Problem

Changing eccentricity threshold, either from the myoquant he-analysis CLI or from myoquant.HE_analysis.run_he_analysis function results in the same dataframe and array output.

Additionally, it's not clear what value range the eccentricity values can take.

Description

Output

Counts for all Features in dataframe output and labels in painted map output stay the same regardless of selected eccentricity threshold.

Expected

Ratio of internalized/peripherical nuclei should change in function of eccentricity threshold.

Possible issue / Proposed solution

I believe the issue is that the param eccentrictiy_thresh in run_he_analysis is not passed to the internal functions predict_all_cells and single_cell_analysis.

Python example output

Running the analysis directly from Python using the run_he_analysis function with different thresholds results in identical values as in plot below:

CLI example output

myoquant he-analysis ./dapi/dapi_00.tif --cellpose-path ./tritc/tritc_00_cp_masks.tif --stardist-path ./dapi/dapi_00_labels.tif --output-path ./ --eccentricity-thresh 2

myoquant he-analysis ./dapi/dapi_00.tif --cellpose-path ./tritc/tritc_00_cp_masks.tif --stardist-path ./dapi/dapi_00_labels.tif --output-path ./ --eccentricity-thresh 0.1

Hello, I am trying to analyze an HE image using your streamlit app.
I get the attached error. Any ideas where it might stem from?
Thanks!