How do I use CellProfiler Data with FCS Express?

CellProfiler is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. De Novo Software has partnered with CellProfiler to allow compatibility with FCS Express. Your image analysis data generated in CellProfiler can be directly exported to FCS Express for further analysis and report generation. FCS Express Image Cytometry Data Analysis Features utilize the FCS Express Flow Cytometry data analysis tools as a backbone. This allows you to quickly and easily analyze and display any number of parameters that define your measured phenotypes.

With FCS Express you can make use of numerous 2D plot visualizations, Histograms, Gates (equivalent to thresholding), and advanced statistics to move between images, plots, and cell galleries to get information on populations, sub-populations, and even the single cells.

The best way to see what FCS Express can do for you is to download a free 30 day trial of the software. You can also watch our short videos and recorded webinars to learn about specific topics, or explore data yourself with one of our many CellProfiler application examples below. Of course if you have any other questions you can contact our knowledgeable support team at

Application Examples

FCS Express can be used to organize, analyze, and get results from any imaging experiment. By using CellProfiler to segment your images you can analyze the simplest single image experiments to complex multi-time point and multi-color assays in FCS Express. See for yourself while learning FCS Express Image Cytometry with our CellProfiler Export tutorial. You may also explore the layout using the free FCS Express ReaderNuclear Translocation Assay with CellProfiler Segmentation .



Previous Do you offer image segmentation or image analysis?
Next How do I use ImageJ with FCS Express?