Welcome
The Pathology area of Gradient Biotech 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.
What you can do today
| Capability | Status |
|---|---|
| Slide upload | TIFF, OME-TIFF, PNG, JPEG, and scanner-format files |
| Tile generation | Thumbnail and multi-level tile manifest for web viewing |
| Tissue detection | Tissue mask, region bounding boxes, focus QC |
| Cell segmentation | Nucleus/cell detection (threshold or watershed) with overlay and cell table |
| Object classifier training | Train a random-forest cell classifier from annotation-labeled regions; predict a class for every cell |
| Color deconvolution | H&E / H-DAB stain separation with per-stain intensity and DAB-positive area fraction |
| Spatial quantification | Density, nearest-neighbor distances, infiltration phenotype, region metrics |
| Multiplex IF phenotyping | Per-cell marker positivity, phenotype rules (e.g. CD8+ T cell, PD-L1+), co-expression and region composition |
| TMA dearraying | Detect tissue cores on a TMA slide and lay them out on a labeled grid |
| Spatial alignment | Coordinate-transform a compbio spatial transcriptomics run onto a pathology slide, with region-level expression summaries |
| Cohort comparison | Group-level statistics (t-test/Mann-Whitney, ANOVA/Kruskal-Wallis, FDR) across sample groups |
| AI interpretation | Grounded summaries citing computed metrics, with research disclaimers |
| OME-TIFF export | Export a processed slide as a pyramidal OME-TIFF for QuPath/Fiji/OMERO |
| Slide viewer | Pan/zoom tiles with tissue mask, cell, phenotype, density heatmap, and spatial-alignment overlay layers |
| Annotation import | GeoJSON and QuPath-compatible region labels |
| Sample/cohort metadata | Per-sample fields plus bulk CSV import |
| Run history | Study-level pipeline run tracking with artifact links |
How the product is organized
Every analysis lives inside a study — your pathology project container. From the pathology dashboard you create or open a study, then work through:
- Study home — upload slides and review run history
- Slide detail — generate tiles, run analysis pipelines, inspect the viewer
- Cohort — assign samples/groups, launch batch runs, compare metrics across slides
- Interpret — AI-assisted summaries of completed runs (open directly at
/areas/pathology/studies/{id}/interpret)
Pipeline jobs run asynchronously. Launch jobs from the slide detail page and refresh when complete.
Who this is for
- Translational and tumor biology researchers quantifying immune infiltration and tissue microenvironment metrics
- Computational pathology groups running reproducible WSI pipelines at scale
- Spatial biology labs grounding molecular assays in tissue morphology (spatial transcriptomics analysis lives in Computational Biology; pathology provides the tissue context layer)
- Pharma tissue biomarker teams exploring histological endpoints with auditable run records
What this is not
- Not a regulated clinical diagnostic or pathologist sign-out system
- Not a passive slide viewer — overlays and metrics support quantitative research
- Not automatic diagnosis — segmentation and quantification outputs are research metrics
Next steps
- Use cases — scenario guides for slide quantification, TME infiltration, annotated compartments, and spatial omics context
- Quick start — upload and analyze your first slide
- Key concepts — studies, slides, runs, and artifacts
- Study workflow — how the main sections fit together
- AI interpretation — grounded summaries of completed runs