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
- Select modality — whole-slide image, region image, TMA, or multiplex IF
- Select stain type — H&E, IHC, IF, multiplex IF, or other
- Optional sample ID — link slide to a cohort sample when known
- Choose file — drag-and-drop or browse
- 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 (requires OpenSlide) |
| NDPI | .ndpi | Hamamatsu scanner format |
| MRXS | .mrxs | 3DHISTECH format |
Very large WSI files may require extended upload time locally. Start with region images or downsampled fixtures for development.
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.