CellProfiler is free, open-source software designed to enable biologists to quantitatively measure cell phenotypes from thousands of images. CellProfiler can automatically find all the cells within a given image and measure parameters from each cell. De Novo Software has teamed up with the developers of CellProfiler to allow analysis of high throughput imaging data in FCS Express. Once your data is properly exported from CellProfiler, FCS Express can import the data and allow visualization of your data set with all of our familiar 2D plots and new plotting features such as picture plots and heat maps.

  In the first two sections of this tutorial you will learn:

•How to export CellProfiler data from a 96 well plate imaging experiment.

•How to import the data into FCS Express.

Note: This tutorial will not focus on how to create and use pipelines in CellProfiler; please refer to CellProfiler manual for extensive information in building pipelines. The focus of this tutorial will be how to modify an existing pipeline in CellProfiler 3.0 in order to export the data in a format that FCS Express can read. If you are using CellProfiler 2.2 or earlier, please visit this page and download the 3.0 release and follow the steps outlined here in this tutorial.

 

 

 

First, we will setup to export 96 well data from CellProfiler.