[github-actions]

🤖 I have created a release beep boop

0.12.0 (2026-10-22)

⚠ BREAKING CHANGES

• omezarr: OME-Zarr support now requires z5 3.0.1 and C++20; xtensor/xsimd are no longer used.

Features

• add 2D test coverage for touch and morphology feature families (3f576d9)
• add IBSI Intensity Histogram features, per-bin HISTOGRAM output, and --mergerois (5b517f4)
• add unittest coverage to all 214 3D features, labeling tests with clear ground truth (b89a9ac)
• Benchmark area fix (#345) (b532f21)
• helpers: add ceil_pow2 (tight next power of two) (d0992dc)
• hounsfield: --preserve-hu CT/Hounsfield intensity preservation (1b5667f)
• hounsfield: keep HU offset base at scanned slide min under fp-options; enable bare CLI --preserve-hu (43f8063)
• hounsfield: wire --preserve-hu through the 3D NIfTI loader (65c9ad9)
• io: add the OME metadata, plane addressing and out-of-core machinery (e500077)
• io: read every pass through one streamed path, addressed by channel and timeframe (773ea75)
• io: stream oversized 3D volumetric ROIs out-of-core across all texture families (04857e2)
• omezarr: migrate to z5 3.0.1 ArrayView API, drop xtensor (225b9b9)
• re-organize and create complete implementation unit test coverage for 492 2D features (#346) (011df60)
• vetting: check_coverage CLI (--check/--write) + drift guard (0ad65ee)
• vetting: check_coverage registry load + schema/token validation (44d2bfa)
• vetting: coverage stats + markdown report generation (0f85581)

