biopb documentation¶
Open bioimage analysis, driven by your agent.
biopb lets you analyze microscopy images by talking to an AI agent — Claude Code, OpenCode, Cursor, or Hermes. You ask the agent to open an image or run an analysis, and it drives biopb for you: loading data, running segmentation and other algorithms, and showing results in a live napari viewer you can watch and tweak.
Get started How it fits together
What you can do¶
- Open and browse large microscopy data — OME-Zarr, OME-TIFF, HDF5, CZI, LIF, ND2, and more — even datasets far larger than your computer's memory.
- Do open-ended analysis in plain language. Filtering, measurements, region properties, spatial statistics — your agent writes the code and you watch results appear in napari.
- Run trained models for segmentation and restoration (Cellpose, UNiFMIR, and others) without writing boilerplate.
- Stay in control. Image results land in the viewer; numbers and tables go to the chat; you decide what to save.
Components¶
You only ever interact with your agent and the napari window. Everything else runs quietly underneath:
| Piece | What it does for you |
|---|---|
| Your AI agent | The thing you talk to. It launches biopb and writes the analysis code. |
| Napari + Data Browser | The viewer where images and results appear. Your agent drives it; you can edit by hand. |
| Data server | Serves your image data, lazily, so huge files just work. |
| Algorithm servers | Run the dedicated algorithms — usually on a GPU machine. |
If you are just getting started, you don't need to think about the last two — the default install wires up a local data server automatically. See How biopb fits together when you want the full picture.
Where to next¶
- Getting started — install and run your first analysis.
- Working with your agent — what to ask and how the workflow feels.
- Working with napari — What do you do in the napari window.
- Troubleshooting — fixes for the common snags.
These docs are for end users
Looking for protocol internals, contributor guides, or the gRPC/Arrow Flight specs? Those live in the source repositories on GitHub.