There are two ways either you can import directly values by using the software of yours or you can do manually. Since I am using the latest version of FloJo, it creates a file directly, you go to the preference logo and from there you can do all these calculations precisely and with fool poof. Hope my answer solves some of your problems...

If you put all your .fcs files in Flowjo's "workspace" (the main window) corresponding to each time point, you can then select them, click the "statistic" button (usually the icon is the greek letter epsilon) and add the mean fluorescent intensity (or median, whatever you want).

Then, to export this in an excel sheet, you can click on the "table editor" icon and drag and drop the statistic corresponding to one of your time points from the workspace to the table editor. Then, in the table editor, click on "create and view table" and it will generate a table of all your results that you can export as a .csv file or as an excel file.

I hope it works, there might be some differences between different versions of FlowJo but the method is generally the same.

Hello Lukas,

I'm a tech support specialist for FlowJo LLC. Can you tell me which version of FlowJo you are currently using? For FlowJo v10, Julien Verdier points one very effective and quick way to export statistics such as mean, mode, count, and other useful stats. However, you can export a CSV or FSC 3.0 file w/ channel values or scale values by right-clicking on the Export/Concatenate feature. Also, you can export a histogram by setting up a univariate histogram and using the Copy Histogram Function in the Edit menu, the data would be stored in your clipboard. 

Of course, if you let us know the version then we can tell you how to export the fluorescent intensities of a range or gate. 

Best regards,

Miguel Velazquez-Palafox

FlowJo Technical Support