This repository hosts notebooks to display microscopy images, videos, as well as image processing and analysis results in a jupyter notebook. These notebooks may be served via nbinteract.
The recommended environment for running image-dashboard is anaconda. The following assumes you have anaconda3 installed and the conda executable is in your $PATH.
After cloning the repo, create a conda environment with
conda create -p ./env
Activate the environment:
conda activate ./env
Install image-dashboards dependencies:
conda install --file requirements.txt
Finally, install image-dashboard into the newly created environment. If you want to develop image-dashboard, add the -e flag. In this way, changes to the image-dashboard sources will be reflected in the installed package:
pip install -e .
That's it.
Active the conda environment:
conda activate ./env
Start your local jupyter notebook server:
jupyter notebook
From the jupyter dashboard, open one of the existing notebooks in notebooks/ or create a new one. If you want the notebook to become part of the repository, don't forget to
git add path/to/new/notebook.ipynb
git commit path/to/new/notebook.ipynb
Please consider working in a forked repository and create merge/pull requests.