Combining ImageJ and Fiji with tools in the Python ecosystem

This repository houses the PyImageJ workshop from the I2K 2020 conference.

Quick start

Install git and conda, then run:

git clone git://github.com/imagej/i2k-2020-pyimagej
cd i2k-2020-pyimagej
conda env create
conda activate i2k-2020-pyimagej
jupyter notebook

For further details and other options, see next section.

git clone git://github.com/imagej/i2k-2020-pyimagej

Remember where you put this i2k-2020-pyimagej directory!

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, that is OK too. In that case, you will need to install the following things:

With pip:

cd i2k-2020-pyimagej
pip install -r requirements.txt

With conda:

conda activate i2k-2020-pyimagej
jupyter notebook

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

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

Name		Name	Last commit message	Last commit date
Latest commit History 40 Commits
example_images		example_images
.gitignore		.gitignore
01-Introduction.ipynb		01-Introduction.ipynb
02-Interactive-ImageJ-GUI.ipynb		02-Interactive-ImageJ-GUI.ipynb
03-Reading-and-Writing-Images.ipynb		03-Reading-and-Writing-Images.ipynb
04-Multidimensional-Images.ipynb		04-Multidimensional-Images.ipynb
05-Macros-Plugins-and-Scripts.ipynb		05-Macros-Plugins-and-Scripts.ipynb
06-Visualizing-Large-Images.ipynb		06-Visualizing-Large-Images.ipynb
07-Under-the-Hood.ipynb		07-Under-the-Hood.ipynb
08-napari.ipynb		08-napari.ipynb
09-Insight-Toolkit.ipynb		09-Insight-Toolkit.ipynb
10-Tips-Tricks-Troubleshooting.ipynb		10-Tips-Tricks-Troubleshooting.ipynb
11-Converting-Between-Image-Types.ipynb		11-Converting-Between-Image-Types.ipynb
README.md		README.md
environment.yml		environment.yml
requirements.txt		requirements.txt