The Image Analysis Field Guide

Essential toolkit to get started in scientific image analysis.

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Installation

Install the packages required to build the book:

pip install -r requirements.txt

If you want to execute the notebooks, install the scientific packages listed in the notebooks/ folder (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

Build and run with docker

Build the image (for the given URLs of your site and JupyterHub):

docker build \
  --build-arg NOTION_KEY=$NOTION_KEY \
  --build-arg DEPLOY_URL=http://localhost:8080/ \
  --build-arg JUPYTERHUB_HOST=localhost \
  --build-arg JUPYTERHUB_PORT=8000 \
  -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