biopb 0.6.6

Python bindings of BioPB: open protobuf/gRPC protocols for biomedical image processing

BioPB - AI-assisted bio-image analysis

The repo provides the core harness framework of the biopb project. The goal is to coordinate a LLM agent with a user in an interactive session to perform complex image ananlysis tasks relavent to scientific researches.

Quick Start

curl -fsSL https://biopb.org/install.sh | bash

biopb-mcp

An MCP server + napari plugin that hands an AI agent a live, shared napari session wired to the data and algorithm servers, so analysis is driven in plain Python instead of fixed GUI buttons. Read More...

• Shared canvas: napari viewer is accessible and mutable by both the agent and the user
• Persistent kernel: agent code runs in a real ipython kernel with namespace persistence and full observability
• Perceive → act → verify: the agent runs code, then screenshots/inspects to confirm the result

biopb-tensor

A blazing-fast imaging data server for sharing your lab's petabyte-scale datasets to LLM agents and human team members alike. Read More...

• Uniform Representation: all source data mapped to a multi-resolution and lazy-read array for client access
• Multi-language: dask array for Python and ImgLib2.CellImg for Java
• Thread-safe & Serializable: compatible with dask.distribute for distributed computing on larger-than-memory dataset
• Metadata Server: full DuckDB SQL support to query your embedded metadata
• On-the-fly Build: keep your data in original format (.zvi, ndtiff etc). No staging or on-boarding process needed
• Built-in Viewer: browse all your data with any browser (e.g., on an ipad)

biopb-image-runtime

Deploy complex image processing algorithms (e.g., large deep-learning models) on the network as services. Read More...

SDK

Schema, utilities and cli for building your own workflow. Explore your data in jupyter notebook etc.

Python

pip install biopb[tensor]

Java

<dependency>
  <groupId>io.github.jiyuuchc</groupId>
  <artifactId>biopb</artifactId>
  <version>CURRENT_VERSION</version>
</dependency>

Related Projects in BioPB

biopb-servers

Specific implementations of biopb-image-runtimes. Read More...

Contributing

Contributions are very welcome. Read the developement document first to understand the overall design architecture.

License

Distributed under the terms of the MIT license,

Issues

If you encounter any problems, please file an issue along with a detailed description.