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.

The quickest way to get up and running with CellProfiler is to:

  1. Download CellProfiler.
  2. Launch it by double clicking. (Windows troubleshooting)
  3. The welcome screen pops up: choose the example pipeline (if you are connected to the internet) and run it.
  4. Find an example pipeline and images (here) that are similar to yours and run it.
  5. Adjust the pipeline to your own images.
  6. Post at the online forum if you have any trouble.