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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

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FAQ

Is this a clinical diagnostic tool?

No. Pathology in Gradient Biotech is a research and translational analysis workspace. Outputs must not be used for clinical diagnosis or pathologist sign-out. This is not a replacement for expert histopathological review.

Do I need QuPath or Fiji installed locally?

No. Upload files through the web UI; all image processing runs in backend-analysis. The application is inspired by QuPath, Fiji, and others.

The slide viewer shows "Tiles not generated yet"

Run Generate tiles from the slide detail page. Segmentation and the tile viewer require a completed tile manifest.

Segmentation is disabled — why?

Segment cells requires a tile manifest. Generate tiles first.

Spatial quantification is disabled — why?

Spatial quantification requires a completed Segment cells run. Run segmentation first.

Segmentation detected too few / too many cells

The current baseline model (threshold_baseline) is a research placeholder. Cell count depends on stain contrast and image resolution. Future phases integrate Cellpose and StarDist — see products/pathology/plan.md.

WSI upload failed or format unsupported

Confirm OpenSlide is installed in the biochem environment for SVS/NDPI/MRXS formats. For local development, start with PNG or TIFF region images.

Where are files stored locally?

Uploads and tiles: data/pathology/
Artifacts: data/pathology/artifacts/{run_id}/
Metadata: Supabase PostgreSQL (biochem_path_* tables) via the metadata API

These paths are gitignored.

How does this relate to Computational Biology spatial analysis?

Computational Biology owns Visium/Xenium/MERFISH ingestion, spatial viewers for omics data, and generic spatial statistics. Pathology owns whole-slide tissue morphology — segmentation, tissue structure, and morphology-guided region context. The areas integrate at the overlay layer, not by duplicating omics pipelines.

How do I add a new pipeline?

Implement in backend-analysis/app/pathology/pipelines/, register in backend-analysis/app/pathology/routers/run.py, and expose via job endpoints. See products/pathology/plan.md and repo root claude.md for conventions.

Is cloud deployment supported?

Production GCP deployment with object storage for tiles and Cloud Tasks for async jobs is planned but not the current local focus. See products/pathology/plan.md Phase 8.