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feat(mirax): add support for fluorescence z-stacks#318

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feat(mirax): add support for fluorescence z-stacks#318
camlloyd wants to merge 2 commits into
glencoesoftware:masterfrom
camlloyd:feat/mirax

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Summary

This PR fixes #42 by adding MRXS fluorescence Z-stack support in MiraxReader.

It:

  • exposes real Z planes as SizeZ > 1
  • excludes ExtFocusLevel from the physical Z axis
  • derives PhysicalSizeZ from OFFSET_IN_MICROMETERS
  • reads fluorescence focus-page blocks from Index.dat
  • preserves the classic path for older/non-stack MRXS files

Validation

The Z-stack behavior was validated with the sample from #42, and also with additional private MRXS Z-stack data.

I also regenerated a full OME-Zarr for the issue sample and checked it visually:

  • main Z-stack opened correctly
  • label image opened correctly
  • fourth channel opened correctly

For regression coverage on non-Z MRXS files, I tested with:

Focused MiraxReader unit tests cover the new parsing and the classic fallback behavior.

I have not yet validated this branch on JPEG-XR-compressed MRXS data.

Notes

This change was developed with assistance from Codex using GPT-5.4.

One small follow-up left out of this PR to keep the diff focused: indexData in MiraxReader.initFile() still uses explicit close logic rather than try-with-resources.

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mrxs Z stacks not supported

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