Bio-Image Analysis with napari

In this course, we will explore ways to analyze and visualize microscopy images with napari, an nD viewer open-source software.

We explore some napari plugins as an interactive and convenient way of performing these analysis, especially the napari-assistant, napari-apoc and napari-clusters-plotter plugins.

We will also perform feature extraction using napari-skimage-regionprops, plot features against each other, and perform a multichannel analysis, where we measure summary statistics of objects in one channel relative to objects in another channel.

All the plugins mentioned above are part of the devbio-napari plugin bundle, which is a collection of plugins for developmental biology image analysis.

Some Jupyter notebooks will be used to illustrate and reproduce the examples.

For this, we will be installing our packages in a conda environment. Please follow the instructions below.

Getting started with Miniforge and Python

Please follow the instructions from this blog post written by Mara Lampert, updated by Stefan Hahmann and by Mara Lampert again under CC BY 4.0 License to install Miniforge on your computer.

Cloning the repository

Clone this repository to your computer (go to the repository page on GitHub here, click the green button Code and choose one option to clone it). The most straight-forward way is to download it as a .zip file. If you do that, unzip the repository in a folder of your choice and remember where you placed it.