Image cytometry export and importing to FCS Express

Hi there,

I have posted this with DeNovo Software, but thought I would also try my luck here.

I’ve been evaluating FCS Express 4 Flow plus Image (details below) in conjunction with CellProfiler.

In particular, I’ve been trying to export from CellProfiler/import to FCS Express. I have followed the instructions at for exporting/importing single image numeric data ( … export.htm) but in the “Open 2D Plots” dialog in FCS Express, when I load my data (.cpout file), no parameters appear in the X- and Y-axis parameter lists. If I try to open the Tutorial Sample Data, the data loads fine and any parameter can be plotted.

I have tried using my own pipeline in CellProfiler as well as using the Tutorial Sample pipeline and modifying the filenames, etc. to fit my data. Yet this still does not work. I have also manually inspected the output (.cptoc and .cpout) files and compared them with the Tutorial Sample Data, and can find no major discrepancies.

If you have any information or suggestions for me to get FCS Express to load my data, please let me know, as we would like to evaluate FCS Express’ image cytometry capabilities and so far have not been able to get it to accept our data.

I will attach 2 example output files.

Version number: 4.00.0054
Serial number: Serial number: 25872
Layout version number: 514
Multicycle version 328-4.2.2011 is installed
Import BD FACSDiva™ Experiment Files enabled
Accuri Import enabled
Proliferation analysis enabled
Your configuration file is C:\Documents and Settings\All Users\Application Data\De Novo Software\FCS Express 4 Plus Research\FCSExpress4PlusDemoResearchDiva25872.config

Drew (853 KB)

Got it sorted guys. Problem was that my regular expression was extracting metadata from the filename and assigning it to a field called “Well”, while I was exporting single image (not multiwell plate) data. Technical support at DeNovo Software tells me “The words Well, Row, Column, Row, and Col prompt FCS Express to look for certain types of data” so it looks like they are reserved and shouldn’t be used.


Good to hear it got sorted out. Hopefully, they’ll update their documentation accordingly to avoid this issue in the future.