Slide upload

Upload slides from the study home page (/areas/pathology/studies/{id}). Each upload creates one slide record and redirects to the slide detail page.

Upload flow

1. Select modality — whole-slide image, region image, TMA, or multiplex IF
2. Select stain type — H&E, IHC, IF, multiplex IF, or other
3. Optional sample ID — link slide to a cohort sample when known
4. Choose file — drag-and-drop or browse
5. Import — writes file to storage and creates the slide record

Supported formats

Format	Extension	Notes
PNG / JPEG	.png, .jpg, .jpeg	Best for local smoke tests and region images
TIFF	.tif, .tiff	Standard pathology scans
OME-TIFF	.ome.tiff	Open Microscopy Environment format
SVS	.svs	Aperio whole-slide format: uploads, but cannot be tiled yet
NDPI	.ndpi	Hamamatsu scanner format: uploads, but cannot be tiled yet
MRXS	.mrxs	3DHISTECH format: uploads, but cannot be tiled yet

Whole-slide scanner formats are stored on upload, but tile generation for them is not available yet (see File formats). Export a region as TIFF, OME-TIFF, or PNG from your scanner software or QuPath instead.

Validation

• File must be a readable image format
• Corrupt or unsupported files are rejected with an error message
• Dimensions and microns-per-pixel are detected when metadata is available

After upload

The slide appears in the study slides grid. Click it to open the slide detail page.

Next step: run Generate tiles before using the slide viewer or segmentation pipelines on large images.

Annotations

Import pathologist annotations from the slide viewer's Annotations panel after upload. Supported sources include GeoJSON and QuPath exports.

Annotations appear as overlays in the slide viewer once imported.

Sample metadata

Optionally link the slide to a cohort sample at upload, or import a batch of samples at once from the study Cohort page (POST /pathology/studies/{id}/samples/import) with a CSV of external_id plus optional clinical and group-label columns.

For full format specifications, see File formats.