CellProfiler: Table of contents

CellProfiler cell image analysis software

Created by
Anne E. Carpenter and Thouis R. Jones

In the laboratories of
David M. Sabatini and Polina Golland at

And now based at

CellProfiler is free and open-source!

If you find it useful, please credit CellProfiler in publications

Cite the website (www.cellprofiler.org)
Cite the publication (check the website for the citation).
Post the reference for your publication on the CellProfiler Forum (accessible from the website) so that we are aware of it.

These steps will help us to maintain funding for the project and continue to improve and support it.

Using CellProfiler

Introduction
- Why Use CellProfiler
- New Features in 2.0
Using CellProfiler
- Navigating The Menu Bar
- Using Module Display Windows
- Setting the Preferences
- How Data Is Handled
- How To Build A Pipeline
- Before The Analysis Run
- Testing Your Pipeline
- Troubleshooting Memory and Speed Issues
- Other Features
  - Batch Processing
  - Running Multiple Pipelines