EM analysis tutorial

Overview

This tutorial shows how to perform and analyze image segmentations in volume Focused Ion Beam Scanning Electron Microscopy (FIBSEM) data. This workshop will take you through the basics of bioimage analysis in Python and napari. We will be performing some analysis on segmented mitochondria using a combination of napari, empanada, and napari-clusters-plotter.

Goals

The aim of this workshop is to provide an introduction to bioimage analysis in Python and napari. By the end of the workshop you should be able to

• use napari as an image viewer

• perform interactive analysis with napari in a jupyter notebook

• make use of the napari plugin ecosystem

Pre-tutorial setup

So that we can best utilize our time together, please do the following before arriving at the tutorial:

1. Install napari and dependencies. Instructions here.

2. Download the notebooks and launch jupyter notebook. Instructions here.

Tutorial instructions

1. Do the introduction to viewing images in napari (part_0_viewer_intro.ipynb).

2. Segment and measure mitochondria using the cellpose plugin (part_1_segment_and_analyze_mitochondria.ipynb).