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Marshall Thompson Glassonion Cognitect United States

Datomic/day-of-datomic 481

Sample Code for Day of Datomic presentation

pmagwene/Duke-BioHaskell-Group 5

A repository for the Duke BioHaskell Interest Group

Glassonion/biosci-scratch 2

Sandbox for biosci-related experimentation

ParkerICI/mibi_processing 0

Tools to process MIBI images

ParkerICI/single_cell_workflows 0

Dockstore wdl workflows for single cell processing (*RNAseq, snATACseq)

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3rd argument to script

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adding channel collapse workflow

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add nuc and wc to mask file names

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fix filename option

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adding rename to sample ID functionality

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quote all the things

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bash, not wdl

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fix spaces in file path

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commit sha 4b149f697f275244e6d5c1ae0a292095693499c2

update deepcell docker image

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back to both

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issue openedvanvalenlab/deepcell-applications

--compartment argument mismatch

In setting up a workflow using vanvalenlab/deepcell-applications:0.3.0 I have hit an issue with the --compartment argument.

Everything works as expected for --compartment "nuclear", however trying with --compartment "both" fails with:

/usr/local/lib/python3.6/dist-packages/tensorflow/python/keras/optimizer_v2/optimizer_v2.py:375: UserWarning: The `lr` argument is deprecated, use `learning_rate` instead.
  "The `lr` argument is deprecated, use `learning_rate` instead.")
usage: run_app.py mesmer [-h] [--output-directory OUTPUT_DIRECTORY]
                         [--output-name OUTPUT_NAME]
                         [-L {DEBUG,INFO,WARN,ERROR,CRITICAL}] [--squeeze]
                         --nuclear-image NUCLEAR_PATH
                         [--nuclear-channel NUCLEAR_CHANNEL [NUCLEAR_CHANNEL ...]]
                         [--membrane-image MEMBRANE_PATH]
                         [--membrane-channel MEMBRANE_CHANNEL [MEMBRANE_CHANNEL ...]]
                         [--image-mpp IMAGE_MPP] [--batch-size BATCH_SIZE]
                         [--compartment {nuclear,membrane,whole-cell}]
run_app.py mesmer: error: argument --compartment/-c: invalid choice: 'both' (choose from 'nuclear', 'membrane', 'whole-cell')

While --compartment "membrane" fails with:

Traceback (most recent call last):
  File "/usr/src/app/run_app.py", line 180, in <module>
    output = app.predict(image, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/deepcell/applications/mesmer.py", line 310, in predict
    postprocess_kwargs=postprocess_kwargs)
  File "/usr/local/lib/python3.6/dist-packages/deepcell/applications/application.py", line 448, in _predict_segmentation
    label_image = self._postprocess(output_images, **postprocess_kwargs)
  File "/usr/local/lib/python3.6/dist-packages/deepcell/applications/application.py", line 215, in _postprocess
    image = self.postprocessing_fn(image, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/deepcell/applications/mesmer.py", line 135, in mesmer_postprocess
    'Must be one of {}'.format(compartment, valid_compartments))
ValueError: Invalid compartment supplied: membrane. Must be one of ['whole-cell', 'nuclear', 'both']

Happy to provide more details if helpful.

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both -> whole-cell

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parameterize compartment, dockerfile, add readme

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test minimal change

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