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Getting Started with MicroMap

This project is about viewing and annotating digital pathology slides. At the moment, it only relies on the openslide python API for the slide serving and the coordinates system.

Install and run instructions

Edit env file

In the .env file, change the SLIDES and ANNOTS variables to point to your slide and annotation folders. Change the REACT_APP_PORT and REACT_APP_FLASK_SERVER_PORT to available ports (they need to be different).

Untested: Change the REACT_APP_FLASK_SERVER_IP to the ip the server is running on. Anything else than 0.0.0.0 (local access) is untested and may not work as intended. If the server is running remotely, putting the ip address of the remote server should work.

Run the dockers

Make sure you have docker and docker-compose installed.

From the main directory (MicroMap), run docker-compose up. The app and server should build and start.

Connect to the app

On your web browser, connect to http://APP_IP:REACT_APP_PORT/ where APP_IP is the ip of the machine app is running on. REACT_APP_PORT is the same as defined in the .env file.