v3.3.0

⚡ Performance

• size filter skips background chunks, uses the CPUs, reports progress
• object tables and the size filter from per-tile sums, with the merge
• relations ~13x faster, and not recomputed when written as csv
• relate reads each parent once for all its children; bundle only when changed

✅ Tests

• two run_multi tests only passed when run as root
• path assertions that hold on Windows too

✨ Features

• workflow: pixi run multi-slurm --config
• plantseg: say who is on the GPU when PlantSeg cannot fit
• connectivity for DoG and threshold labelling, matched by the merge

🏗️ Build

• pixi: ️ the workflow takes patchworks from GitHub main

🐛 Bug Fixes

• pixi: every pixi run failed on the plantseg-careamics solve
• workflow: a PlantSeg config run from the default env failed on the GPU
• pixi: plantseg environment's Snakemake rejected --slurm-jobname-prefix
• workflow: ️ say what seed_labels grows from, loudly when no config makes it
• types: mypy rejects ndarray[bool].sum() under numpy 2.5's stubs
• workflow: seed_labels accepted nuclei still being segmented
• plantseg: tiles failed in PlantSeg's own patch-size search
• types: drop an unused type: ignore in the PlantSeg plugin
• plantseg: thin z-tiles and 2-plane tiles failed with real PlantSeg
• plantseg: depth padding mirrored nuclei into competing seeds
• plantseg: PlantSeg's "OOM error will happen" did not shrink the patch
• workflow: keep a segment job on the GPU SLURM gave it
• workflow: a config failing on a left-over lock says how to unlock
• workflow: one run_multi per work_dir
• workflow: driver liveness check without /proc (macOS, Windows)
• workflow: relations on missing label images fail up front, named
• workflow: cupy in the plantseg environment, checked up front
• relabel progress reaches 100%; SLURM job logs line-buffered
• a position rule's reference table is loaded, and waited for
• OME-Zarr conformance: dimension_names, label levels, 0.4 stores
• a deleted label image left in the labels list

👷 CI

• macOS and Windows jobs are required now that they pass

📝 Documentation

• the plantseg environment on a login node without a GPU
• workflow: multi.yaml: what relate's cpus are for

👥 Contributors

• @claude