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@tckumarasekara tckumarasekara commented Jan 26, 2026

This PR adds,

  • stainwarpy/register

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 #9702

  • 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 force-pushed the pr-register branch 3 times, most recently from 5fa1915 to d042459 Compare January 26, 2026 17:37
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new module: stainwarpy/register

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