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Towards #228

Replace the code to load the Xenium segmentation masks to use Dask to greatly reduce the memory consumption of the Xenium reader.

I abandoned the idea of saving each element to free up memory because the Xenium reader is already mostly Dask-compatible, so it will not bring any advantage.

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codecov-commenter commented Oct 28, 2025

Codecov Report

❌ Patch coverage is 86.04651% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 55.25%. Comparing base (5f829f5) to head (54a24a0).

Files with missing lines Patch % Lines
src/spatialdata_io/readers/xenium.py 86.04% 6 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #337      +/-   ##
==========================================
- Coverage   55.30%   55.25%   -0.05%     
==========================================
  Files          26       26              
  Lines        2846     2843       -3     
==========================================
- Hits         1574     1571       -3     
  Misses       1272     1272              
Files with missing lines Coverage Δ
src/spatialdata_io/readers/xenium.py 72.70% <86.04%> (-0.25%) ⬇️

... and 2 files with indirect coverage changes

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@LucaMarconato
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LucaMarconato commented Jan 6, 2026

Hi @marcovarrone, my apologies for the delay in reviewing this (or the other PR).

Great idea! In this PR the tests fail because the temporary directory where we extract the zip data is cleaned up when the function exits. I think opening the .zarr.zip file using a ZipStore should do the trick.

Meanwhile, to benchmark the performance gain in a more transparent way, I rely on an explicit extraction. I'll do some benchmarks and document the changes.

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3 participants