This project accompanies the course given by the Science IT Support unit at Bern University.
It contains as series of Notebooks exposing how to do mostly basic and some advanced image processing using Python. It uses standard packages (Numpy, Maplotlib) and for the image processing parts is heavily based on the scikit-image package.
Most of the examples datasets are biology microscopy images taken from open repositories and can be downloaded using the Data_setup_local notebook.
One can install all necessary packages manually. However we provide some information to facilitate the installation of all parts (for UNIX machines) in the Instructions_local.md guide.
The course is originally run using a JupyterHub based on The Littlest JupyterHub and installed on a switchEngine. We also give instructions to create such as JupyterHub in the Instructions_SwitchEngine.md guide.