feat: Allen atlas improvements and RAS alignment#101
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FIrgolitsch wants to merge 3 commits intomainfrom
Open
feat: Allen atlas improvements and RAS alignment#101FIrgolitsch wants to merge 3 commits intomainfrom
FIrgolitsch wants to merge 3 commits intomainfrom
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- Replace setup.py + requirements.txt with pyproject.toml (uv) - Add .pre-commit-config.yaml (ruff-format, ruff lint, ty advisory) - Update CI workflow to use uv + ruff + ty - Update Dockerfile for uv - Add uv.lock, linumpy/py.typed - Delete setup.py, requirements.txt, requirements-pytest.txt - Run ruff format on all Python files - Run ruff check --fix (341 auto-fixes applied)
…visualization New library modules: - linumpy/preproc/normalization.py, resampling.py - linumpy/utils/image_quality.py, orientation.py, visualization.py New scripts: - linum_fix_galvo_shift_zarr.py, linum_clean_raw_data.py - linum_compare_stitching.py, linum_extract_pyramid_levels.py - linum_normalize_z_intensity.py, linum_aip_png.py - linum_screenshot_omezarr_annotated.py, linum_generate_mosaic_aips.py Updated: preprocessing, stitching, registration, I/O, metrics modules Added tests for normalization, resampling, xyzcorr, orientation, visualization
- scripts/linum_align_to_ras.py — new script for RAS alignment - scripts/linum_download_allen.py — updated Allen atlas download - linumpy/io/allen.py — improved Allen I/O module
This was referenced Apr 1, 2026
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PR H — Allen Atlas & RAS Alignment
Changes
scripts/linum_align_to_ras.py— Align volumes to RAS orientationscripts/linum_download_allen.py— Improved Allen atlas downloadlinumpy/io/allen.py— Newnumpy_to_sitk_image()utility, improved Allen I/ODependencies