Cell geometery

cellprofiler

#1

I would like to ask how I can measure cell geometry, cell volume or size. Looking forward to hear back from you.


#2

Hi,

You’re in luck; CellProfiler is fully capable of doing most of that. Probably not cell volume just yet, since that would probably involve a 3-D stack of images. But it can certainly do the rest.

I suggest trying out some of the example pipelines and data that you can obtain from our webpage: cellprofiler.org/examples.htm. In particular, the “Human cells” and “Fruit fly cells” include cellular morphological measurements, i.e., geometry and size.

The key modules of the pipeline that you would want to take a closer look at are the IdentifyPrimAutomatic module (for identifying the cells) and the MeasureObjectAreaShape module (for measuring the morphology of the cells previously identified). Since you can define “geometry” in several different ways, you would need to decide which morphological parameter is appropriate for your situation. Fortunately, MeasureObjectAreaShape quantifies a variety of them (such as area, perimeter, etc) and you can take your pick.

I hope this gets you started. Let us know if you have more questions.
-Mark