use shards when writing ome zarr datasets

[akhanf]

instead of ozx

Also increase mem and resources for jobs

[Copilot]

Pull request overview

This PR updates SPIMquant’s Snakemake workflow to write segmentation-derived datasets as directory-based OME-Zarr stores (rather than .ozx zipstores), with shared writer kwargs intended to enable chunking/sharding, and adjusts resource settings for several jobs. It also expands input discovery to include Imaris .ims files.

Changes:

• Switch many mask/dist outputs from *.ozx to *.ome.zarr and mark most as directory(...) outputs in rules.
• Standardize OME-Zarr writing in multiple scripts via match_scale_factors_from=... and **config["zarrnii_out_kwargs"].
• Increase memory/resources for some rules and add .ims as an allowed SPIM input extension.

Reviewed changes

Copilot reviewed 17 out of 17 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
spimquant/workflow/scripts/vesselfm.py	Writes vessel masks to .ome.zarr with scale-factor matching and shared writer kwargs.
spimquant/workflow/scripts/threshold.py	Writes threshold masks to .ome.zarr with scale-factor matching and shared writer kwargs.
spimquant/workflow/scripts/skeletonize_vessels_mask.py	Writes skeleton masks to .ome.zarr with scale-factor matching and shared writer kwargs.
spimquant/workflow/scripts/signed_distance_transform.py	Writes SDT outputs to .ome.zarr with scale-factor matching and shared writer kwargs.
spimquant/workflow/scripts/n4_biasfield.py	Adds .ims-specific execution behavior for N4 processing.
spimquant/workflow/scripts/gmmthresh.py	Writes GMM threshold masks with shared writer kwargs.
spimquant/workflow/scripts/clean_segmentation.py	Writes cleaned masks with scale-factor matching and shared writer kwargs.
spimquant/workflow/rules/vessels.smk	Converts vessel intermediates to .ome.zarr directories and adjusts threads/mem/runtime.
spimquant/workflow/rules/templatereg.smk	Updates some template-registration outputs to .ome.zarr and increases memory for selected rules.
spimquant/workflow/rules/segmentation.smk	Converts segmentation outputs to .ome.zarr directories.
spimquant/workflow/rules/regionprops.smk	Updates inputs to consume .ome.zarr masks/dist outputs.
spimquant/workflow/rules/qc.smk	Updates QC rules to consume .ome.zarr masks.
spimquant/workflow/rules/patches.smk	Updates patch generation inputs to consume .ome.zarr masks.
spimquant/workflow/rules/heatmaps.smk	Increases memory for heatmap generation rules.
spimquant/workflow/rules/fieldfrac.smk	Updates inputs to consume .ome.zarr masks and increases memory for mapping step.
spimquant/workflow/rules/common.smk	Minor formatting-only change.
spimquant/config/snakebids.yml	Adds .ims input extension support and introduces zarrnii_out_kwargs for writer configuration.