Bio-Image Analysis with napari

In this workshop, 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-flim-phasor-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.

Finally, we will analyze higher dimensional FLIM data with the napari-flim-phasor-plotter plugin.

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

For this, we will be using different 3 environments. Please follow the instructions below.

Getting started with Miniforge and Python

If you are attending this course in presence, most of these environments will be already set up for you. Skip to Third environment: napari-flim-phasor-env to update the last environment.

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

First environment: napari-intro-env

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 being downloading it as a .zip file). After that, open a terminal, navigate to where you cloned the repository locally in your computer and create a conda environment by running:

mamba env create -f environment.yml

or

mamba env create -f https://github.com/BiAPoL/BioImage-Analysis-and-Data-Processing-Workshop-2024/raw/main/environment.yml

After successful installation, activate your environment with:

mamba activate napari-intro-env

Second environemnt: devbio-napari

Open a terminal and type (or copy the line below):

mamba create --name devbio-napari python=3.9 devbio-napari pyqt -c conda-forge -c pytorch

Hit ENTER to answer yes when asked to install packages. Activate your environment with:

mamba activate devbio-napari

Third environment: napari-flim-phasor-env

Open a terminal and type (or copy the line below):

mamba create -n napari-flim-phasor-env python=3.9 napari pyqt git

Hit ENTER to answer yes when asked to install packages.

Activate your environment with:

mamba activate napari-flim-phasor-env

Then install napari-flim-phasor-plotter with pip:

pip install napari-flim-phasor-plotter

Finally, include the devbio-napari bundle package with:

mamba install -c conda-forge devbio-napari=0.10.0 scikit-image=0.24.0