folder:Elsewhere...\x7C 137 | Saved movie format:avi 138 | -------------------------------------------------------------------------------- /cellpainting_u2os_63x_phenix_bin2/qc.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160418141927 4 | GitHash:9969f42 5 | ModuleCount:4 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Default Input Folder sub-folder\x7CDownloads 10 | Name of the file:load_data_with_illum.csv 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Site,Well 17 | Rescale intensities?:Yes 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:All loaded images 21 | Image count:1 22 | Scale count:4 23 | Threshold count:1 24 | Select the images to measure: 25 | Include the image rescaling value?:Yes 26 | Calculate blur metrics?:Yes 27 | Spatial scale for blur measurements:5 28 | Spatial scale for blur measurements:10 29 | Spatial scale for blur measurements:20 30 | Spatial scale for blur measurements:50 31 | Calculate saturation metrics?:Yes 32 | Calculate intensity metrics?:Yes 33 | Calculate thresholds?:No 34 | Use all thresholding methods?:Yes 35 | Select a thresholding method:Otsu 36 | Typical fraction of the image covered by objects:0.1 37 | Two-class or three-class thresholding?:Two classes 38 | Minimize the weighted variance or the entropy?:Weighted variance 39 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:Select... 43 | Image count:2 44 | Scale count:1 45 | Threshold count:1 46 | Scale count:1 47 | Threshold count:1 48 | Select the images to measure:OrigDNA 49 | Include the image rescaling value?:No 50 | Calculate blur metrics?:No 51 | Spatial scale for blur measurements:20 52 | Calculate saturation metrics?:No 53 | Calculate intensity metrics?:No 54 | Calculate thresholds?:Yes 55 | Use all thresholding methods?:No 56 | Select a thresholding method:Otsu 57 | Typical fraction of the image covered by objects:0.1 58 | Two-class or three-class thresholding?:Two classes 59 | Minimize the weighted variance or the entropy?:Weighted variance 60 | Assign pixels in the middle intensity class to the foreground or the background?:Background 61 | Select the images to measure:OrigMito 62 | Include the image rescaling value?:No 63 | Calculate blur metrics?:No 64 | Spatial scale for blur measurements:20 65 | Calculate saturation metrics?:No 66 | Calculate intensity metrics?:No 67 | Calculate thresholds?:Yes 68 | Use all thresholding methods?:No 69 | Select a thresholding method:Otsu 70 | Typical fraction of the image covered by objects:0.1 71 | Two-class or three-class thresholding?:Three classes 72 | Minimize the weighted variance or the entropy?:Weighted variance 73 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:Comma (",") 77 | Add image metadata columns to your object data file?:No 78 | Limit output to a size that is allowed in Excel?:No 79 | Select the measurements to export:No 80 | Calculate the per-image mean values for object measurements?:No 81 | Calculate the per-image median values for object measurements?:No 82 | Calculate the per-image standard deviation values for object measurements?:No 83 | Output file location:Default Output Folder\x7C 84 | Create a GenePattern GCT file?:No 85 | Select source of sample row name:Metadata 86 | Select the image to use as the identifier:None 87 | Select the metadata to use as the identifier:None 88 | Export all measurement types?:Yes 89 | : 90 | Representation of Nan/Inf:NaN 91 | Add a prefix to file names?:No 92 | Filename prefix:AlzheimersQC_ 93 | Overwrite existing files without warning?:No 94 | Data to export:Do not use 95 | Combine these object measurements with those of the previous object?:No 96 | File name:DATA.csv 97 | Use the object name for the file name?:Yes 98 | -------------------------------------------------------------------------------- /cellpainting_u2os_63x_phenix_bin2/qc_without_batchfile.