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Introduction to image analysis with Python

This tutorial provides several Jupyter notebooks that together provide an introduction to understanding image data with Python.

Running the notebooks requires:

  1. Either installing Jupyter directly, or through Docker (see details below).
  2. Getting the sample data file (again see below).

Running the notebooks directly

Firstly install Jupyter. There are some instructions here.

To get the data file used in the examples, download from Figshare then unzip the file. You'll need to alter the path to the Hypocotyl.czi file within the Jupyter notebooks to wherever you put the file.

## Running the notebooks with Docker

You can also run Jupyter in a self contained environment called Docker. To do this:

  1. Install Docker.
  2. Run the build script build_docker_image.sh
  3. Run the docker image with docker run -d -p 8888:8888 dtp2017
  4. Open a web browser and point it at http://localhost:8888