Access object area data

cellprofiler

#1

Hello,

Can anyone tell me how to access the data generated by the MeasureObjectAreaShape module? I need to know the area of my objects, but the only data that seems to be stored about my objects for export is their location.

Thanks!
Jo


#2

Hello,
There are 2 ways of exporting your results of the measure modules (in your case, MeasureObjectAreaShape). If you have already run your pipeline, you can use the DefaultOUT.mat file to export your results by openning CellProfiler, clicking on the menu “Data Tools”, then “ExportData.”

Alternatively, you can add the module “ExportToExcel” to your pipeline. Then, select the object you would like to export.

Both methods will export your data to an Excel file.

~martha


#3

I had been using the ExportToExcel module, but it was only exporting the location of the colonies. I inserted another MeasureObjectAreaShape module after my FilterByObjectMeasurement for another purpose and got the desired result:

IdentifyPrimAutomatic
MeasureObjectAreaShape (original)
FilterByObjectMeasurement
MeasureObjectAreaShape (second copy)
ExportToExcel

Just out of curiosity, why is it necessary to remeasure the objects after they’ve been filtered? I had assumed that once they had been measured the data attached to each object was associated with it from then on, even if other objects from its group had been filtered out. Or is it a matter of module placement (i.e. must the export module directly follow the Measure module of interest?).

Thanks for the quick response,
Jo


#4

Hi Jo,
Yes, you need another MeasureObjectAreaShape module after the FilterByObjectMeasurement because the objects are renumbered once you remove objects. Alternatively, you could always perform post-processing of your data outside of CellProfiler (for example, in a database).

~martha