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:20160418141927 4 | GitHash:9969f42 5 | ModuleCount:5 6 | HasImagePlaneDetails:False 7 | 8 | LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | Input data file location:Default Input Folder sub-folder\x7CDownloads 10 | Name of the file:load_data_with_illum.csv 11 | Load images based on this data?:Yes 12 | Base image location:Default Input Folder\x7C 13 | Process just a range of rows?:No 14 | Rows to process:1,100000 15 | Group images by metadata?:Yes 16 | Select metadata tags for grouping:Plate,Site,Well 17 | Rescale intensities?:Yes 18 | 19 | MeasureImageQuality:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 20 | Calculate metrics for which images?:All loaded images 21 | Image count:1 22 | Scale count:4 23 | Threshold count:1 24 | Select the images to measure: 25 | Include the image rescaling value?:Yes 26 | Calculate blur metrics?:Yes 27 | Spatial scale for blur measurements:5 28 | Spatial scale for blur measurements:10 29 | Spatial scale for blur measurements:20 30 | Spatial scale for blur measurements:50 31 | Calculate saturation metrics?:Yes 32 | Calculate intensity metrics?:Yes 33 | Calculate thresholds?:No 34 | Use all thresholding methods?:Yes 35 | Select a thresholding method:Otsu 36 | Typical fraction of the image covered by objects:0.1 37 | Two-class or three-class thresholding?:Two classes 38 | Minimize the weighted variance or the entropy?:Weighted variance 39 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 40 | 41 | MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 42 | Calculate metrics for which images?:Select... 43 | Image count:2 44 | Scale count:1 45 | Threshold count:1 46 | Scale count:1 47 | Threshold count:1 48 | Select the images to measure:OrigDNA 49 | Include the image rescaling value?:No 50 | Calculate blur metrics?:No 51 | Spatial scale for blur measurements:20 52 | Calculate saturation metrics?:No 53 | Calculate intensity metrics?:No 54 | Calculate thresholds?:Yes 55 | Use all thresholding methods?:No 56 | Select a thresholding method:Otsu 57 | Typical fraction of the image covered by objects:0.1 58 | Two-class or three-class thresholding?:Two classes 59 | Minimize the weighted variance or the entropy?:Weighted variance 60 | Assign pixels in the middle intensity class to the foreground or the background?:Background 61 | Select the images to measure:OrigMito 62 | Include the image rescaling value?:No 63 | Calculate blur metrics?:No 64 | Spatial scale for blur measurements:20 65 | Calculate saturation metrics?:No 66 | Calculate intensity metrics?:No 67 | Calculate thresholds?:Yes 68 | Use all thresholding methods?:No 69 | Select a thresholding method:Otsu 70 | Typical fraction of the image covered by objects:0.1 71 | Two-class or three-class thresholding?:Three classes 72 | Minimize the weighted variance or the entropy?:Weighted variance 73 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 74 | 75 | ExportToSpreadsheet:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 76 | Select the column delimiter:Comma (",") 77 | Add image metadata columns to your object data file?:No 78 | Limit output to a size that is allowed in Excel?:No 79 | Select the measurements to export:No 80 | Calculate the per-image mean values for object measurements?:No 81 | Calculate the per-image median values for object measurements?:No 82 | Calculate the per-image standard deviation values for object measurements?:No 83 | Output file location:Default Output Folder\x7C 84 | Create a GenePattern GCT file?:No 85 | Select source of sample row name:Metadata 86 | Select the image to use as the identifier:None 87 | Select the metadata to use as the identifier:None 88 | Export all measurement types?:Yes 89 | : 90 | Representation of Nan/Inf:NaN 91 | Add a prefix to file names?:No 92 | Filename prefix:AlzheimersQC_ 93 | Overwrite existing files without warning?:No 94 | Data to export:Do not use 95 | Combine these object measurements with those of the previous object?:No 96 | File name:DATA.csv 97 | Use the object name for the file name?:Yes 98 | 99 | CreateBatchFiles:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:False|wants_pause:False] 100 | Store batch files in default output folder?:Yes 101 | Output folder path:/Users/shsingh 102 | Are the cluster computers running Windows?:No 103 | Hidden\x3A in batch mode:No 104 | Hidden\x3A in distributed mode:No 105 | Hidden\x3A default input folder at time of save:/Users/shsingh/Desktop 106 | Hidden\x3A revision number:0 107 | Hidden\x3A from old matlab:No 108 | Launch BatchProfiler:No 109 | -------------------------------------------------------------------------------- /tracking_neutrophiles_matrix_comparison/readme.md: -------------------------------------------------------------------------------- 1 | # Tracking pipeline 2 | 3 | Pipleline to track neutrophile granulocytes in time series acquired with bright field microscopy. 