PathoLens

Overview

• PathoLens is a work-in-progress pathology tooling repo that bundles:
  • wsi-viewer-local: a lightweight Flask Web UI and backend for viewing WSIs (via OpenSeadragon) and proxying DICOMweb. It includes a MedSigLIP prediction endpoint as a component.
  • path-foundation-demo: a stripped, static copy of Google’s Path Foundation demo assets for reference. All Git history and attributes have been removed.
  • data/: local storage for large WSI files (e.g., .svs). These are ignored by Git.

Repo Layout

• wsi-viewer-local/: Viewer service with Dockerfile, simple server, example scripts, and tests.
• path-foundation-demo/: Self-contained demo (static artifacts + minimal server).
• data/: Place your .svs files here for local experiments (ignored by Git).

Quick Start: WSI Viewer

Option A: Local virtualenv

1. Create and activate a venv

   cd wsi-viewer-local python3 -m venv .venv source .venv/bin/activate

2. Install dependencies (note: downloads PyTorch/Transformers; this is large)

   pip install -U pip pip install -r requirements.txt

3. Run the server

   Optional: set a DICOMweb endpoint to proxy

   export DICOM_SERVER_URL="http://localhost:8042/dicom-web"

   export PORT=8081 python server.py

4. Open the UI

   • Shell page: http://localhost:8081/
   • OpenSeadragon demo: http://localhost:8081/osd

Option B: Docker

From repo root or from wsi-viewer-local/:

docker build -t patholens-viewer ./wsi-viewer-local docker run --rm -p 8081:8081
-e PORT=8081
# Optionally, to proxy an Orthanc DICOMweb # -e DICOM_SERVER_URL=http://host.docker.internal:8042/dicom-web
patholens-viewer

Smoke Tests

The smoke tests validate that the viewer server starts and serves local pages without external dependencies (model downloads, Orthanc) using Flask’s test client.

cd wsi-viewer-local

If you created the venv above:

. .venv/bin/activate python tests/server_smoke.py

Orthanc and DICOM Data (optional)

• An example Orthanc setup is included under wsi-viewer-local/orthanc/ (with docker-compose.yml).
• Scripts to convert WSIs to DICOM and import them are under wsi-viewer-local/scripts/.
• Once Orthanc is populated, set DICOM_SERVER_URL for the viewer, then exercise the /predict endpoint using examples/ in the same folder.

Notes

• Large WSI files (.svs, .tiff) are ignored by Git and should be placed in data/.
• The path-foundation-demo folder is included without its original Git attributes/history, per request.