biopb 0.1.4

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

Documentation

Documentation

Python binding

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

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-lacss is a FIJI plugin and a biopb.image client, designed as a cell detector/segmentor for trackmate. It works with any biopb.image servers.
• biopb-server implement ready-to-deploy biopb servers (as Docker containers).