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AllenCell / EMT_image_analysis

Repository for EMT image analysis code
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Colony mask training/inference instructions #27

Open mfs4rd opened 3 days ago

mfs4rd commented 3 days ago

This issue is about the work-in-progress branch for colony mask inference reproducibility, sm_colony_mask_pred_test_v0.

Report on improvements for the all colony mask inference repo instructions

1) Make clearer in step 1 that the data directory should be a subdirectory of Colony_mask_training_inference earlier in the step

2) Attempting to pip install . the repo when data directory is present causes issues where pip believes it is a module directory. Consider adding a setting in the setup files to prevent this

3) the way the paths/default.yaml file is set up doesn't check the folder the repo has been cloned into, or CYTODL_CONFIG_PATH=$PWD/configs does not work as intended

4) eval_scale*.yaml files have predict_all_cells_mask_zarr_aws_v0.csv as the default csv file, but predict_all_cells_mask_v0.csv is the one currently provided. You will likely be changing this for the final release but make sure the default matches then

pgarrison commented 2 days ago

Love this! Thanks @mfs4rd

  1. is partially captured in #25. I've added it there.