Spatial biology processing suite
The AstroPath Pipeline was developed to process whole slide multiplex immunofluorescence data from microscope to database at single cell resolution.
OME-Zarr whole-slide images to patch- and slide-level foundation-model embeddings - cloud-native, FAIR, model- and backend-agnostic.
An R package for modeling asymmetric spatial associations between cell types in tissue images using a multilevel Bayesian framework.
This is a pipeline for ingestion, cleaning, and spatial analysis of Akoya PCF images
Configurable fingerprint-based cell-type annotation for CODEX and QuPath tables
A reproducible framework for modeling spatial cell–cell interactions in the tumor microenvironment using multitype Gibbs point processes and multiplexed imaging data.
Python implementation of Spatial Patterning Analysis of Cellular Ensembles
Python workflows for tile-based feature extraction, clustering, and visualization of multiplex whole-slide imaging data.
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