4 | 5 | * The pipeline ```tracking_neutrophiles_4CP3.cppipe``` is tested with CP3.0.0rc 6 | -------------------------------------------------------------------------------- /tracking_neutrophiles_matrix_comparison/tracking_neutrophiles_4CP3.cppipe: -------------------------------------------------------------------------------- 1 | CellProfiler Pipeline: http://www.cellprofiler.org 2 | Version:3 3 | DateRevision:300 4 | GitHash: 5 | ModuleCount:17 6 | HasImagePlaneDetails:False 7 | 8 | Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 9 | : 10 | Filter images?:Images only 11 | Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "\x5B\\\\\\\\\\\\\\\\/\x5D\\\\\\\\.") 12 | 13 | Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 14 | Extract metadata?:Yes 15 | Metadata data type:Text 16 | Metadata types:{} 17 | Extraction method count:1 18 | Metadata extraction method:Extract from file/folder names 19 | Metadata source:File name 20 | Regular expression:^(?P\x5B0-9\x5D{8})_(?P\x5BA-Z\x5D{2})_(?P\x5Ba-z\x5D{4})_(?P\x5B0-9\x5D{4}) 21 | Regular expression:(?P\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$ 22 | Extract metadata from:All images 23 | Select the filtering criteria:and (file does contain "") 24 | Metadata file location: 25 | Match file and image metadata:\x5B\x5D 26 | Use case insensitive matching?:No 27 | 28 | NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:7|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 29 | Assign a name to:All images 30 | Select the image type:Grayscale image 31 | Name to assign these images:neutrophils 32 | Match metadata:\x5B\x5D 33 | Image set matching method:Order 34 | Set intensity range from:Image metadata 35 | Assignments count:1 36 | Single images count:0 37 | Maximum intensity:255.0 38 | Volumetric:No 39 | x:1.0 40 | y:1.0 41 | z:1.0 42 | Select the rule criteria:and (file does contain "") 43 | Name to assign these images:DNA 44 | Name to assign these objects:Cell 45 | Select the image type:Grayscale image 46 | Set intensity range from:Image metadata 47 | Retain outlines of loaded objects?:No 48 | Name the outline image:LoadedOutlines 49 | Maximum intensity:255.0 50 | 51 | Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 52 | Do you want to group your images?:Yes 53 | grouping metadata count:3 54 | Metadata category:condition 55 | Metadata category:matrix 56 | Metadata category:dateCreated 57 | 58 | Crop:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 59 | Select the input image:neutrophils 60 | Name the output image:neutrophilesCropped 61 | Select the cropping shape:Rectangle 62 | Select the cropping method:Coordinates 63 | Apply which cycle\'s cropping pattern?:First 64 | Left and right rectangle positions:50,1300 65 | Top and bottom rectangle positions:0,end 66 | Coordinates of ellipse center:500,500 67 | Ellipse radius, X direction:400 68 | Ellipse radius, Y direction:200 69 | Remove empty rows and columns?:All 70 | Select the masking image:None 71 | Select the image with a cropping mask:None 72 | Select the objects:None 73 | 74 | CorrectIlluminationCalculate:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 75 | Select the input image:neutrophilesCropped 76 | Name the output image:illumination 77 | Select how the illumination function is calculated:Regular 78 | Dilate objects in the final averaged image?:Yes 79 | Dilation radius:10 80 | Block size:60 81 | Rescale the illumination function?:No 82 | Calculate function for each image individually, or