Pipeline for Wheat germ agglutinin staining




I’m new to Cellprofiler and I would like to set up a pipeline to measure cell area of cardiac cells in heart tissue using wheat germ agglutinin stain (WGA). I have saw some posts from the this forum and I get a pipeline for this. But, when I download the sample image and run the pipeline, it comes out with no information. The pipeline, the output file, and the sample image are enclosed below, would some one help with this? Many thanks!

By the way, my images are similar with the sample image that only one staining with green color in it.

FilteredCellsWGA.txt (489 Bytes)
WGA pipe modified.cpproj (441.2 KB)


Hello there,

Not sure if you already came across this discussion : Trouble identifying objects

Applying same method may give you a good start, for example: test.cpproj (639.9 KB)

You may have to play with the following adjustment to get better result:

  • object minimum/maximum size
  • size for smoothing filter
  • local maxima

Good luck.


Hi, thanks for the reply. This pipeline works quite good for me. But I am
wondering if this can be modified to analyze multiple images (say image1
for sample1, image2 for sample2…) , then output with an excel file with
cell size data.

I try to add two modules in it, the one is Measuresizeshape and the other
one is exporttospartesheet. It also works but not quite well…

Best Regards,


Hi there,

analyze multiple images (say image1 for sample1, image2 for sample2…)

Yes, certainly. You can just drag and drop images into the Images module.

then output with an excel file with cell size data.
add two modules MeasureSizSshape and Exporttospartesheet. It also works but not quite well.

Can you tell us more what doesn’t work? Because it’s exactly what we need to add.


Oh, hi, Minh,

Sorry for the late reply. I here attached one of my image that I can not
adjust the pipeline to get better results…would you please help? Many
thanks! I also attached the pipeline (This pipeline is quite good for my
other images)…

And I am wondering if that possible that the pipeline can measure the image
of WGA staining with DAPI in it? Many thanks!

Best Regards,

wga.cppipe (10.2 KB)



In your previous example picture, it was color. So example pipeline_v1 was aimed to use such color input.
However your actual image is grayscale, with higher solution, you should thus modify the pipeline accordingly wga.cpproj (129.6 KB)

For other question, we would encourage you to visit basic tutorials and FAQs, which are very useful for a first start.