biopb 0.1.1

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

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.
2. biopb.image Image processing protocols. Current focus is single-cell segmentation, designed originally for the Lacss project.

Public Servers

Below are public servers that implements the biopb protocol

• cellpose.biopb.org:443
  • Protocol: biopb.image.ObjectDetection
  • Model: Cellpose single-cell segmentation (cyto3 variant).
• lacss.biopb.org:443
  • Protocol: biopb.image.ObjectDetection
  • Model: LACSS base variant. Support 2D and 3D input.
• osilab.biopb.org:443
  • Protocol: biopb.image.ObjectDetection
  • Model: segformer as reported in NIPS challenge paper.

Related project

• 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, such as those listed above.

Documentation

Documentation