Microglia IBA1 DAB staining


I am trying to use CellProfiler to analyze the area including the cell body and processes (as separate measures) and shape of microglia. Currently we are using ImageJ to threshold these cells however, we don’t feel it is accuratre and we want something more automated. We attempted to create a CellProfiler pipeline but we were wondering if someone can help improve its accuracy. Right now only part of the processes are selected and some smaller stained regions are being selected as cell bodies. So we’d like to increase sensitivity for processes and decrease it for cell bodies.

I appreciate any recommendations
Thanks !

Pipline_Microglia.cpproj (417.8 KB)

This is another picture in the cortex.


While waiting for others to give more expert tips, you can try this pipeline, in which I made a series of “Smoothing keep edges” to make the neurites stand out of the background neurites.cpproj (643.8 KB)

Then I use EnhanceOrSuppressFeatures > Neurites > Tube size = 2.0 on one of the filter images.

After these enhancements, I first identify the bodies of microglials, and subsequently the neurite processes.

You may try to tune it for better result.

Good luck.

Thank you so much ! This is very helpful I appreciate the help !!


this might be useful