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Expand MCQUANT with glcm features #49

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@LukasHats LukasHats commented Aug 7, 2024

Expanded MCQUANT for GLCM and associated graycoprops:

  • Included glcm calculation per cell label and associated graycoprops calculation in the MaskChannel function
  • made use of the --intensity_props argument to determine, whether a user-specified a glcm feature
  • included CLI inputs for angle and distance to calculate the GLCM. Currently limited to 1 angle and 1 distance (otherwise it overblows the CSV result table). The default is set to angle 0 and distance 1 pixel. Included these CLI options in all functions in the main script. Can be changed if necessary, as GLCM features are normally calculated for various angles.
  • Added qptiff as accepted bioformat. For future maybe adding ome zarr/ngff should be considered
  • Added intensity standard deviation (intensity_std) as additional option
  • Adjusted the README, including the script call that was not updated
  • Successfully tested on exemplar001 (using ome.tif and segmentation mask)

LukasHats and others added 16 commits August 5, 2024 14:25
…d MCQUANT main file to handle additional glcm features, resizing of the loaded image to uint8 for glcm calculation, adjusted extra property handling of the regionprops_table function. Version importing has to be adjusted next
Expansion of MCQUANT with glcm features
@LukasHats LukasHats mentioned this pull request Aug 8, 2024
@jmuhlich jmuhlich force-pushed the master branch 4 times, most recently from e361552 to 1d94184 Compare August 9, 2024 15:28
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2 participants