based on all images?:Each 83 | Smoothing method:Gaussian Filter 84 | Method to calculate smoothing filter size:Manually 85 | Approximate object size:10 86 | Smoothing filter size:60 87 | Retain the averaged image?:No 88 | Name the averaged image:IllumBlueAvg 89 | Retain the dilated image?:No 90 | Name the dilated image:IllumBlueDilated 91 | Automatically calculate spline parameters?:Yes 92 | Background mode:auto 93 | Number of spline points:5 94 | Background threshold:2.0 95 | Image resampling factor:2.0 96 | Maximum number of iterations:40 97 | Residual value for convergence:0.001 98 | 99 | CorrectIlluminationApply:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 100 | Select the input image:neutrophilesCropped 101 | Name the output image:neutrosIlluCorrected 102 | Select the illumination function:illumination 103 | Select how the illumination function is applied:Divide 104 | 105 | EnhanceEdges:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 106 | Select the input image:neutrosIlluCorrected 107 | Name the output image:neutrosEdgeImage 108 | Automatically calculate the threshold?:Yes 109 | Absolute threshold:0.2 110 | Threshold adjustment factor:1.0 111 | Select an edge-finding method:Sobel 112 | Select edge direction to enhance:All 113 | Calculate Gaussian\'s sigma automatically?:Yes 114 | Gaussian\'s sigma value:10.0 115 | Calculate value for low threshold automatically?:Yes 116 | Low threshold value:0.1 117 | 118 | EdgeDetection:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:False|wants_pause:False] 119 | Input:neutrosIlluCorrected 120 | Output:edgeImage 121 | Mask:Leave blank 122 | 123 | ImageMath:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 124 | Operation:Invert 125 | Raise the power of the result by:1.0 126 | Multiply the result by:1.0 127 | Add to result:0.0 128 | Set values less than 0 equal to 0?:Yes 129 | Set values greater than 1 equal to 1?:Yes 130 | Ignore the image masks?:No 131 | Name the output image:neutrosInverted 132 | Image or measurement?:Image 133 | Select the first image:neutrosIlluCorrected 134 | Multiply the first image by:1.0 135 | Measurement: 136 | Image or measurement?:Image 137 | Select the second image: 138 | Multiply the second image by:1.0 139 | Measurement: 140 | 141 | ImageMath:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 142 | Operation:Average 143 | Raise the power of the result by:1.0 144 | Multiply the result by:1.0 145 | Add to result:0.0 146 | Set values less than 0 equal to 0?:Yes 147 | Set values greater than 1 equal to 1?:Yes 148 | Ignore the image masks?:Yes 149 | Name the output image:ImageAfterMath 150 | Image or measurement?:Image 151 | Select the first image:neutrosEdgeImage 152 | Multiply the first image by:1.0 153 | Measurement: 154 | Image or measurement?:Image 155 | Select the second image:neutrosInverted 156 | Multiply the second image by:1.0 157 | Measurement: 158 | 159 | ApplyThreshold:[module_num:12|svn_version:\'Unknown\'|variable_revision_number:10|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 160 | Input:ImageAfterMath 161 | Output:BW 162 | Threshold strategy:Global 163 | Thresholding method:Minimum cross entropy 164 | Threshold smoothing scale:0 165 | Threshold correction factor:1 166 | Lower and upper bounds on threshold:0.0,1.0 167 | Manual threshold:0.0 168 | Select the measurement to threshold with:None 169 | Two-class or three-class thresholding?:Two classes 170 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 171 | Size of adaptive window:50 172 | Lower outlier fraction:0.05 173 | Upper outlier fraction:0.05 174 | Averaging method:Mean 175 | Variance method:Standard deviation 176 | # of deviations:2.0 177 | Thresholding method:Otsu 178 | 179 | Closing:[module_num:13|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 180 | Input:BW 181 | Output:BWClosed 182 | Structuring element:disk,3 183 | 184 | IdentifyPrimaryObjects:[module_num:14|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 185 | Select the input image:BWClosed 186 | Name the primary objects to be identified:NEUTROS 187 | Typical