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Add new module stainwarpy/extractchannel #9776

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@tckumarasekara tckumarasekara commented Jan 26, 2026 •
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This PR adds,

  • stainwarpy/extractchannel

stainwarpy
modules for registration of H&E tissue images with their corresponding multiplexed images and to transform the segmentation masks of one image type to be able to use with the other type.

  • As first step, stainwarpy/extractchannel extracts the alignable channel (preferably DAPI) from multiplexed image.
  • As second step, stainwarpy/register registers H&E and multiplexed images and output the registered image, transformation maps and evaluation metrics for the registration performed.
  • As third step, stainwarpy/transformsegmask transforms the segmentation mask of one image using the transformation maps created from the second module.

PR checklist

Closes #9701

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@tckumarasekara tckumarasekara changed the title Adding new module stainwarpy/extractchannel Add new module stainwarpy/extractchannel Jan 27, 2026
itrujnara
itrujnara reviewed Jan 27, 2026
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Hi, the module already looks quite good. I have left some questions to consider. They probably apply to the other subcommand modules as well.

modules/nf-core/stainwarpy/extractchannel/tests/main.nf.test
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.single_ch_image.get(0).get(1)).exists(),
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Is the file in question indeterministic? Is there any data in the channel that is not checked here?

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@tckumarasekara tckumarasekara Jan 27, 2026

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Hi, yes, the output file is non-deterministic between runs due to metadata (ef: UUIDs) and minor floating-point differences. This is the case for the other modules also. This module emits just one file in a tuple.

modules/nf-core/stainwarpy/extractchannel/meta.yml Outdated
type: file
description: Single channel extracted image file in OME-TIFF format
pattern: "multiplexed_single_channel_img.ome.tif"
ontologies: []
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Is this the correct ontology?
https://edamontology.github.io/edam-browser/#format_3727
Keep in mind that there have been some issues with the ontology server, so linting/CI might misbehave.

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@tckumarasekara tckumarasekara Jan 27, 2026

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Yes, thank you. I`ll update the meta.yml

modules/nf-core/stainwarpy/extractchannel/main.nf Outdated
label 'process_single'

conda "${moduleDir}/environment.yml"
container "community.wave.seqera.io/library/stainwarpy:0.2.3--2c8b18a5e6d93e4a"
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Can you add a link to a dedicated Singularity container?

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@tckumarasekara tckumarasekara Jan 27, 2026

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I`ll add that, thanks.

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@tckumarasekara tckumarasekara Jan 27, 2026

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and I realized I accidentally pushed some branches (pr-extractchannel, pr-register, pr-transformsegmask) to this repository (nf-core/modules). Could these be safely removed? This won’t affect the PR itself. Thanks a lot!

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new modules: stainwarpy/extractchannel

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