[mohsenhariri]

Repair extraction for small, edge-touching, and 3D masks, including the original files in #121. Correct SVD orientation, centered neighborhoods, the documented 13-feature mapping, maximal correlation, and difference-variance selection. Version 0.4.0 changes numerical results: cached 0.3.x features must be recomputed; the public import and output axis order remain compatible.

Complete the medical-image CLI and repair Slicer labelmaps, segmentations, both-angle outputs, parameter forwarding, progress, cancellation, and geometry. Share typed validation/I/O/statistics helpers. Refresh dependencies, examples, documentation, container targets, Conda support, and release validation. Slicer dependency installation now requires an explicit Install action.

Validation: 110 tests pass on the minimum Python 3.10 stack and current Python 3.11 stack; CI covers 3.10–3.13. Eight integration tests pass in native Slicer 5.12.4. The original #121 case returns finite features for all 92,918 masked pixels. Documentation builds with warnings as errors; the notebook executes headlessly; Conda packages build and run 2D/3D tests; both Docker targets pass extraction/notebook smoke tests. Core and CLI distributions rebuild from sdists, pass strict Twine checks, and install together in a fresh environment. The refreshed lockfile passes pip-audit.

Supersedes Dependabot PRs #123, #125, and #126 with a coordinated dependency refresh. Catalog/feedstock acceptance and service ownership (#25, #73, #78, #83) remain external follow-ups with prepared contribution files; publishing is not triggered by merging this PR.

Closes #11, closes #24, closes #43, closes #52, closes #53, closes #54, closes #55, closes #59, closes #60, closes #62, closes #63, closes #68, closes #69, closes #77, closes #80, closes #81, closes #84, closes #85, closes #86, closes #90, closes #91, closes #97, closes #121, closes #124.