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 5. 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:

Note: This tutorial will not focus on how to create and use pipelines in CellProfiler (please refer to CellProfiler manual for this topic). The focus of this tutorial will be on how to modify an existing pipeline to export the data in a format that FCS Express can read. .

 

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