Bug Fixes

• 2d zernike: seed the angular tables at repetition 0, not 1 (2eb3cc3)
• 3d gldzm: hold the ROI mark in the distance cube, and index the vetted features (334936c)
• 3d gldzm: keep a ROI voxel whose grey level is zero, and say what the family costs (ea9dd3a)
• 3d gldzm: over the ROI, at 26-connectivity, at the IBSI distance (cf5d971)
• 3d gldzm: refuse an out-of-core box whose border distance outgrows its 16-bit buffer (2eed988)
• 3d morphology: compute 3MESH_VOLUME out-of-core too, and keep 3AREA as on main (d457455)
• 3d morphology: hull the mesh vertices, and sum both volumes exactly (8cbe064)
• 3d morphology: integrate the ROI surface mesh, and build the hull in double (9b9be52)
• 3d morphology: make the convex hull exact on lattice voxels (8b7ba7c)
• 3d ngtdm: default the neighbourhood radius so the family is not NaN (53b04b5)
• 3d-ngldm: DCNU/DCNUN summed the wrong marginal (== GLNU) (d3198e5)
• 3d-shape: correct mislabeled axis lengths + vet 7 morphology features (0af100b)
• 3d: compute 3ROBUST_MEAN (was hardcoded 0) + vet 18 3D first-order features (79d0974)
• anisotropy: measure an oversized 2D ROI's geometry on the resampled ROI (933d243)
• anisotropy: measure intensity and texture on the voxels as acquired (62a0f88)
• anisotropy: measure the intensity-weighted 2D geometry on the pixels as acquired (3949f10)
• anisotropy: size an anisotropic whole slide for its pass as acquired (427fa9c)
• anisotropy: split the 2D passes by feature method, and carry on past an emptied ROI (10b346e)
• audit and fix 2D feature tests 1/n (c5cf260)
• caliper: correct Martin/Nassenstein diameters + vet 12 features vs imea (bc3e92a)
• caliper: float-precision hull rotation + address PR #381 review (3377183)
• categorize and name feature unit tests and expected values (d854679)
• chords: correct max-chord angle index and all-chords histogram source (bd9a930)
• cleare state and start fresh to avoid random test failure. (495f05c)
• convex-hull: Pick's-theorem hull area so SOLIDITY <= 1 (0319932)
• emit per-bin HISTOGRAM values in arrow/parquet output (01ac9c2)
• feature settings: resolve a feature's settings by its dynamic type (981add1)
• feature settings: resolve the oversized 3D pass's settings by the dynamic type (2828f8f)
• feature_mgr: extend check_11_correspondence() to Feature3D (b188e50)
• feature_mgr: loop 3D correspondence check from Feature3D::FIRST (9287f3c)
• fractal-dim: adaptive box counting and a clean divider perimeter (c981743)
• fractal-dim: address PR review comments (98a4f2d)
• fractal-dim: align the ROI to the box-counting grid (98e53ec)
• fractal-dim: mean log-log slope for box-count, Richardson D for perimeter (af37142)
• gabor: keep filter-response magnitudes real-valued, then vet GABOR vs scikit-image (2b2c7d7)
• glcm: default co-occurrence offset to 1 and exclude background (02c5a75)
• glcm: normalize HOM2/ENTROPY by sum_p (2D+3D) + fully oracle-vet GLCM (60a1ebb)
• gldm: exclude background from the dependence matrix (f1f8eb4)
• gldzm: build zones from the full 8-neighbourhood (fc0bbde)
• handle multi-valued HISTOGRAM in buffer output (Python pandas/arrow) (246f4dd)
• hexagonality,lstsq: use std::abs so gcc/Linux doesn't truncate doubles to int (88a6f53)
• imq: average LOCAL_FOCUS_SCORE over every tile, and return on a thin ROI (feb8603)
• imq: correct FOCUS_SCORE overflow + abs()-variance, vet 4 imq features vs OpenCV and CellProfiler (7eed701)
• imq: score oversized ROIs like in-RAM ones and give a thin ROI the soft-NaN (76c0b59)
• intensity_histogram: report IH_ROBUST_MEAN_IDX as a 1-based bin index (0527f48)
• intensity: keep a header-rescaled slide's stored integers, and carry the rescale in the inverse (c79c822)
• intensity: make the recorded map match what the loaders actually store (ce5f74b)
• intensity: mirror the loaders' upper clamp, and survive degenerate input (6bf9735)
• intensity: one narrowing for every load-time map, saturated at both ends (ed36627)
• intensity: report first-order features in the slide's own intensity domain (1a4e956)
• intensity: restore the HU rounding, and finish the guards it skipped (b243ff5)
• intensity: settle a slide that measured nothing, and close the last unguarded cast (f25d7e1)
• io: read compressed striped TIFFs past the first strip, and refuse a failed scanline (a02393a)
• io: refuse an unsupported file type at every loader dispatch (fe5586b)
• io: refuse the complex TIFF sample formats in all four loaders (b413ffd)
• io: release the pair an image loader holds when it opens another (71aa025)
• io: stream a single-ROI mask's whole foreground, and fail a pair whose out-of-core feature fails (9e24e70)
• io: write the CLI test's volume fixture as Z-planes, not RGBA (e06fc2f)
• issue 327 single roi polus (#330) (03eeb0c)
• loader: clamp negative signed-int pixels so int16 CT doesn't wrap to a huge unsigned value (fac1bac)
• make imagecodecs PIP_ONLY_BINARY (b5fa20a)
• migrate build_and_test from macos-15-intel to macos-14 (ac70de1)
• mitigate exposed bug due to incorrect reading of bx in 3d_surface (24d18ee)
• moments: correct Hu invariant h5/h6 formulas (9x bracket, stray +eta03) (73f6ca8)
• moments: use fractional centroid in 2D central moments (drop (int) truncation) (5cbf94a)
• morphology: geodetic length/thickness from real perimeter (was size_t-truncated) (ce7716f)
• morphology: report ROI radii as distances, taken exactly (5bb289b)
• neighbors: exact min distance for the touch/radius test (PERCENT_TOUCHING) (92de774)
• neighbors: implement closest-neighbor dist/ang and cap PERCENT_TOUCHING (4322c88)
• nested: carry every non-feature column into the nested-ROI table (f60d8d0)
• ngldm: compute the 3D NGLDM over the ROI, over 26 neighbours, at the IBSI dependence count (558aa79)
• ome: read only named TIFF extensions and keep X and Y units apart (8ec6b03)
• ome: refuse a plane count past size_t and a non-object Zarr axis (9dada69)
• omezarr: say why a store will not open, and where its image is (455c13a)
• ooc: make the 2D out-of-core feature paths match the in-RAM path (9a9ad02)
• python: release an instance's Environment so a recycled id() cannot inherit it (6dd550f)
• remove redundant calculations and avoid flushing valid old values (cdf48cf)
• review comments on PR 352 (ec42edc)
• roi buffers: refuse a pixel outside the box that sizes its buffer (2273638)
• stop featurize() mutating its shared default name lists (372172e)
• upgrade Docker build to CUDA 12.6 and Python 3.11 (80b548d)
• use raw docstrings to silence invalid escape sequence SyntaxWarning (e3bf05c)
• vetting: band the 3D GLSZM entropy pin for a platform, not for a machine (ab8573e)
• vetting: correct radial follow-up records (7c4657a)
• vetting: let the NGTDM coverage scanner read one-line TEST registrations (51df88e)
• vetting: normalize oracle_coverage.csv to LF, drop dead current_test notes (7dc26ed)
• vetting: write every generated CSV and report with LF (91eb35e)

