Quantification step fails with skimage.morphology.convex_hull ModuleNotFoundError error

[emir-radkevich]

Hi.

I am using mcmicro on our lab's image from Orion machine.
I am using your pipeline on HPC starting at segmentation. So far, unmicst and s3seg are working.

I am getting this error during quantification step though:

Command executed:

  shopt -s nullglob
  mcquant --image HIMC_52231_Ovarian_200x_MSSM_EM_Q143_BV_Test_000226--unmicst.ome.tif        --masks cell*.tif *_cp_masks*.tif --output . --channel_names markers.csv

Command exit status:
  1

Command output:
  {'masks': ['cell.ome.tif'], 'image': 'HIMC_52231_Ovarian_200x_MSSM_EM_Q143_BV_Test_000226--unmicst.ome.tif', 'channel_names': 'markers.csv', 'output': '.', 'intensity_props': {'intensity_mean'}, 'mask_props': None}
  Extracting single-cell data for HIMC_52231_Ovarian_200x_MSSM_EM_Q143_BV_Test_000226--unmicst.ome.tif...
  Finished 0
  Finished 1
  Finished 2
  Finished 3
  Finished 4
  Finished 5
  Finished 6
  Finished 7
  Finished 8
  Finished 9
  Finished 10
  Finished 11
  Finished 12
  Finished 13
  Finished 14
  Finished 15
  Finished 16
  Finished 17
  Finished 18
  Finished 19

Command error:
  WARNING: Could not find any nv files on this host!
  INFO:    Converting SIF file to temporary sandbox...
  Traceback (most recent call last):
    File "/usr/local/bin/mcquant", line 8, in <module>
    File "/usr/local/lib/python3.11/site-packages/mcquant/cli.py", line 11, in main
    File "/usr/local/lib/python3.11/site-packages/mcquant/SingleCellDataExtraction.py", line 272, in MultiExtractSingleCells
    File "/usr/local/lib/python3.11/site-packages/mcquant/SingleCellDataExtraction.py", line 245, in ExtractSingleCells
    File "/usr/local/lib/python3.11/site-packages/mcquant/SingleCellDataExtraction.py", line 194, in MaskZstack
    File "/usr/local/lib/python3.11/site-packages/mcquant/SingleCellDataExtraction.py", line 62, in MaskIDs
    File "/usr/local/lib/python3.11/site-packages/skimage/measure/_regionprops.py", line 1097, in regionprops_table
    File "/usr/local/lib/python3.11/site-packages/skimage/measure/_regionprops.py", line 882, in _props_to_dict
    File "/usr/local/lib/python3.11/site-packages/skimage/measure/_regionprops.py", line 666, in solidity
    File "/usr/local/lib/python3.11/site-packages/skimage/measure/_regionprops.py", line 242, in wrapper
    File "/usr/local/lib/python3.11/site-packages/skimage/measure/_regionprops.py", line 452, in area_convex
    File "/usr/local/lib/python3.11/site-packages/skimage/measure/_regionprops.py", line 242, in wrapper
    File "/usr/local/lib/python3.11/site-packages/skimage/measure/_regionprops.py", line 457, in image_convex
  ModuleNotFoundError: No module named 'skimage.morphology.convex_hull'
  INFO:    Cleaning up image...

I tried to look into the error inside the contatiner:

>singularity shell work/singularity/labsyspharm-quantification-1.6.0.img

Singularity> cat /usr/local/lib/python3.11/site-packages/skimage/measure/_regionprops.py | grep -n convex_hull
457:        from ..morphology.convex_hull import convex_hull_image
459:        return convex_hull_image(self.image)
499:        identity_convex_hull = np.pad(
504:                find_contours(identity_convex_hull, 0.5, fully_connected='high')
507:            coordinates, _, _, _ = marching_cubes(identity_convex_hull, level=0.5)

Singularity> ls /usr/local/lib/python3.11/site-packages/skimage/morphology/ | grep convex
_convex_hull.cpython-311-x86_64-linux-gnu.so
convex_hull.py

Looks like this module exists.
Do not understand the error.

Could you please help me?

[jmuhlich]

What kind of computer and operating system are you running mcmicro on?

[jmuhlich]

I re-read your report and I see now you said "HPC" so I figure it's x86_64 machines running Linux, but it would still be good to verify that.

[emir-radkevich]

I re-read your report and I see now you said "HPC" so I figure it's x86_64 machines running Linux, but it would still be good to verify that.

Yes, you are right.