Awesome

neuroglancer-docker

The project is a docker image for the neuroglancer project so that neuroglancer python interface can be more easily deployed in a production environment. A demo video with over 1GB of PETCT imaging data can be seen here

Getting Start

Binder

You can use a prebuilt image on binder inside Jupyter Notebook or Jupyter Lab

Notebooks

Docker

Building the Image

In the main directory of the project you can run

docker build -t 4quant/neuroglancer .

To build the docker image with the tag 4quant/neuroglancer

Running the image

To just run the image in the default mode (notebook), you simple type

docker run -i -p 8989:8989 -p 8888:8888 -t 4quant/neuroglancer

Running with the notebooks saved locally (instead of lost inside docker)

docker run -i -p 8989:8989 -p 8888:8888 -v $PWD/notebooks:/home/neuroglancer_user/local_notebooks -t 4quant/neuroglancer

Running with local notebooks and data

In this case the data is located in the current directory in a folder called data but this can be changed to anything

docker run -i -p 8989:8989 -p 8888:8888 -v $PWD/notebooks:/home/neuroglancer_user/local_notebooks -v $PWD/data/:/home/neuroglancer_user/local_data -t 4quant/neuroglancer

Note

If you have not built the image locally it will be downloaded from docker hub.

You can then navigate to http://localhost:8888 and you will be taken to the notebook interface where you can run a demo by simply running the blocks in the SimpleNumpyDemo notebook (inside the notebooks directory)

Run the notebook interface

docker run -i -p 8989:8989 -p 8888:8888 -t 4quant/neuroglancer jupyter notebook --ip='0.0.0.0'

Run just the python demo

docker run -i -p 8989:8989 -t 4quant/neuroglancer python -i docker_demo.py