PyImageJ: Integrating ImageJ and Fiji with tools in the Python ecosystem

This repository houses the PyImageJ workshop from the I2K 2022 conference.

Quick start

Install git and conda, then run:

git clone https://github.com/imagej/i2k-2022-pyimagej
cd i2k-2022-pyimagej
conda env create
conda activate i2k-2022-pyimagej
jupyter notebook

For further details and other options, see next section.

Setup and Installation

1. Obtain the materials

git clone https://github.com/imagej/i2k-2022-pyimagej

Or use your favorite graphical git tool. Or download the tarball.

Remember where you put this i2k-2022-pyimagej directory!

2. Install prerequisites

We recommend using conda with PyImageJ. You can install it via the miniconda installer.

If you prefer to use plain pip, or pip with virtualenv, you will need to install the following things:

• Python 3.8
  • 3.9 works, but may not be compatible with some dependencies (ITK?)
  • 3.10 works in general, but you may encounter problems on Windows
• OpenJDK 8 or 11 – any flavor is fine; Zulu JDK+FX 8 works well
• Apache Maven

3. Install packages

• With conda:

  cd i2k-2022-pyimagej
  conda env create
  

• With pip:

  cd i2k-2022-pyimagej
  pip install -r requirements.txt
  

4. Open the notebooks

• With conda:

  conda activate i2k-2022-pyimagej
  jupyter notebook
  

• With pip:

  jupyter notebook
  

And then, in your web browser, click on the notebooks of interest!

Pitfalls and Troubleshooting

• DO NOT run your terminal as an administrator (Windows), or your conda or pip commands as sudo (Mac/Linux).