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Claude Code Instructions for biahub

Environment

  • Conda envs: /hpc/mydata/$USER/envs/
  • biautils (iohub, biahub CLI): module load anaconda; module load comp_micro; conda activate biautils
  • neuroglancer: conda activate /hpc/mydata/$USER/envs/neuroglancer_iohub

Repository Structure

Single package, managed with uv (migration in progress from setuptools).

biahub/
├── pyproject.toml       # uv-managed project
├── biahub/              # Main package
│   ├── cli/             # Click CLI + Hydra pipeline CLI
│   ├── *.py             # Processing modules
│   └── vendor/          # Vendored dependencies
├── settings/            # Example YAML configs
├── tests/
└── plans/               # Migration plans

Reference Data

  • Widefield (Hummingbird): /hpc/projects/intracellular_dashboard/virtual_stain_ft_infected/2026_01_29_A549_H2B_CAAX_DAPI_DENV_ZIKV/
  • Light-sheet (Mantis): /hpc/projects/intracellular_dashboard/organelle_dynamics/2025_08_26_A549_SEC61_TOMM20_ZIKV/
  • Test data: /hpc/projects/intracellular_dashboard/refactor_biahub/

Plans

  • plans/biahub-uv.md — Migrate packaging from setuptools to uv
  • plans/biahub-cli-refactor.md — Add Hydra pipeline CLI and config templates

Code Conventions

  • Click for CLI, Pydantic v2 for settings (extra="forbid")
  • Absolute imports: from biahub.X import Y
  • OME-Zarr format via iohub library
  • Use absolute HPC paths

Viewing Data

# Neuroglancer (preferred)
neuroglancer_view.py /path/to/data.zarr --position A/1/0

# Browser dashboard (nd-embedding-atlas)
python /hpc/mydata/$USER/code/nd-embedding-atlas/scripts/ndimg_view.py /path/to/data.zarr --position A/1/0

Related PRs

  • PR #200 (feature/merge-mantis-analysis-template): Do NOT merge