ApplyThreshold module

Hi,

My images contain both speckles which is what I am interested in, and dead cells which I would like to threshold out. Unfortunately, the speckles are within the same intensity range as the dead cells and therefore I cannot simply threshold based on an intensity level. However, the dead cells are much larger than the speckles so I could theoretically threshold based on intensity and area. Is there a way to do this in CellProfiler?

Thanks,
Lin

Hi Lin,

Have a look at the FilterByObjectMeasurement module. For a given set of objects with a prior measurement, you can filter the objects based on that measurement (i.e, min and/or max allowable value).

One note: The filtered objects are a new set of objects, so you have to perform measurements on the new ones if you want to perform additional rounds of filtering based on another measurement; you can’t use the original objects and filter on two measurements simultaneously.

Regards,
-Mark

Hi Mark,

Thanks for your reply. Is there a way that I can threshold or filter the pixels of particular objects out, and then use the rest of the image for processing/segmentation? The problem is that I don’t simply want to filter objects by measurement because I’m not interested in calculating measurements only for the unfiltered objects, but for the rest of the image (the non-thresholded pixels).

Thanks again for your help!
Lin

Hi Lin,

If the objects that you want to get rid of are light (i.e., high intensity) on a dark (i.e, low intensity) background, have you considered using ImageMath to invert the image intensity, and running IdentifyPrimAutomatic on the result? That way, instead of thresholding the objects, you are thresholding everything else, and you end up with an object(s) that excludes the image regions you don’t want. Just remember to turn off ‘Fill holes’ in the IdentifyPrimAutomatic module, and turn off declumping if necessary.

Regards,
-Mark