Skip to content
main
Switch branches/tags
Go to file
Code

README.md

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.

Setup and Installation

1. Obtain the materials

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

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

Remember where you put this i2k-2020-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, that is OK too. In that case, you will need to install the following things:

3. Install packages

  • With conda:

    cd i2k-2020-pyimagej
    conda env create
    
  • With pip:

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

4. Open the notebooks

  • With conda:
    conda activate i2k-2020-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).

About

Workshop materials for "Images to Knowledge with ImageJ and Friends" 2020 conference

Resources

Releases

No releases published

Packages

No packages published