├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── CellProfiler_features.csv ├── JUMPExperimentMasterTable.csv ├── LICENSE ├── README.md ├── figures ├── ExtendedData1.svg ├── ExtendedData1.tiff ├── ExtendedData2.svg ├── ExtendedData2.tiff ├── ExtendedData2_diff.svg ├── ExtendedData2_diff.tiff ├── ExtendedData3.svg ├── ExtendedData3.tiff ├── ExtendedData3_diff.svg ├── ExtendedData3_diff.tiff ├── ExtendedData4.svg ├── ExtendedData4.tiff ├── ExtendedData5.svg ├── ExtendedData5.tiff ├── ExtendedData6.svg ├── ExtendedData6.tiff ├── ExtendedData7.svg ├── ExtendedData7.tiff ├── ExtendedData8.svg ├── ExtendedData8.tiff ├── ExtendedData9.svg ├── ExtendedData9.tiff ├── Figure1.pdf ├── Figure1.svg ├── Figure2.pdf ├── Figure2.svg ├── Figure3.pdf ├── Figure3.svg ├── Figure3_diff.pdf ├── Figure3_diff.svg ├── Figure4.pdf ├── Figure4.svg ├── Figure5.pdf ├── Figure5.svg ├── Figure6.pdf ├── Figure6.svg ├── InPaper │ ├── Main │ │ ├── # of times imaged-Percent Replicating-Batch-None-None.svg │ │ ├── Cell Type-Percent Matching-Treatment timepoint-Modality Match.svg │ │ ├── Days between staining and imaging-Percent Replicating-Batch-Cell Type-None.svg │ │ ├── Fields of view-Percent Replicating-Batch-None-None.svg │ │ ├── JUMP-MOA.svg │ │ ├── JUMP-Target-CRISPR.svg │ │ ├── JUMP-Target-ORF.svg │ │ ├── JUMP-Target1-Compound.svg │ │ ├── JUMP-Target2-Compound.svg │ │ ├── Mean Percent Replicating by Compartments Present.svg │ │ ├── Mean Percent Replicating by Measurements Present.svg │ │ ├── Percent Replicating-Percent Matching-Batch-Binning-None-None.svg │ │ ├── Percent Replicating-Percent Matching-Batch-Exposure level-None-None.svg │ │ ├── Percent Replicating-Percent Matching-Batch-Imaging modality-None-None.svg │ │ ├── Percent Replicating-Percent Matching-Batch-None-None-Reagent source.svg │ │ ├── Percent Replicating-Percent Matching-Batch-Stains - Official CellPainting Versions-None-None.svg │ │ ├── Percent Replicating-Percent Matching-Clone type-Cell Type-None-Density.svg │ │ └── Percent Replicating-Percent Matching-Measurement scales-None-None-None.svg │ └── Supplemental │ │ ├── ChannelAdditionPercentReplicating-AGP.svg │ │ ├── ChannelAdditionPercentReplicating-BFHigh.svg │ │ ├── ChannelAdditionPercentReplicating-BFLow.svg │ │ ├── ChannelAdditionPercentReplicating-Brightfield.svg │ │ ├── ChannelAdditionPercentReplicating-DNA.svg │ │ ├── ChannelAdditionPercentReplicating-ER.svg │ │ ├── ChannelAdditionPercentReplicating-Mito.svg │ │ ├── ChannelAdditionPercentReplicating-RNA.svg │ │ ├── Drug selection-Percent Matching-Treatment timepoint-Modality Match.svg │ │ ├── Drug selection-Percent Replicating-Treatment timepoint-Modality-None.svg │ │ ├── Dye [concentration]-Batch.svg │ │ ├── JUMP-MOA_Replicates.svg │ │ ├── Matching between parental and Cas9-Percent Matching-Treatment timepoint-Modality Match.svg │ │ ├── Mean Percent Replicating by Measurements Present - AGP Only.svg │ │ ├── Mean Percent Replicating by Measurements Present - BFHigh Only.svg │ │ ├── Mean Percent Replicating by Measurements Present - BFLow Only.svg │ │ ├── Mean Percent Replicating by Measurements Present - Brightfield Only.svg │ │ ├── Mean Percent Replicating by Measurements Present - DNA Only.svg │ │ ├── Mean Percent Replicating by Measurements Present - ER Only.svg │ │ ├── Mean Percent Replicating by Measurements Present - Mito Only.svg │ │ ├── Mean Percent Replicating by Measurements Present - RNA Only.svg │ │ ├── Mean Percent Replicating by Stains Present.svg │ │ ├── Percent Replicating-Percent Matching-Batch-Microscope-None-None.svg │ │ ├── Percent Replicating-Percent Matching-Batch-None-None-Multiplane.svg │ │ ├── Percent Replicating-Percent Matching-Batch-None-None-Stains - Overall stain level.svg │ │ ├── Percent Replicating-Percent Matching-Density-None-None-Stains - Permeabilization with dyes.svg │ │ ├── Percent Replicating-Percent Matching-Plate type-None-None-None.svg │ │ ├── Plating density-Percent Matching-Treatment timepoint-Modality Match.svg │ │ ├── Polybrene effect on compounds and matching-Percent Matching-Treatment timepoint.svg │ │ ├── Polybrene effect on compounds and matching-Percent Replicating-Plate Comparison.svg │ │ └── Treatment timepoint-Percent Replicating-Cell Type-Modality-None.svg ├── NotInPaper │ ├── Binning-Percent Matching-Batch-None-None.png │ ├── Binning-Percent Replicating-Batch-None-None.png │ ├── Cell Type-Percent Matching-Treatment timepoint-Modality Match -AGP.png │ ├── Clone type-Percent Matching-Density-Cell Type-None.png │ ├── Clone type-Percent Replicating-Density-Cell Type-None.png │ ├── Clone type-Percent Replicating-Density-None-Cell Type.png │ ├── Compartments Present-Mean Percent Replicating-None-None-None.png │ ├── Compartments Present-Mean Percent Replicating-None-None-None.svg │ ├── Density-PercentMatch-JustShowMatching.png │ ├── Drug selection-Percent Replicating-Treatment timepoint-Modality-None.png │ ├── Dye [concentration]-Percent Replicating-Batch-Dye-None.png │ ├── Exposure level-Percent Matching-Batch-None-None.png │ ├── Exposure level-Percent Replicating-Batch-None-None.png │ ├── Imaging modality-Percent Matching-Batch-None-None.png │ ├── Imaging modality-Percent Replicating-Batch-None-None.png │ ├── Matching between parental and Cas9-Percent Replicating-Treatment timepoint-None-None.png │ ├── Measurement scales-Percent Matching-Batch-None-None.png │ ├── Measurement scales-Percent Replicating-Batch-None-None.png │ ├── Microscope-Percent Matching-Batch-None-None.png │ ├── Microscope-Percent Replicating-Batch-None-None.png │ ├── Multiplane-Percent Matching-Batch-None-None.png │ ├── Multiplane-Percent Replicating-Batch-None-None.png │ ├── Percent Replicating-Percent Matching-Batch-Reagent source-None-None.png │ ├── Plate type-Percent Matching-Batch-None-None.png │ ├── Plate type-Percent Replicating-Batch-None-None.png │ ├── Plating density-Percent Replicating-Treatment timepoint-Modality-None.png │ ├── Polybrene effect on compounds and matching-Percent Replicating-Polybrene effect on compounds and matching-None-None.png │ ├── Reagent source-Percent Matching-Batch-None-None.png │ ├── Reagent source-Percent Replicating-Batch-None-None.png │ ├── Stains - Official CellPainting Versions-Percent Matching-Batch-None-None.png │ ├── Stains - Official CellPainting Versions-Percent Replicating-Batch-None-None.png │ ├── Stains - Overall stain level-Percent Matching-Batch-None-None.png │ ├── Stains - Overall stain level-Percent Replicating-Batch-None-None.png │ ├── Stains - Permeabilization with dyes-Percent Matching-Density-None-None.png │ ├── Stains - Permeabilization with dyes-Percent Replicating-Density-None-None.png │ ├── Target1 vs Target2-Percent Replicating-Batch-None-None.png │ └── Target1 vs Target2-Percent Replicating-Plate Comparison.png └── image_crops │ ├── 2020_06_25_Stain2_Batch2_Redone-BR00113819__2020-07-07T19_08_17-Measurement1.bmp │ ├── 2020_06_25_Stain2_Batch2_Redone-BR00113819__2020-07-07T19_08_17-Measurement1.svg │ ├── 2020_06_25_Stain2_Batch2_Redone-BR00113819__2020-07-07T19_08_17-Measurement1_montage.bmp │ ├── 2020_06_25_Stain2_Batch2_Redone-BR00113819__2020-07-07T19_08_17-Measurement1_montage.svg │ ├── 2020_06_25_Stain2_Batch2_Redone-BR00113819__2020-07-07T19_08_17-Measurement1_montage_gray.bmp │ └── 2020_06_25_Stain2_Batch2_Redone-BR00113819__2020-07-07T19_08_17-Measurement1_montage_gray.svg ├── notebooks ├── AssessBinning.ipynb ├── AssessBleaching.ipynb ├── AssessCompoundsInCas9.ipynb ├── AssessDensity.ipynb ├── AssessDrugSelection.ipynb ├── AssessExposure.ipynb ├── AssessFOVs.ipynb ├── AssessMeasurementScales.ipynb ├── AssessMicroscope.ipynb ├── AssessMultiplane.ipynb ├── AssessPlates.ipynb ├── AssessPolybreneOnCompounds.ipynb ├── AssessPolyclonesVsMonoclones.ipynb ├── AssessReagents.ipynb ├── AssessStains.ipynb ├── AssessTarget1vsTarget2.ipynb ├── AssessTimedelay.ipynb ├── AssessTreatmentTimepoint.ipynb ├── AssessTreatmentTimepoint_NoAGP.ipynb ├── AssessWidefieldVConfocal.ipynb ├── DescribePlates.ipynb ├── FeatureDropout.ipynb ├── FijiNiceImageScript.py ├── MakePrettyPlatemap.ipynb ├── MakeSourceDataFiles.ipynb ├── MasterFigureTemplate-MOA.ipynb ├── MasterFigureTemplate-Target.ipynb ├── MatrixedFeatureDropout.ipynb ├── PlotFeatureDropout.ipynb ├── PlotPies.ipynb ├── checkpoint_csvs │ ├── AGP_only_feature_dropout_combinations.csv │ ├── AssessCompoundsInCas9-Matching.csv │ ├── AssessCompoundsInCas9-Replicating.csv │ ├── AssessDensity-Matching.csv │ ├── AssessDensity-Replicating.csv │ ├── AssessPolyclonesMonoclones-Matching.csv │ ├── AssessPolyclonesMonoclones-Replicating.csv │ ├── AssessStains-OfficialVersions.csv │ ├── AssessStains-Permeabilization.csv │ ├── AssessStains-ReduceAllStains.csv │ ├── AssessStains-ReduceSomeStains.csv │ ├── BFHigh_only_feature_dropout_combinations.csv │ ├── BFLow_only_feature_dropout_combinations.csv │ ├── Binning.csv │ ├── Brightfield_only_feature_dropout_combinations.csv │ ├── DNA_only_feature_dropout_combinations.csv │ ├── Days_between_staining_and_imaging-replicating.csv │ ├── Drug_selection-matching.csv │ ├── Drug_selection-replicating.csv │ ├── ER_only_feature_dropout_combinations.csv │ ├── Exposure_level.csv │ ├── Fields_of_view-replicating.csv │ ├── Imaging_modality.csv │ ├── Measurement_scales.csv │ ├── Microscope.csv │ ├── Mito_only_feature_dropout_combinations.csv │ ├── Multiplane.csv │ ├── Number_of_times_imaged-replicating.csv │ ├── Plate_type.csv │ ├── Polybrene_effect_on_compounds_and_matching-cross-plate-replication.csv │ ├── Polybrene_effect_on_compounds_and_matching-matching.csv │ ├── Polybrene_effect_on_compounds_and_matching-replicating.csv │ ├── RNA_only_feature_dropout_combinations.csv │ ├── Reagent_source.csv │ ├── Target1_vs_Target2-cross-plate-replication.csv │ ├── Target1_vs_Target2-matching.csv │ ├── Target1_vs_Target2-replicating.csv │ ├── Treatment_timepoint-matching-noAGP.csv │ ├── Treatment_timepoint-matching.csv │ ├── Treatment_timepoint-replicating.csv │ ├── channel_dropout_combinations.csv │ ├── compartment_dropout_combinations.csv │ ├── feature_dropout_combinations.csv │ └── single_dropout.csv ├── requirements.txt └── utils.py ├── pipelines ├── analysis.cppipe ├── illum.cppipe ├── qc.cppipe └── segment.cppipe └── source_data_files ├── Extended_Data_Figure_1_SourceData.xlsx ├── Extended_Data_Figure_2_SourceData.xlsx ├── Extended_Data_Figure_3_SourceData.xlsx ├── Extended_Data_Figure_4_SourceData.xlsx ├── Extended_Data_Figure_5_SourceData.xlsx ├── Extended_Data_Figure_6_SourceData.xlsx ├── Extended_Data_Figure_9_SourceData.xlsx ├── Extended_Data_Figures_7_and_8_SourceData.xlsx ├── Figure_2_SourceData.xlsx ├── Figure_3_SourceData.xlsx ├── Figure_4_SourceData.xlsx ├── Figure_5_SourceData.xlsx └── Figure_6_SourceData.xlsx /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/carpenter-singh-lab/2023_Cimini_NatureProtocols/HEAD/.gitignore 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