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Description
I am attempting to process Patient1.mcd from the Immucan dataset: https://zenodo.org/records/5949116 using your pipeline. At the prepare step:
imc prepare --ilastik --n-crops 0 --ilastik-compartment nuclear Patient1.mcd
I receive the following error:
Started analyzing 'Patient1.mcd'.
1 2 Traceback (most recent call last):
File "/home/admin/anaconda3/envs/imc_elemento/bin/imc", line 7, in <module>
sys.exit(main())
File "/home/admin/anaconda3/envs/imc_elemento/lib/python3.9/site-packages/imc/cli.py", line 35, in main
return eval(main_args.command)(cmd_args)
File "/home/admin/anaconda3/envs/imc_elemento/lib/python3.9/site-packages/imc/scripts/prepare.py", line 73, in main
mcd_to_dir(**sargs)
File "/home/admin/anaconda3/envs/imc_elemento/lib/python3.9/site-packages/imc/utils.py", line 690, in mcd_to_dir
write_ometiff(
File "/home/admin/anaconda3/envs/imc_elemento/lib/python3.9/site-packages/imc/utils.py", line 840, in write_ometiff
tifffile.imwrite(
File "/home/admin/anaconda3/envs/imc_elemento/lib/python3.9/site-packages/tifffile/tifffile.py", line 966, in imwrite
result = tif.write(data, shape, dtype, **kwargs)
TypeError: write() got an unexpected keyword argument 'resolutionunit'
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