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Add image converter module - issue #22#131

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TCFig wants to merge 2 commits intonf-core:devfrom
TCFig:dev
Open

Add image converter module - issue #22#131
TCFig wants to merge 2 commits intonf-core:devfrom
TCFig:dev

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@TCFig TCFig commented Mar 13, 2026

In the following pull request I tried to create a new module that converts the morphology.ome.tiff image into several png images depending on the amount of resolutions and series present in the original ome.tiff.

The module uses bftools by bioformats. The main command used is bfconvert, additional information on how to use the command is here.

Since this was the first time I did any type of contribution to nf-core I did not follow the usual workflow for creating a module and adding it to the pipeline 😅. Therefore there are multiple files/folders missing (such as test.nf and meta.yml). Additionally I was not able to integrate the module into the main spatialxe pipeline.

I did test the module and everything appears to be working as intended!

PR checklist

  • 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 pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/spatialxe branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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