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 and the platform handles image processing. 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 detector is a research placeholder, and cell count depends on stain contrast and image resolution. More advanced detection models are planned.

WSI upload failed or format unsupported

SVS, NDPI, and MRXS files upload, but tile generation for them is not yet available: it needs the OpenSlide library, which is not installed, and full-size whole-slide images exceed the current tiler's memory limits. Export a region as TIFF, OME-TIFF, or PNG instead. See File formats.

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.