Merge pull request #76 from AllenCell/cellprofiler_project_file

add cellprofiler cpproj file
AllenCell · Dec 10, 2024 · b20fcf5 · b20fcf5
2 parents 7f9374a + 070c783
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diff --git a/docs/USAGE.md b/docs/USAGE.md
@@ -190,8 +190,12 @@ You can download our pre-computed embeddings here.
 | other_punctate    | `python src/br/analysis/run_analysis.py --save_path "./outputs_other_punctate/" --embeddings_path "./morphology_appropriate_representation_learning/model_embeddings/other_punctate" --dataset_name "other_punctate" --run_name "Rotation_invariant_pointcloud_structurenorm" --sdf False`            |
 | pcna              | `python src/br/analysis/run_analysis.py --save_path "./outputs_pcna/" --embeddings_path "./morphology_appropriate_representation_learning/model_embeddings/pcna" --dataset_name "pcna" --run_name "Rotation_invariant_pointcloud_jitter" --sdf False`                                                    |
 
-3. To run drug perturbation analysis, run
+3. To run drug perturbation analysis using the pre-computed features, run
 
 ```
 python src/br/analysis/run_drugdata_analysis.py --save_path "./outputs_npm1_perturb/" --embeddings_path "./morphology_appropriate_representation_learning/model_embeddings/npm1_perturb/" --dataset_name "npm1_perturb"
 ```
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+To compute cellprofiler features, open the [project file](../src/br/analysis/cellprofiler/npm1_perturb_cellprofiler.cpproj) using cellprofiler, and point to the single cell images of nucleoli in the [npm1 perturbation dataset](https://open.quiltdata.com/b/allencell/tree/aics/NPM1_single_cell_drug_perturbations/). This will generate a csv named `MyExpt_Image.csv` that contains mean, median, and stdev statistics per image across the different computed features.
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diff --git a/src/br/analysis/cellprofiler/npm1_perturb_cellprofiler.cpproj b/src/br/analysis/cellprofiler/npm1_perturb_cellprofiler.cpproj