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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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Slide viewer

The slide viewer on the slide detail page provides pan/zoom navigation over tiled whole-slide and region images with analysis overlay layers.

Prerequisites

Run Generate tiles first. Without a tile manifest, the viewer shows a placeholder with a tile-generation button.

Navigation

  • Pan — click and drag
  • Zoom — scroll wheel or pinch
  • Tiles load on demand from GET /pathology/slides/{id}/tiles/{level}/{x}_{y}.jpg

A thumbnail preview loads when the full pyramid is not yet available.

Overlay layers

Toggle layers when corresponding pipeline runs have completed:

LayerSource pipelineWhat it shows
Tissue masktissue_detectForeground tissue boundary
Cell overlaysegment_cellsDetected nucleus/cell boundaries
Density heatmapspatial_quantificationLocal cell density visualization
AnnotationsImported GeoJSON / QuPathLabeled region boundaries

Overlays are semi-transparent PNG artifacts composited over the base tile layer.

Cell inspection

When segmentation completes, detected cells appear in the Detected Cells table below the viewer:

  • Centroid coordinates
  • Area in pixels
  • Class label and confidence score

Click cells in the table to highlight them in the viewer when supported.

Region context

Tissue detection produces region bounding boxes (tumor, stroma, etc. depending on detection output). Regions feed the Region Metrics table after spatial quantification.

QC signals

Review alongside the viewer:

  • Tissue fraction — proportion of slide area classified as tissue
  • Focus score — blur/focus quality indicator
  • Focus warnings — tile-level QC flags
  • Cell count and median confidence — segmentation quality summary

Export

After spatial quantification, export links provide:

  • Cell spatial CSV — per-cell measurements
  • Region metrics JSON — compartment-level statistics

Links appear in the Spatial Metrics panel on the slide detail page.

Performance notes

Large WSI pyramids generate many tiles. Local development works best with region images (640×480 to 5000×5000 px) before scaling to full scanner exports.