diameter of objects, in pixel units (Min,Max):10,50 188 | Discard objects outside the diameter range?:Yes 189 | Discard objects touching the border of the image?:Yes 190 | Method to distinguish clumped objects:None 191 | Method to draw dividing lines between clumped objects:Shape 192 | Size of smoothing filter:10 193 | Suppress local maxima that are closer than this minimum allowed distance:7.0 194 | Speed up by using lower-resolution image to find local maxima?:Yes 195 | Fill holes in identified objects?:After both thresholding and declumping 196 | Automatically calculate size of smoothing filter for declumping?:No 197 | Automatically calculate minimum allowed distance between local maxima?:Yes 198 | Handling of objects if excessive number of objects identified:Continue 199 | Maximum number of objects:10 200 | Use advanced settings?:No 201 | Threshold setting version:10 202 | Threshold strategy:Global 203 | Thresholding method:Otsu 204 | Threshold smoothing scale:1.3488 205 | Threshold correction factor:1.0 206 | Lower and upper bounds on threshold:0.0,1.0 207 | Manual threshold:0.5 208 | Select the measurement to threshold with:None 209 | Two-class or three-class thresholding?:Two classes 210 | Assign pixels in the middle intensity class to the foreground or the background?:Foreground 211 | Size of adaptive window:50 212 | Lower outlier fraction:0.05 213 | Upper outlier fraction:0.05 214 | Averaging method:Mean 215 | Variance method:Standard deviation 216 | # of deviations:2.0 217 | Thresholding method:Otsu 218 | 219 | TrackObjects:[module_num:15|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 220 | Choose a tracking method:LAP 221 | Select the objects to track:NEUTROS 222 | Select object measurement to use for tracking:None 223 | Maximum pixel distance to consider matches:50 224 | Select display option:Color and Number 225 | Save color-coded image?:Yes 226 | Name the output image:TrackedCells_ 227 | Select the movement model:Both 228 | Number of standard deviations for search radius:3.0 229 | Search radius limit, in pixel units (Min,Max):2.0,10.0 230 | Run the second phase of the LAP algorithm?:Yes 231 | Gap closing cost:40 232 | Split alternative cost:40 233 | Merge alternative cost:40 234 | Maximum gap displacement, in pixel units:5 235 | Maximum split score:50 236 | Maximum merge score:50 237 | Maximum temporal gap, in frames:5 238 | Filter objects by lifetime?:No 239 | Filter using a minimum lifetime?:Yes 240 | Minimum lifetime:1 241 | Filter using a maximum lifetime?:No 242 | Maximum lifetime:100 243 | Mitosis alternative cost:80 244 | Maximum mitosis distance, in pixel units:40 245 | 246 | MeasureObjectSizeShape:[module_num:16|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 247 | Select objects to measure:NEUTROS 248 | Calculate the Zernike features?:Yes 249 | 250 | ExportToSpreadsheet:[module_num:17|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] 251 | Select the column delimiter:Comma (",") 252 | Add image metadata columns to your object data file?:Yes 253 | Limit output to a size that is allowed in Excel?:No 254 | Select the measurements to export:No 255 | Calculate the per-image mean values for object measurements?:No 256 | Calculate the per-image median values for object measurements?:No 257 | Calculate the per-image standard deviation values for object measurements?:No 258 | Output file location:Default Output Folder sub-folder\x7Ctmp 259 | Create a GenePattern GCT file?:No 260 | Select source of sample row name:Metadata 261 | Select the image to use as the identifier:None 262 | Select the metadata to use as the identifier:None 263 | Export all measurement types?:Yes 264 | : 265 | Representation of Nan/Inf:NaN 266 | Add a prefix to file names?:Yes 267 | Filename prefix:Tracked 268 | Overwrite existing files without warning?:No 269 | Data to export:Image 270 | Combine these object measurements with those of the previous object?:No 271 | File name:DATA.csv 272 | Use the object name for the file name?:Yes 273 | --------------------------------------------------------------------------------