raacampbell / at-image

registration playground code

Source

This was copied from Stelios's repo -> https://github.com/cajal/at-image.git

To extract

The function in the pipeline that runs a rigid, affine, and nonrigid slice to volume registration. should be here -> (https://github.com/cajal/pipeline/blob/55a68e7404490a730bddba6051ef51aaced76a4e/python/pipeline/stack.py#L1637)

at-image

image processing and registration utilities of the Tolias Lab

Requirements

• Install Docker and sign into the application. Check it works by typing docker version at the CLI.
• You will also need Docker Compose. This may have been installed with Docker. If so, docker compose version will return something. If not, visit the above link.

To deploy image and launch into jupyterlab:

1. clone repository
2. navigate to the deploy folder
3. in the deploy folder add an empty file called .env
4. in terminal run:

docker compose build jupyterlab

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

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