Performance Improvements

• 3d gldzm: gather the ROI's mark and grey levels in one pass (c37f58b)
• imq: read the out-of-core focus-score image a row at a time (d418b9d)
• io: decode each row of a striped TIFF once per tile-row scan (c1bacd1)
• morphology: read ROI radii from a distance transform where it is cheaper (14a67eb)
• ngldm: build the 3D NGLDM from the ROI's voxels, in one pass for the mask and grey levels (685da53)
• omezarr: open the z5 dataset once, not per tile (9b36f84)

Documentation

• 3d gldzm: record what the retired coverage sweep checked, and what it did not (483dbbc)
• 3d morphology: compare 3MESH_VOLUME with PyRadiomics MeshVolume (75a2ea7)
• 3d morphology: correct the PyRadiomics mesh comparison (69fb83d)
• 3d morphology: correct the PyRadiomics mesh comparison for orientation and spacing (202f9f9)
• 3d morphology: tighten the PyRadiomics mesh comparison (4ea101d)
• 3d ngldm: say what the generator verifies, and what the Ns agreement proves (9310932)
• add CLAUDE.md codebase and workflow guide (e301fe6)
• answer the second review of the pages, scripts and registry (f3f54c3)
• api: rewrite the Python docstrings in numpydoc style and check them against the code (c76f641)
• build: build the site without the compiled extension and fail CI on warnings (1ded975)
• caliper: correct inaccurate/stale comments (no code change) (cc5b4de)
• CLAUDE: add git workflow and tests/vetting conformance rules (a548b57)
• CLAUDE: address PR #388 review — C++20; agentic git workflow (466c038)
• CLAUDE: address PR #388 review — generalize paths, drop z5py pin, add no-local-paths rule (4235e0c)
• cli: generate the command-line reference and correct the usage pages (428b1f8)
• correct the pages, scripts and registry rows named in review (2c2f295)
• devguide: rewrite the developer guide and correct the project notes (8fccc2b)
• features: add the 3D intensity, shape and texture pages (c92ac6b)
• features: generate the feature list, the groups and the family indexes (91c3573)
• features: rewrite the 2D intensity, histogram and image quality pages (e2b0286)
• features: rewrite the 2D morphology, erosion, fractal and radial pages (3cd4a4d)
• features: rewrite the GLCM, GLRLM and GLSZM pages (0eaa6f3)
• features: rewrite the GLDM, GLDZM, NGLDM and NGTDM pages (0a87b6e)
• features: rewrite the moments, Zernike and Gabor pages (cb7616e)
• guide: add IBSI mode, validation and troubleshooting pages (dde7609)
• imq: say in the matrix that this pass vets the in-RAM paths only (1591760)
• io: describe the supported formats, the output and the shared conventions (9c2e03b)
• io: state the strip band's memory footprint and that ram_limit omits it (ab01215)
• link the known defects to their issues (8b23ce6)
• morphology: describe the ROI radius features rather than the change to them (edb9f5d)
• readme: slim the README and add the entry pages (494352d)
• scale: document large images, volumes and GPU acceleration (2daf705)
• test: correct IQR/QCoD _IDX framing — discrete percentile is IBSI-conformant, not a bug (29214ba)
• tests: add vetting audit baseline, fraclac oracle, and README (e5232c0)
• tests: box-count golden is FracLac-vetted, not a self-consistency pin (8ccc76b)
• tests: neighbor features are partly tool-vetted (CellProfiler), not analytic-only (7910549)
• tests: oracle tool local-setup research (TOOLS.md) (65e0b79)
• tests: spec for the oracle-vetting test framework (f44ff25)
• vetting: add skimage to the SPEC 4 oracle-token set (3ee1dfd)
• vetting: add the 2D morphology CellProfiler vetting report (9d0db5f)
• vetting: add the missing radial config matrix (fe4ef56)
