Skip to content

resolutionunit error on imc prepare #18

@matt-sd-watson

Description

@matt-sd-watson

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'

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions