Pathology quickstart
Run a whole slide image through tile extraction or tissue detection and download the results.
You want tile-level and tissue-level readouts from a whole slide image — a grid of quality-filtered tiles, a tissue mask and coverage percentage, or a matrix of deep-learning features. This runs digital pathology analysis over your histology data end to end: open the slide, run the workflow you pick, and hand back downloadable artifacts.
Before you start
Have your slide in the platform's workspace storage as an S3 URI — the tool reads it from there. Supported formats are SVS, TIFF, NDPI, and standard images (PNG/JPG). Decide which workflow you need (see step 2).
Step-by-step
Upload or locate your slide
Make sure the whole slide image is in workspace storage. You will reference it by its slide_url (an s3://… URI).
Choose a workflow
- tile_extraction (default) — cut the slide into tiles and keep the ones that pass tissue and blur filters.
- tissue_detection — segment tissue from background and measure how much of the slide is covered.
- feature_extraction — extract ResNet-50 features from each retained tile.
Submit the job
Ask for the analysis in chat, naming the slide and workflow. For example:
"Run tile extraction on my slide at s3://workspace/slides/case01.svs at 20x, tile size 256."
The orchestrator selects pathology analysis and fills in the parameters (see inputs).
Wait for processing
The job runs on GPU asynchronously and can take 10–60 minutes depending on slide size and workflow. A progress phase and heartbeat appear while it runs; large slides are processed tile by tile.
Read and download results
When the job completes, an intelligence card appears on the canvas with the headline numbers, and the artifacts land in workspace storage for download — a tiles.zip archive, a tissue_mask.png, or a features.npy file depending on the workflow. See outputs for the full result shape.
A worked example
You have an H&E slide and want a clean tile set for a downstream classifier:
- Upload
case01.svsto workspace storage. - Prompt: "Extract tiles from s3://workspace/slides/case01.svs at 20x magnification, tile size 256, tissue threshold 0.5."
- The tool grids the slide, drops tiles that are mostly background (
tissue_percentagebelow 0.5) or blurry (Laplacian variance below the blur threshold), and zips the survivors. - The card reports the tile count and slide dimensions;
tiles.zipis available to download and feed into feature extraction next.
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