• vetting: audit the 2D GLCM goldens against fresh oracle runs (0484103)
• vetting: audit the 2D GLRLM goldens against fresh oracle runs (67f24ed)
• vetting: correct 3D first-order oracle accounting (f6ad06a)
• vetting: correct split to 16 ibsi + 4 analytic; file IQR_IDX flooring bug (726b082)
• vetting: correct the 3D NGLDM report's file-inventory claim, and widen the generator's shift (1a762a1)
• vetting: correct what the 3D first-order MATLAB oracle backs (2ccd560)
• vetting: design for IBSI-vetted IH dispersion/index tests (07b1b75)
• vetting: drop the references to the deleted 3D morphology MATLAB header (071b52d)
• vetting: fix stale token count in plan example (16 ibsi + 4 analytic) (3255fef)
• vetting: give the constant-ROI cell a SPEC disposition, not an invented one (834e59d)
• vetting: give the neighbour rows a tier, a test name, a benchmark and a matrix (7981b2a)
• vetting: implementation plan for IBSI-vetted IH dispersion/index tests (4dfb1ff)
• vetting: lead the 3D first-order report with the current state (004bfc5)
• vetting: lead the 3D first-order report with the current state (25c57f2)
• vetting: migration map + seeded oracle_coverage.csv (Phase 1, no code changes) (77f3d07)
• vetting: name BasicMorphologyFeatures as MASS_DISPLACEMENT's producer (d33a168)
• vetting: name Octave wherever the matlab oracle is presented (d70e3fe)
• vetting: narrow what the 3D coverage sweep asserts that nothing else does (2a75d34)
• vetting: point the IMQ mechanics-guard comment at scan_other_tests (bb1981c)
• vetting: record licensed 2D first-order provenance (06ad1be)
• vetting: record licensed 2D morphology provenance (3d039d6)
• vetting: record reconciled IBSI IH phantom config + index base (99df244)
• vetting: record the 2D GLDM audit (3ee009d)
• vetting: record the 2D GLDZM audit (f29924d)
• vetting: record the 2D GLSZM audit (176476a)
• vetting: record the 2D neighbour audit (50d0ff8)
• vetting: record the 2D NGTDM audit (23c609f)
• vetting: record the 3D GLDM default cell and the degenerate ROI it discards (12ef315)
• vetting: record the 3D GLDM recipes, matrix, benchmarks and audit (cac4e99)
• vetting: record the 3D GLSZM audit, its recipes and its benchmark (33e0fbe)
• vetting: record the 3D NGTDM audit, its recipes and its benchmark (55d5e90)
• vetting: record the config scope of the gldm promotions (7 are mode-invariant) (0780912)
• vetting: record the config scope of the glrlm promotions (285bc39)
• vetting: record the config scope of the glszm promotions (c4bb8b1)
• vetting: record what the 3D GLSZM review round measured (b7126de)
• vetting: resolve missing oracles via deep-dive research (Phase 2) (2fa0515)
• vetting: resolve the Phase-2 reconciliation decisions (SPEC 6) (8b45ddd)
• vetting: retract unproven 3D NGLDM "ibsi" promotions; document MIRP disagreement (b924f8e)
• vetting: scaffold matrix/ and oracles/gen_ conventions (GLCM example) (61fdc66)
• vetting: seed config_recipes.md (b64c82b)
• vetting: separate unproven provenance from unreproducible provenance (058cb00)
• vetting: update golden_regen doc for the flat rel=1e-8 tolerance (f84773f)

Code Refactoring

• 3d surface: describe the eigenvalue ordering rather than the defect it replaced (34a74c2)
• address PR #351 review nits (c623405)
• feature settings: key the settings registry by std::type_index (9381158)
• tests: route fractal fixture through the shared masked-loader helper (050e672)

Build System

• arrow: require Boost for Arrow instead of Z5 (43a584f)

Continuous Integration

• release-please: use manifest config so 0.x breaking = minor, and pin 0.12.0 (a500bd9)

---

This PR was generated with Release Please. See documentation.