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Genericize repo for public release + add turntable proofreading tools - #1
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…, and datasets - make_review_page: remove hardcoded internal Neuroglancer mesh/EM sources, dataset position, and EM contrast window; NG links only render when sources are passed on the CLI - render_slices: default --contrast to auto instead of a dataset-tuned window; generic example paths - export_run: default --runs-root to ./runs (gitignored) - README / design doc / AGENTS.md / agent_prompt.md: replace internal paths and dataset ids with placeholders (<collection_dir>, /path/to/...); drop cellmap-analyze migration notes - rubrics: make the shared structural guidance organelle-agnostic (mito-specific wording stays in the mitochondrion rubric) - README: list get_image_legend and fix get_rubric's signature
…scan prompt) - tools/render_turntable.py: rotating MP4 or N labeled still viewpoints of one object's mesh under a fixed orthographic camera with a stationary grid overlay, plus a <id>.turntable.json sidecar describing the exact geometry - tools/turntable_geometry.py: pure-numpy camera/grid/rotation geometry - tools/grid_to_voxel.py: invert a (view/frame, grid cell or point) hit to a voxel coordinate by ray-casting the un-rotated mesh; returns a local slice orientation (surface normal + PCA axes) - tools/mesh_sources.py: support standalone remote precomputed mesh layers - prompts/turntable_scan.md: VLM scan prompt whose JSON output feeds grid_to_voxel - tests/test_turntable.py: geometry + end-to-end ray-cast tests (skip without numpy/pyvista) - new [video] extra (imageio + imageio-ffmpeg); TESTING_ROADMAP.md
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Summary
Two commits:
Genericize repo for public release — removes project-specific data so the repo can be made public:
tools/make_review_page.py: drop hardcoded internal Neuroglancer mesh/EM sources, dataset position, and EM contrast window. Neuroglancer links now only render when--ng-mesh-sources/--ng-em-sourceare passed.tools/render_slices.py:--contrastdefaults toautoinstead of a dataset-tuned window; generic example paths.tools/export_run.py:--runs-rootdefaults to./runs(gitignored).AGENTS.md/agent_prompt.md: internal paths and dataset ids replaced with placeholders (<collection_dir>,/path/to/...); downstream-migration notes removed.rubrics.py: shared structural guidance is now organelle-agnostic (mito-specific wording stays in the mitochondrion rubric).get_image_legendand fixesget_rubric's signature.Add mesh-driven turntable proofreading tools —
render_turntable.py(rotating MP4 or labeled stills + geometry sidecar),turntable_geometry.py,grid_to_voxel.py(ray-cast a view/grid hit back to a voxel + local slice orientation), standalone remote precomputed mesh support inmesh_sources.py, a VLM scan prompt, tests, and a new[video]extra.Behavior changes
export_run.pywrites to./runs/by default (wasignore/runs/); pass--runs-rootto override.--contrast lo,hifor a fixed window.Testing
ruff check .andruff format --check .clean.pytest: 41 passed locally (turntable tests skip without numpy/pyvista, as in CI's[dev]install).make_review_page.pywith and without Neuroglancer sources, andexport_run.pywith the new default runs root.Note
Earlier commits on
mainstill contain the old internal paths/URLs in history; consider squashing or publishing from a fresh repo if history matters before making the repo public.