Bug (mask_2d) - The output NPY mask isn't seem to be the stardist output

marcnol / pyHiM

Multiplexed DNA-FISH data analysis pipeline

GNU Lesser General Public License v3.0

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Bug (mask_2d) - The output NPY mask isn't seem to be the stardist output #199

Closed XDevos closed 9 months ago

XDevos commented 11 months ago

pyHiM generate two PNG:

scan_001_DAPI_005_ROI_converted_decon_ch00_segmentedMasks.png
scan_001_DAPI_005_ROI_converted_decon_ch00_stardist_segmentedMasks.png

and when we visualize the npy mask (scan_001_DAPI_005_ROI_converted_decon_ch00_Masks.npy) with napari, the data seems to be the first png without stardist.

Configuration: "background_method": "stardist" "tesselation": false

scan_001_DAPI_005_ROI_converted_decon_ch00_segmentedMasks

XDevos commented 11 months ago

It's the same issue with: "background_method": "stardist" "tesselation": true