Use temporary local Zarr for regionprops to prevent file errors

[akhanf]

This pull request introduces several important improvements to the workflow's resource allocation and file handling for region property computation and segmentation statistics merging. The main changes focus on increasing resource limits for memory-intensive tasks and ensuring robust extraction and handling of zipped OME-Zarr files.

Resource allocation improvements:

• Increased memory and runtime limits for the compute_filtered_regionprops rule in regionprops.smk to better handle large datasets (mem_mb from 256000 to 500000, runtime from 180 to 360).
• Increased memory allocation for the merge_into_segstats_tsv rule in segstats.smk (mem_mb from 1500 to 16000) to prevent out-of-memory errors during merging.

File handling and robustness:

• Updated compute_filtered_regionprops.py to extract the input OME-Zarr zip archive to a secure temporary directory before analysis, improving compatibility and preventing issues with direct zip file access.

Workflow configuration:

• Added an acq wildcard constraint to the workflow's wildcard_constraints for more robust pattern matching in group-level analyses.

[Copilot]

Pull request overview

This PR improves robustness and scalability of the Snakemake workflow for segmentation region property computation by increasing resources for memory-intensive steps, adding an additional wildcard constraint for group-level analysis, and adjusting regionprops processing to use a temporary local extracted Zarr store when inputs are zip-based.

Changes:

• Increased memory/runtime resources for compute_filtered_regionprops and increased memory for merge_into_segstats_tsv to reduce OOM/timeouts on large datasets.
• Updated compute_filtered_regionprops.py to extract zip-based OME-Zarr inputs into a temporary directory before computing region properties.
• Added an acq wildcard constraint for group-level workflows to improve pattern matching.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 3 comments.

File	Description
spimquant/workflow/Snakefile	Adds acq to wildcard_constraints for group-level analyses.
spimquant/workflow/scripts/compute_filtered_regionprops.py	Changes regionprops computation to operate on a temporary extracted local store rather than reading directly from a zip-based store.
spimquant/workflow/rules/segstats.smk	Increases memory allocation for TSV merging to reduce OOM risk.
spimquant/workflow/rules/regionprops.smk	Increases memory/runtime allocation for regionprops computation to better handle large datasets.