Introduction to CellProfiler, Free Open-Source Software for Image Analysis

The Presenters

Beth Cimini and Kyle Karhohs
Broad Institute of Harvard and MIT

Session Summary

Microscopy experiments have proven to be a powerful means of generating information-rich data for biological applications. From small-scale microscopy experiments to time-lapse movies and high-throughput screens, automatic image analysis is more objective and quantitative and less tedious than visual inspection. This course will introduce users to the free open-source image analysis program CellProfiler and its companion data exploration program CellProfiler Analyst. We will show how CellProfiler can be used to analyze a variety of types of imaging experiments. We will also briefly discuss the basic principles of supervised machine learning with CellProfiler Analyst in order to score complex and subtle phenotypes.

Session Outline

• Basics of image analysis.
• Methods of distinguishing objects of interest from the image background.
• Methods of separating clusters of touching objects.
• Obtaining measurements from the cell.
• Exporting measurements and images.

CMLE Credit: 1.0