Using CellProfiler for Biological Image Analysis

Mark-Anthony Bray, Ph.D. will present a webinar Using CellProfiler for Biological Image Analysis. Mark earned his B.S. in biomedical engineering from Tulane University in 1996 and his Ph.D. in biomedical engineering from Vanderbilt University in 2003, followed by postdoctoral work in cellular bioengineering at Harvard University. In 2008, he joined the Imaging Platform at the Broad Institute as a computational biologist under the direction of Anne Carpenter. Using his biology and image assay development expertise, he is now involved in the adaptation of image analysis software to specific image-based screens.

Image-based screens increasingly require the use of automated microscopes which generates hundreds, if not thousands of images at a time. With such large image sets, automatic image analysis is more objective and quantitative and less tedious then visual inspection alone. This webinar is meant to instruct biologists in the use of CellProfiler, an open-source, freely-downloadable software package designed for analyzing such images via a user-friendly interface. Material will begin an introduction of CellProfiler, followed by details for the construction and use of a pipeline for analyzing typical image data. We will also include some of the more important considerations in cellular image analysis, by demonstrating the software on sample images as a realistic use case. Lastly, we will cover measurement export and preparation for additional analysis using  machine-learning tools.

At the completion of this tutorial, the attendee will have knowledge of the following:

  • Understand the basics of the CellProfiler environment;
  • Design a simple pipeline using the graphic user interface;
  • Test their pipeline and adjust the settings for optimal performance.


Who Should Attend:This tutorial is intended for beginners to quantitative cellular image analysis. No programming skills are required. However, basic knowledge of fluorescence microscopy and digital image acquisition is expected.


Seminar Information
Date Presented:
January 14, 2014 12:00 PM Eastern
1 hour, 15 minutes
Using CellProfiler for Biological Image Analysis
Speaker Information
Mark-Anthony Bray Ph.D.   [ view bio ]
Individual topic purchase: Selected
American Society for Clinical Pathology
CMLE: 1.00
This continuing medical laboratory education activity is recognized by the American Society for Clinical Pathology for 1 CMLE credit. ASCP CMLE credits are acceptable for the ASCP Board of Registry Certification Maintenance Program.
This Seminar is presented free of charge.