Migrate ClearEx ingestion and analysis stores to Zarr v3#11
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AdvancedImagingUTSW wants to merge 11 commits intomainfrom
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Migrate ClearEx ingestion and analysis stores to Zarr v3#11AdvancedImagingUTSW wants to merge 11 commits intomainfrom
AdvancedImagingUTSW wants to merge 11 commits intomainfrom
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Update CODEX.md to document store-level spatial calibration and other recent runtime changes. Adds a root store attribute `spatial_calibration` as the canonical stage-to-world axis mapping (missing attrs default to identity), records canonical text form (`z=...,y=...,x=...`) and allowed bindings (`+/-x`, `+/-y`, `+/-z`, `+/-f`, `none`). Notes that WorkflowConfig now carries SpatialCalibrationConfig, setup exposes a per-experiment "Spatial Calibration" control that prefills existing stores and writes resolved mappings on Next, headless workflows accept `--stage-axis-map`, visualization affines derive world z/y/x translations (including Navigate F and `none` behavior), and provenance records the effective calibration. Adds a dated "Recent Runtime Updates (2026-03-20)" section summarizing these changes.
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Summary
clearex migrate-storeand sibling staging/materialization flows for external Zarr, OME-Zarr, and N5 inputs_ARRAY_DIMENSIONS, and legacyaxeszarr,dask,distributed,tifffile,ome-zarr, andnapari-ome-zarrTesting
uv run pytest -q tests/io/test_cli.py tests/io/test_experiment.py tests/io/test_read.py tests/io/test_provenance.pyuv run pytest -q tests/test_workflow.py tests/io/test_cli.py tests/io/test_experiment.py tests/io/test_provenance.pyuv run ruff check src/clearex/main.py src/clearex/workflow.py src/clearex/gui/app.py src/clearex/io/cli.py src/clearex/io/experiment.py src/clearex/io/provenance.py src/clearex/io/read.py src/clearex/io/zarr_storage.py src/clearex/visualization/pipeline.py src/clearex/flatfield/pipeline.py src/clearex/detect/pipeline.py src/clearex/deconvolution/pipeline.py src/clearex/mip_export/pipeline.py tests/test_workflow.py tests/io/test_cli.py tests/io/test_experiment.py tests/io/test_provenance.py tests/io/test_read.pyuv run --extra viewer python -c "import neuroglancer, ome_zarr, napari_ome_zarr; print('viewer-extra-ok')"conda env create --dry-run -f environment.yml