at-image

image processing and registration utilities of the Tolias Lab

Requirements

• Docker link
• docker compose link

To deploy image and launch into jupyterlab:

1. clone repository
2. navigate to the deploy folder
3. in terminal run:

docker compose build jupyterlab

On the first time it will take several minutes to download the Docker image and build.

4. in the deploy folder add an empty file called .env

5. Optional

   In the .env file the following environment variables can be added:

    `JUPYTER_PORT_CONTAINER=8888` # desired port w/o this variable the default is 8888
    `JUPYTER_PASSWORD=some password` # desired password for jupyterlab
   

6. in terminal run:

docker compose up -d jupyterlab

7. In browser, navigate to localhost:8888 or to whatever port set with JUPYTER_PORT_CONTAINER if changed from the default