How to export to excel?


Hi, team
my Question: after run the pipeline for 10cycles, why I open the Excel file, the only measurements I see are for the last image set (i.e., cycle) processed?
my pipeline are:
identifyPrimAutomatic(for blue)
identifyPrimAutomatic(for red)
identifyPrimAutomatic(for green)
identifysecondary(for blue and red)
identifysecondary(for blue and green)
MeasureObjectAreaShape(for B/R/G area)
MeasureObjectintensity(for red)
MeasureObjectintensity(for green)



For your experiment, are looking at measurements generated for each image (per-image, e.g, in a file called DefaultOUT_Image.xls) or generated for each object in an image (per-object, e.g, in a file called DefaultOUT_Nuclei.xls, or whatever your objects are called)?

If the measurements you are examining are per-image, then this would be odd behavior, since it should show at least an image number (if not more) for each image set.

If they are per-object, then this behavior can occur if no objects are being found in the “missing” images. You may want to generate a per-image spreadsheet (if you haven’t already), and look at the object count under a column called “Count_” (where is the object in question). If those counts are zero for the image sets 1 through 9 and non-zero for the 10, you may want to check that your objects are being identified correctly.

Hope this helps!


Dear Mark
After I fellow your replay, I have got each output excel files and 1 to 10 set were show in them.
Every time I run this pipeline only can see the data in windows, these “DefaultOUT_****.xls” were never be export before.
I don’t know why…maybe some problem with my PC…
now I can get every data which I want to export, thank you!!!


Hello All

Im a newbie to CellProfiler, I have Windows version 10997 while our collaborator runs a Linux version v11248. He has ability to change the output parameters in the “ExporttoExcel” pipeline, while we in windows do not have the ability to modify the parameters we want to export into excel, and therefore we get alot of unnecessary info at this early point of using the software. Is there a latest version of windows Cellprofiler where we have the same “ExporttoExcel” pipeline sheet in windows as our collaborator has in Linux?


Both these versions should be able to do the same thing. If you check the box next to “Select the columns of measurements to export,” a new button will appear allowing you to specify the measurements you want written out,