Measurements for Batch Processing




I processed a batch of four images yesterday using the basic earthworm pipeline to identify single nuclei and measure the intensity of Hoechst staining. At the end of the process I exported the data as an xls file, but the data exported seems to only be a summary and averages of all the objects identified in each image. Is there a way to extract the measurements for each object measured in a single image when batch processing? Thank you for your time.


Chris Roden


Are you sure that you have included a Measure module that measures something about the objects in your images (e.g. MeasureObjectAreaShape)?

If so, then when you export data using the DataTool “ExportData”, it will say “The following measurements were found: Image, Object”, except that instead of “Object” it will say whatever you have actually called your objects in the pipeline. Both should be checked by default. As long as the checkbox next to "Object "is checked, the exporting of individual object measurements should work exactly in the same way as the image measurements, which apparently you are already able to export. The Object measurements will be in a separate file from the image measurements.

Does this explain it?


Hi Anne-

Thanks for your help. I am using the Measure Intensity module in my pipeline so that was not a problem. When I unchecked the “Image” option when exporting data I was successful in getting an xls file with all of the individual measurements broken down per image analyzed. When leaving both the “Image” and “Option” boxes checked I only get one xls file with a summary of averaged intensity measurements for and entire image (so only one measurement per image). I was expecting that when both boxes were checked that an xls file would be exported with two worksheets. I’m not sure if this is how the program is designed to work, but nonetheless I’ve figured out how to get what I need.



Hi Chris,

What version of CellProfiler are you using? I can’t seem to reproduce the error. You are using the pipeline which is posted in the Examples section?


P.S. As you suggested, the program normally creates a separate excel file for everything which is checked.