v3.0.0

♻️ Refactoring

• ️ one chunk_slices helper; vectorise per-object accounting

⚡ Performance

• ome_zarr: unlocked shard writes
• ome_zarr: pyramid downsampling on strided views
• dog: cache the deconvolution setup per worker; dup_rev_z auto

✅ Tests

• napari: drive view_in_napari itself, not just its resolvers
• make the allocation and ISO-export tests machine-independent
• codec check portable across zarr releases

✨ Features

• workflow: a separate pixi workspace for viewing results
• ome_zarr: block-average image pyramids; labels stay nearest
• workflow: resume a retried segment batch per tile
• ome_zarr: majority-vote label pyramids keep small objects
• merge: IoU stitching and resumable tile_process
• seams: seam_report -- does the tiling show in the labels?
• io: configurable compression codec
• cli: a patchworks command: convert, segment, seams, info, view
• dog: DoG sigmas in micrometres (sigma_units="um")
• io: remote stores (s3://, gs://, https://) without local litter
• provenance: label images record how they were made
• core: several GPUs in one tile_process run (gpus=)
• core: dry_run: plan a run before submitting it
• postprocess: fill_holes and open_labels
• autotune: suggest_overlap -- pick the overlap from the data
• launcher: bring in the Streamlit launcher, updated for the current settings and multi runs

🏗️ Build

• ️ require zarr 3 and Python 3.11; drop the dead zarr-2 paths
• ️ ship a py.typed marker
• ️ dependency floors verified by a minimum-versions CI job

🐛 Bug Fixes

• workflow: let the viewer environment solve off the cluster
• workflow: keep the workspace linux-64, platforms belong to the feature
• workflow: drop the per-feature platforms; they are not scoped
• napari: recognise a .zip bundle as a zarr source
• core: unique stage stores, cleanup on failure, no default log file
• merge: pin fork for the relabel pool on Linux
• merge: release the LUT after an in-process relabel; open arrays once
• merge: never wrap label ids in a narrow dtype
• relabel: keep the smallest object when there is no background
• relations: overlap_fraction is over the whole a label
• postprocess: dilate_labels grows into background only
• core: name the function when fn returns the wrong shape
• io: keep auto_empty_threshold's sample windows inside the image
• io: only a path component ending in .zip is a bundle
• chunks: find the job's own cgroup; count headroom, not the ceiling
• ome_zarr: pyramid levels pin the configured codec
• ome_zarr: crash-safe reshard swap
• cluster: give make_local_cluster workers a real memory limit
• gpu: release GPU memory outside the except block before backing off
• geometry: labels segmented at level > 0 take that level's calibration
• napari: view_in_napari opens non-zarr files

👷 CI

• run the test suite in CI
• build the docs strictly on every pull request
• run docstring examples; report macOS and Windows
• type-check with mypy
• head-vs-base benchmarks on pull requests

📝 Documentation

• occupancy: build_occupancy_map names the sibling store
• ome_zarr: drop a doubled blank line markdownlint flags
• gpu: drop a doubled blank line markdownlint flags
• launcher: add a user guide for the Streamlit launcher

🔧 Chores

• pre-commit hooks mirroring the lint workflow

👥 Contributors

• @lguerard
• @claude