Add Docker-based Minian (Python 3.8) processing support#67
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kushalbakshi wants to merge 36 commits intodatajoint:main_external-storagefrom
Open
Add Docker-based Minian (Python 3.8) processing support#67kushalbakshi wants to merge 36 commits intodatajoint:main_external-storagefrom
kushalbakshi wants to merge 36 commits intodatajoint:main_external-storagefrom
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When extra_dj_params.docker_image is set in ProcessingParamSet, the make_compute() method spawns a sibling Python 3.8 container running the original denisecailab/minian instead of the inline modernized path. This ensures result parity with the customer team's original pipeline. Co-Authored-By: Claude Opus 4.6 <[email protected]>
Remove the ~650 lines of inline minian processing + compatibility patches. The minian method now always runs via the py38 sibling container. Docker image configurable via MINIAN_DOCKER_IMAGE env var. Co-Authored-By: Claude Opus 4.6 <[email protected]>
…tuning - Change default image to minian-py38:latest (conda-forge based) - Refactor _run_minian_in_container: write params as unified config JSON, translate container paths to host paths via HOST_S3_ROOT/HOST_OUTBOX env vars, pass Dask timeout and memory allocator env vars to container - Add test_minian_pipeline.py for end-to-end Minian integration testing Co-Authored-By: Claude Opus 4.6 <[email protected]>
MinianLoader: - Load ref_image and mean_proj zarrs directly instead of computing from full varr_ref video (which was never in the final output) - Remove dead varr_ref fallback from max_proj_image _run_minian_in_container: - Pass through Dask env vars from environment instead of hardcoding - Include DASK_DISTRIBUTED__WORKER__MEMORY__* vars - Fix MINIAN_CONTAINER_MEMORY -> MINIAN_CONTAINER_MEM_LIMIT to match docker-compose naming - Remove unused /data/params/params.json CLI argument Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
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Summary
Processing.make_compute(), running the minian pipeline in an isolated container via sibling container executionMinianLoaderclass for loading minian zarr outputs (A, C, S, motion, summary images) without requiring minian to be installedMotionCorrection,Segmentation,Fluorescence, andActivitytables_run_minian_in_container()helper with host path translation for sibling container Docker execution, real-time log streaming, and configurable Dask env var passthroughsetup.pydependenciestest_minian_pipeline.pynotebook for integration testingTest plan
MinianLoadercorrectly loads all zarr arrays and exposes them via properties (masks, motion_shifts, summary images)Processing->MotionCorrection->Segmentation->Fluorescence->Activity🤖 Generated with Claude Code