How do I use ImageJ with FCS Express?

ImageJ is free open-source software designed to process and analyze images and image data sets. Through the use of macros and plugins users can automate tasks and create custom tools. De Novo Software has created macros and plugins for ImageJ that allow you to export your imaging data from ImageJ to FCS Express . 

Once your data is properly exported from ImageJ,  you can use FCS Express for 2D plot visualizations, Histograms, Gates (equivalent to thresholding), and advanced statistics and 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 your ImageJ data sets 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 ImageJ application examples below. Of course if you have any other questions you can contact our knowledgeable support team at

ImageJ Macros for FCS Express Image Cytometry Data Analysis

Application Examples

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