[uermel]

Summary

v2.0 (Zarr v3) counterpart of #111. ChimeraX support for copick's filaments and instance / panoptic segmentations, with editing tools, a Copick Annotate window and a Copick Edit toolbar tab.

Display and data

• Filaments:
  • a Filaments tab with a stepper (<< k of N >>, fp / fn);
  • filament sets drawn as tubes in instance colours, with direction arrowheads;
  • control-point handles while editing.
• Segmentations:
  • the Segmentations tab shows types (binary, multilabel, instance, panoptic);
  • instance and panoptic segmentations are drawn as per-instance surfaces;
  • deleting a segmentation now passes its type, so a same-key segmentation of another type is kept (data-loss fix).
• Tables: compact two-line object tables (swatch, name, type chip / "user · session"), a header sort menu, outline selection, search across user / session / type, and wrap-around arrow keys.

Editing

• Filaments:
  • trace mouse mode (add / drag / remove control points) and cut mode;
  • join (also on tubes selected in the 3D view; the 3D selection and the filament list share one selection), reverse, delete, convert;
  • save, optionally with sampled picks.
  • Every filament edit is a step on ChimeraX's undo stack: Cmd/Ctrl+Z, including in copick's keyboard-shortcut mode.
• Instances: paint / erase / pick-ID mouse modes, brush sizes, new ID, merge, delete, undo, save.
• Copick Annotate window:
  • Filaments, Instances and Pick instances pages, using the shared instance browser;
  • tabbed with the right-hand panel group and kept in front when ArtiaX raises its options panel.
• Copick Edit toolbar tab (31 buttons, at most as many as the Copick tab):
  • annotate, new picks / filaments / instances, save all;
  • common particle tools;
  • filaments, instances, brush sizes and pick colours.
  • Particle tools stay in the Copick tab as before.
• Commands, shortcuts, docs: copick filament …, copick instance …, copick annotate, copick save, copick colorpicks; filament / instance shortcuts; documentation pages.

Depends on

• Stacked on fix: keep pick shifts, and default score and id for new picks (v2.0) #110 (v2.0 port of fix: keep pick shifts, and default score and id for new picks #108); this PR's diff is only the new work.
• copick-shared-ui >= 2.0.0a3, the alpha that will contain feat: filaments, instance segmentations and compact instance browsing (v2.0) copick-shared-ui#74 (2.0.0a2 does not)
• copick >= 2.0.0a3 (released; the first published v2.0 alpha with feat: filament objects, pick identity, and RELION/EM pick geometry fixes (v2.0) copick#481, #482, #493, #495). CI installs copick-shared-ui from PyPI, so it passes once 2.0.0a3 (with chore(main): release chimerax-copick 1.9.1 #74) is published.

Testing

• pytest tests -m "not chimerax": 35 passed.
• Scripted self-tests driving ChimeraX Daily over REST, on a CryoET Data Portal test project with filaments, picks, instance and panoptic segmentations:
  • display, tables, stepper, saving: 39 checks;
  • undo / cut / join / 3D-selection: 53 checks.

🤖 Generated with Claude Code