Computational pathology and whole-slide imaging research
The Pathology area is a web workspace for computational pathology and whole-slide imaging research. Upload tissue slides or region images; generate tile manifests for browser viewing; run tissue detection, cell segmentation, and spatial quantification; inspect overlays in the slide viewer; and track reproducible pipeline runs.
Use cases
Guided workflows map common questions to data requirements, analysis steps, and documentation — pick the scenario closest to your study.
Research question: What is the tissue composition of this slide, how many cells are detected, and what spatial metrics characterize the tissue architecture?
Run the full computational pathology pipeline on a tissue slide — tile generation, tissue detection, cell segmentation, and spatial quantification with interactive viewer review.
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Research question: How infiltrated is the tissue, what is the spatial organization of detected cells, and does the infiltration pattern suggest immune-desert, excluded, or inflamed phenotypes at the tissue level?
Quantify tumor microenvironment architecture — cell density patterns, immune infiltration phenotype, and spatial proximity metrics from segmented tissue slides.
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Research question: What are the cell counts, densities, and spatial statistics within each labeled tissue compartment rather than across the whole slide?
Quantify cell density and spatial metrics within pathologist-defined regions — tumor, stroma, necrosis, or lymphoid compartments imported from GeoJSON or QuPath exports.
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Research question: Where do spatial gene expression signals originate relative to tissue structure, and how can morphology-guided regions connect molecular data to what pathologists see on the slide?
Ground spatial transcriptomics in tissue morphology — pathology provides the WSI tissue context layer that makes Visium, Xenium, and MERFISH results interpretable in histological space.
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Capabilities
Everything available in the Pathology workspace today — pipelines, explorers, exports, and provenance.