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Research Areas

Computational BiologySingle-cell, bulk RNA-seq, spatial, and biomarkers
CardiologyCardiovascular signals, cohorts, and interpretationImmunologyImmune cell states, signaling networks, and repertoire dynamicsNeurologyBrain connectivity, functional imaging, and electrophysiologyOncologyTumor microenvironment, immune response, mutations, and survivalPathologyWhole-slide imaging, tissue quantification, and spatial pathology

Application

Documentation

Documentation

Back to studies

Study workflow

Pathology follows a left-to-right research flow. Tile generation is required before browser viewing and segmentation on large slides.

Create study → Upload slides → Generate tiles → Tissue detect → Segment cells → Spatial quantification

Dashboard — area home

The pathology dashboard (/areas/pathology/dashboard) shows recent studies and links to create a new study.

Readiness signal: at least one study with one uploaded slide and a completed tile or analysis run.

Study home — project overview

The study page (/areas/pathology/studies/{id}) is your project hub:

  • Slide ingestion — upload form with modality and stain type selectors
  • Slides grid — thumbnail cards linking to slide detail pages
  • Run history — all pipeline runs for this study

Slide detail — analyze and inspect

Each slide opens at /areas/pathology/studies/{id}/slides/{slideId}:

  • Slide viewer — pan/zoom with overlay layers
  • Pipeline controls — tile, tissue detect, segment, spatial quantification
  • QC panels — tissue fraction, cell count, spatial metrics
  • Cell table — detected objects with area and confidence
  • Region metrics table — compartment-level density and cell statistics

See Slide viewer.

Typical paths

Study typePath
Region image demoUpload PNG → tiles → tissue detect → segment → quantify
WSI reviewUpload SVS/OME-TIFF → tiles → tissue QC → segmentation at scale
TME quantificationSegment → spatial quantification → export region metrics CSV
Annotated regionsImport GeoJSON → tissue detect → quantify within labeled compartments

Integration with Computational Biology

Spatial transcriptomics ingestion, deconvolution, and generic spatial statistics are owned by the Computational Biology area. Pathology contributes the WSI tissue context layer — morphology-guided region extraction and overlay alignment — without duplicating compbio spatial pipelines.

See products/pathology/product.md for the multimodal integration roadmap.

Future workflow (planned)

  • Cohort comparison across sample groups (cohort_compare pipeline)
  • Multiplex IF phenotyping
  • AI interpretation grounded in spatial metrics
  • Publication-ready report export

See products/pathology/plan.md for phase status.