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 after upload via the metadata API (POST /pathology/slides/{id}/annotations/import). Supported sources include GeoJSON and QuPath exports.
Annotations appear as overlays in the slide viewer once imported.
Sample metadata
Optional sample_id on upload links the slide to a cohort sample. Full CSV sample import is planned — see products/pathology/plan.md Phase 4.
For full format specifications, see File formats.