Getting Started

CellProfiler is free, open-source software for quantitative analysis of biological images. No prior experience in programming or computer vision is required - this page is intended to help you get up and running. If you find these tools helpful, please remember to cite our work to help keep the project funded.

Manuals

CellProfiler	2.0	1.0
CellProfiler Analyst	2.0	1.0

Tutorials

Get started quickly using one of our tutorials introducing you to the features of CellProfiler and demonstrating how to set up your first pipeline. Once you understand the basics, our advanced tutorials will help you learn to optimize settings.

Examples

Download an example pipeline that you can load in CellProfiler to see how it works. The examples page also has a guide to choosing the right example pipeline to modify for your images. For CellProfiler Analyst, download an example data set and configuration file so you can become familiar with the data exploration and machine-learning tools.

Frequently Asked Questions

Find answers to frequently asked questions about CellProfiler.

Online Forum

Still have questions? Post your problem in our forum to get an answer from our image assay developer team or from the larger CellProfiler community.

Still stuck? The Broad Institute Imaging Platform is available for non-profit consulting on challenging image analysis and data mining projects. Learn more and contact us via the Carpenter lab website to explore a collaboration.