v2.0.0

♻️ Refactoring

• workflow: ️ keep the method list in one place

⚡ Performance

• workflow: segment a batch of tiles per job to amortize model load
• merge: derive global ids from tile counts, dropping two full passes
• ome_zarr: stream pyramid levels instead of rechunking through dask
• workflow: run the segmentation configs concurrently
• merge: parallelize the boundary scan and give every pool its cores
• merge: skip chunks that hold no labels, and size occupancy blocks
• merge: segment into the label group and relabel it in place

✨ Features

• distributed: accept a per-axis overlap halo
• workflow: use a per-axis overlap and reject halos wider than the tile
• workflow: log which z-tiling regime prepare picked

🐛 Bug Fixes

• occupancy: decide skipped tiles from the whole tile, not its centre
• cluster: size work against the SLURM allocation, not the whole node
• gpu: catch cupy OOM, read the granted GPU, validate configs in prepare
• occupancy: keep the map out of image.zarr and build it once
• workflow: read merge's label counts by path, not from snakemake.input
• ome_zarr: guard in-place re-merges and match NGFF layout to zarr version

📝 Documentation

• document the pipeline changes and ship the optimized defaults
• document the in-place merge, empty-chunk skipping and block sizing

🔄 Other

• Merge dev: pipeline overhaul (v2.0.0)

👥 Contributors

• @lguerard