CellProfiler – practical

Trainer: Beth Cimini, Le Liu, Paula Llanos, Esteban Miglietta, Suganya Sivagurunathan, Shatavisha Dasgupta and Callum Tromans-Coia

Overview:  In this exercise, you are given a subset of the data from IDR and a partially completed CellProfiler pipeline; you must create a pipeline that finds and measures several organelles and the entire cell body. You will gain experience tuning a pipeline that can cope with not only different cell phenotypes but also images of empty wells, blurry wells, debris, and other real-world potential screen confounders.

Learning outcomes:

After this section you should be able to:

• Create a pipeline that finds and measures several organelles and the entire cell body
• Tune a pipeline that can cope with not only different cell phenotypes but also images of empty wells, blurry wells, debris, and other real-world potential screen confounders

Materials:

• This tutorial can be accessed at https://tutorials.cellprofiler.org/ under the heading “Beginner Segmentation”