Cleanup pc preprocessing #79
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fatwir
approved these changes
Dec 13, 2024
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This PR cleans up the preprocessing scripts for generating point clouds for punctate structures after the image_preprocessing is done. Tested on the outputs of the image_preprocessing step.
For the PCNA dataset, run
python src/br/data/preprocessing/pc_preprocessing/pcna --save_path "./make_pcs_test" --preprocessed_manifest "./subpackages/image_preprocessing/tmp_output_pcna/processed/manifest.parquet" --global_path "./subpackages/image_preprocessing/"For nuclear structures from the variance dataset, run
python src/br/data/preprocessing/pc_preprocessing/punctate_nuc.py --save_path "./make_pcs_test" --preprocessed_manifest "./subpackages/image_preprocessing/tmp_output_variance/processed/manifest.parquet" --global_path "./subpackages/image_preprocessing/"For cytoplasmic structures from the variance dataset, run
python src/br/data/preprocessing/pc_preprocessing/punctate_cyto.py --save_path "./make_pcs_test" --preprocessed_manifest "./subpackages/image_preprocessing/tmp_output_variance/processed/manifest.parquet" --global_path "./subpackages/image_preprocessing/"