Overview
Pathology workflows connect slide ingestion, tissue analysis, spatial quantification, and interactive review in a single study workspace. Each use case below maps a common research question to platform capabilities, data requirements, and a suggested analysis path.
Use case index
| Use case | Research question | Key capabilities |
|---|---|---|
| Slide quantification | How many cells are present and what are the spatial tissue metrics? | Tile generation, tissue detection, segmentation, spatial quantification |
| TME infiltration | What is the immune infiltration pattern and tumor-stroma organization? | Cell density, nearest-neighbor distances, infiltration phenotype scoring |
| Annotated compartments | What are the metrics within pathologist-defined regions? | GeoJSON/QuPath import, region-level density and cell statistics |
| Spatial omics context | Where do molecular signals originate in tissue morphology? | WSI tissue context layer integrated with Computational Biology spatial pipelines |
Who these use cases serve
| Audience | Typical goals |
|---|---|
| Translational and tumor biology researchers | TIL quantification, spatial immune analysis, biomarker discovery |
| Computational pathology groups | Reproducible WSI pipelines, segmentation at scale, spatial statistics |
| Spatial biology labs | Ground Visium/Xenium/MERFISH in tissue morphology |
| Pharma tissue biomarker teams | Histological endpoints, heterogeneity scoring, treatment-response correlation |
| Pathology research departments | Digital workflow exploration, annotation, quantitative morphology |
Common data requirements
Most use cases start with a pathology study containing:
- Slides — PNG/TIFF region images or whole-slide scans (SVS, OME-TIFF, NDPI)
- Modality and stain metadata — whole-slide image, region image, H&E, IHC, IF
- Sample metadata (for cohort work) — diagnosis, tumor grade, treatment, response status, group label
Tile generation is required before browser viewing and segmentation on large slides.
Choosing a starting point
| If your primary goal is… | Start with… |
|---|---|
| End-to-end slide analysis from upload | Slide quantification |
| Immune infiltration or TME metrics | TME infiltration |
| Metrics within labeled tumor/stroma regions | Annotated compartments |
| Morphology context for spatial transcriptomics | Spatial omics context |
What these use cases are not
These workflows support research and translational pathology. They are not clinical diagnostic or pathologist sign-out systems. Segmentation and quantification outputs are research metrics, not diagnoses.
Next steps
- Quick start — analyze your first slide
- Study workflow — how study pages fit together
- Pipelines reference — API endpoints and parameters