The Image Analysis Field Guide

Essential toolkit to get started in scientific image analysis.

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Installation

Option 1: Install and build the Jupyter book website locally

Install the packages required to build the jupyter book website:

pip install -r requirements.txt

Install the scientific packages required to run the notebooks:

pip install -r jupyterhub/sections/spawn-image/requirements.txt

Build the Jupyter book:

jupyter-book build src/

Then, drag and drop _build/html/index.html in a web browser.

To check external links:

jb build src --builder linkcheck

Option 2: Build and run with docker

Build the image:

docker build --build-arg NOTION_KEY=$NOTION_KEY -t $(whoami)/$(basename ${PWD}) .

Run the jupyter book in a container on http://localhost:8080/.

Quick test:

docker run --rm -it -p 8080:80 $(whoami)/$(basename ${PWD}):latest

Persistent:

docker run -dp 8080:80 --name image-analysis-field-guide $(whoami)/$(basename ${PWD}):latest

Set up a JupyterHub and link it to the site

We provide a configuration to set up and run a JupyterHub for users and contributors. The JupyterHub can be linked to the website via the jupyterhub_url parameter in _config.yml. Users can run notebooks in the Jupyter Hub environment via the launch icon.

Build and run the JupyterHub

From the jupyterhub/ directory:

docker compose up -d

This command will

• Build the [./jupyterhub/spawn-image/Dockerfile](spawn image).
• Build the [./jupyterhub/Dockerfile.jupyterhub](JupyterHub image).
• Run the JupyterHub on http://localhost:8000/.

Our JupyterHub configuration is derived from JupyterHub Imaging.