Add Fractal tasks for object and single-cell registration

fmi-basel / gliberal-scMultipleX

Feature extraction and linking of multiplexing data.

BSD 3-Clause "New" or "Revised" License

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Add Fractal tasks for object and single-cell registration #99

Closed jluethi closed 9 months ago

jluethi commented 9 months ago

@nrepina I'm opening the PR so that when we push to the branch, Github CI reruns the automated tests :) Not to be merged yet

What this is adding

[x] Label-based registration for organoids (3 tasks)
[x] Label-based registration for single cells

Minor changes:

[x] Updates scmultiplex measurements task to Fractal-tasks-core 0.14.0a0
[x] Updates test data to have new ROI tables with correct metadata
[x] Fixes overwrite bug in scmultiplex task
[x] Refactor of scmultiplex task to use more library functions, less edge-case handling in the task code

Once fractal-tasks-core 0.14.0 is released:

[x] Update the new tasks to 0.14.0
[ ] Add test data for new tasks

codecov-commenter commented 9 months ago

Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (4b46ca5) 98.91% compared to head (c3dd4af) 98.13%. Report is 13 commits behind head on main.

Files	Patch %	Lines
tests/fractal/test_fractal_measurement.py	96.66%	2 Missing :warning:

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #99 +/- ## ========================================== - Coverage 98.91% 98.13% -0.79% ========================================== Files 10 10 Lines 461 482 +21 ========================================== + Hits 456 473 +17 - Misses 5 9 +4 ```

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nrepina commented 9 months ago

Adding 4 new tasks:

[x] calculate_object_linking --> organoid linking across rounds with phase cross-correlation of segmentations; outputs linking table
[x] calculate_platymatch_registration --> single-cell linking and registration across rounds; outputs linking table and affine or free-form deformation transformation matrix saved to disk
[x] calculate_linking_consensus --> calculates master consensus table for organoids or single cells that are successfully linked across rounds, output: master table stored in reference round directory
[x] relabel_by_linking_consensus --> relabels segmentation images and ROI tables based on master consensus.

The places where the i/o code could use a refactor is noted with # TODOs. In particular the calculate_platymatch_registration is huge and can benefit from some i/o helper functions.