BioPB

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

biopb.ome Microscopy data representation modeled after OME-XML.
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.

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.

Name		Name	Last commit message	Last commit date
Latest commit History 17 Commits
biopb		biopb
docs		docs
examples		examples
gen/python/biopb/image		gen/python/biopb/image
scripts		scripts
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
pyproject.toml		pyproject.toml