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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

Quick start

This walkthrough covers a region image from upload through tissue detection, segmentation, and spatial quantification.

1. Create a study

Click Create study. Enter a name (for example TME demo) and optional disease area or tissue type metadata.

2. Upload a slide

On the study page, choose modality and stain type, then upload an image file:

  • PNG or JPEG — best for local smoke tests
  • TIFF / OME-TIFF — standard pathology image formats
  • WSI formats — SVS, NDPI, MRXS (when OpenSlide is available locally)

3. Generate tiles

Click Generate tiles. Wait for the job to complete — the slide viewer loads with pan/zoom tile navigation.

4. Run tissue detection

Click Detect tissue. Review tissue fraction, focus score, and detected regions in the Tissue QC panel. A tissue mask overlay appears in the viewer.

5. Segment cells

Click Segment cells (requires tiles). Review cell count, model name, and mean area in the Segmentation Summary panel. Cell overlay and detected-cell table populate.

6. Spatial quantification

Click Spatial quantification (requires segmentation). Review overall density, infiltration phenotype, nearest-neighbor distances, and region metrics. Export CSV and JSON artifacts from the metrics panel.

Next steps