AttributeError: module 'deepcell.utils' has no attribute 'get_image'

[ArtemSokolov]

I am getting the following error when attempting to run the Docker container:

Traceback (most recent call last):
  File "main.py", line 156, in <module>
    compartment=ARGS.compartment
  File "main.py", line 77, in run
    nuclear_img = deepcell.utils.get_image(nuclear_path)
AttributeError: module 'deepcell.utils' has no attribute 'get_image'

Command executed:

docker run --rm -v "$PWD":/data vanvalenlab/deepcell-applications --nuclear-image /data/exemplar-001.ome.tif --output-directory /data

where exemplar-001.ome.tif is a stitched and registered image from MCMICRO's minimal working dataset. Assuming nextflow and Docker are installed, the .ome.tif can be reproduced with:

nextflow run labsyspharm/mcmicro/exemplar.nf --name exemplar-001 --path .
nextflow run labsyspharm/mcmicro --in ./exemplar-001 --stop-at registration
ls ./exemplar-001/registration/exemplar-001.ome.tif

[willgraf]

Can you please confirm which version of deepcell you are using?

Also, the Docker image tag you are using (if using a pre-built image).

[ArtemSokolov]

Hi @willgraf,

The container image was built directly from the GitHub repo (commit 4f71fb2) by running

docker build -t vanvalenlab/deepcell-applications .

as suggested in the README.

[willgraf]

Thank you! It looks like this is an issue with breaking changes between deepcell 0.6.x and 0.8.x.

A fix is in-progress, but in the meantime, the get_image function can be imported from deepcell.utils.io_utils as a patch.