WEHI SODA-Hub

Spatial Omics Data Analytics (SODA) Hub supports spatial research at the Walter and Eliza Hall Institute of Medical Research (WEHI) in Parkville, Australia. The Hub is providing streamlined data management and analysis environment to accelerate research in spatial omics.

SODA is building and contributing to open-source software. Please see the WEHI-SODA-Hub GitHub page for a complete list of our public repositories.

Analysis tools and pipelines

• spatialvpt: Segmentation and QC workflow for MERSCOPE using vizgen-postprocessing tool.
• vizgen-postprocessing_container: Container for running vizgen-postprocessing tool with the cellpose2 plugin.
• spatialVis: R package for downstream plots and spatial analyses for spatial proteomics.
• MibiSegmentation: A CLI for Mesmer segmentation of MIBI TIFFs.
• cellmeasurement: Groovy app for calcuating cell measurements from whole-cell and nuclear masks.

Metadata tools

• rdfpytest: Framework for running SHACL tests over RDF data in Python.
• RdfNav: Utilities for navigating an RDF graph in Python.
• RdfCrate: Library for building RO-Crates using rdflib.
• OmeroCrate: Tools for uploading an RO-Crate dataset to Omero.
• proclaim: RO-Crate profile generator from LinkML.
• cordful: LinkML implementation of various linked data schemas, profiles vocabularies and ontologies.