Samples of images segmented by Cellpose Classical segmentation with PartSeg#

By Kasia Kedziora 🔬

Learning Objectives#

In this lesson, you’ll learn how to use and configure the PartSeg plugin in napari to complete a classical segmentation workflow.

  1. An introduction to classical segmentation

  2. Detecting and segmenting nuclei as individual objects

  3. Detecting and segmenting foci as individual objects

  4. Quantifying segmentation regions based on your masks

  • Time to learn: 1 hour

Prerequisites#

Napari version and plugins

Importance

Notes

napari v 0.4.17

Mandatory

Tested with this napari version. Verify your version by going to the Help menu and choosing napari info.

PartSeg v 0.14.6

Mandatory

Install this plugin from within the napari viewer, by going to the Plugin menu, then clicking on Install/uninstall plugins. Search for PartSeg and click install.

Napari-segment-blobs-and-things-with-membranes v 0.2.22

Mandatory

Install this plugin from within the napari viewer, by going to the Plugin menu, then clicking on Install/uninstall plugins. Search for Napari-segment-blobs-and-things-with-membranes and click install.

Sample data

2D data used in lesson

Optional

What is a classical segmentation pipeline?#

A classical segmentation pipeline is built around a thresholding algorithm to detect objects with intensities that vary from their surrounding background. It can be divided into 3 main parts:

  • preprocessing: preparation of images for thresholding (e.g. filtering to remove noise).

  • thresholding: finding an intensity value that separates objects from the background.

  • postprocessing: a set of operations designed to refine the shape of detected objects.

Video introduction to classical segmentation#

Supporting materials#