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Refactor task topology#9

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rcannood wants to merge 15 commits intomainfrom
add-prediction-processor
Open

Refactor task topology#9
rcannood wants to merge 15 commits intomainfrom
add-prediction-processor

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@rcannood
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@rcannood rcannood commented Apr 30, 2026

Describe your changes

  • Adds a process_prediction component that assigns transcripts to segmented cells using label image lookup.
  • Refactors process_dataset to split its output into spatial_unlabelled (image + transcripts only, no cell assignments) for methods and spatial_solution (ground truth labels, shapes, reference table) for metrics and control methods only.
  • Updates all API specs, the benchmark workflow, and the cellpose method to reflect this separation.

Checklist before requesting a review

  • I have performed a self-review of my code

  • Check the correct box. Does this PR contain:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Bug fixes
  • Proposed changes are described in the CHANGELOG.md

  • CI Tests succeed and look good!

rcannood and others added 10 commits April 30, 2026 13:26
Co-authored-by: Florian Heyl <flo.minion.info@gmail.com>
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
@rcannood rcannood changed the title Add prediction processor Refactor task topology Apr 30, 2026
rcannood and others added 5 commits April 30, 2026 14:24
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
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Only found one slight thing. Rest looks fine.

Comment thread README.md
evaluation.

Example file:
`resources_test/task_spatial_segmentation/mouse_brain_combined/processed_prediction.h5ad`
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Suggested change
`resources_test/task_spatial_segmentation/mouse_brain_combined/processed_prediction.h5ad`
`resources_test/task_spatial_segmentation/mouse_brain_combined/processed_prediction.zarr`

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2 participants