Metadata-Version: 2.2
Name: biopb
Version: 0.1.1
Summary: Python bindings of BioPB: open protobuf/gRPC protocols for biomedical image processing
Author-email: Ji Yu <jyu@uchc.edu>
License: MIT License
        
        Copyright (c) 2024 Ji Yu
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
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Project-URL: Homepage, https://github.com/jiyuuchc/biopb
Project-URL: Documentation, https://jiyuuchc.github.io/biopb/
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE

# BioPB
A place for collecting protobuf/gRPC definitions for bio-research data. Currently it has only two packages

1. `biopb.ome` Microscopy data representation modeled after [OME-XML](https://ome-model.readthedocs.io/en/stable/ome-xml/index.html).
2. `biopb.image` Image processing protocols. Current focus is single-cell segmentation, designed originally for the [Lacss](https://github.com/jiyuuchc/lacss/) project.

## Public Servers
Below are public servers that implements the biopb protocol

* `cellpose.biopb.org:443`
  - Protocol: `biopb.image.ObjectDetection`
  - Model: [Cellpose](https://www.cellpose.org/) single-cell segmentation (cyto3 variant).
* `lacss.biopb.org:443`
  - Protocol: `biopb.image.ObjectDetection`
  - Model: [LACSS](https://github.com/jiyuuchc/lacss) base variant. Support 2D and 3D input.
* `osilab.biopb.org:443`
  - Protocol: `biopb.image.ObjectDetection`
  - Model: segformer as reported in [NIPS challenge paper](https://www.nature.com/articles/s41592-024-02233-6).

## Related project
* [`trackmate-lacss`](https://github.com/jiyuuchc/TrackMate-Lacss) is a [`FIJI`](https://imagej.net/software/fiji/) plugin and a `biopb.image` client, designed as a cell detector/segmentor for [trackmate](https://imagej.net/plugins/trackmate/index). It works with any `biopb.image` servers, such as those listed above.

## Documentation
[Documentation](https://jiyuuchc.github.io/biopb/)
