biopb 0.5.0

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

BioPB

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

1. biopb.image Image processing protocols. Current focus is single-cell segmentation, designed originally for the Lacss project.
2. biopb.ome Microscopy data representation modeled after OME-XML.

Documentation

Documentation

Language bindings

Python

A python binding of schema is included in this repo. The package additionally implements some utility functions for data conversion between numpy <--> protobuf.

pip install biopb

Java

The Java binding contains util functions based on imglib2. To use in Maven based project:

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

Other languages

For all other languages use the automatically generated SDK from buf.build

Related project

• napari-biopb is a napari widget and a biopb.image client, allowing users to perform 2D/3D single-cell segmentation within the Napari environement.
• trackmate-bipb is a FIJI plugin and a biopb.image client, designed as a cell detector/segmentor for trackmate, but also works a stand-alone unit.
• biopb-server implement ready-to-deploy biopb servers (as Docker containers).