Delete mode in EditObjectsManually module

Hello!

I am having some trouble with the delete mode in the EditObjectsManually module. I am simply identifying cells that are roughly circular & fluorescent so it is quite simple to detect using IdentifyPrimaryObjects (and I’m happy with the results I am getting). However, I have some images that are catching some noise from the edges of the image which is contaminating the results with undesired objects that are not circular. I tried the EditObjectsManually module, but the Delete Mode (hotkey ‘X’) does not seem to be working on my end. That means I need to manually click on all of the objects, which works but takes a very long time.

Any idea of how to:
a) Use the Delete Mode ? I am able to form a rectangle using the left mouse but when I release it nothing happens to the objects that were in that rectangle
b) Discard objects based on the shape (ie: not circular) ?

I’ve attached an image showing on the right the circular shapes I’m happy with and on the left those I want to remove from the count.

Thanks in advance for your help!
Hugo

cellprofilerhelp

Hi @hsinha,

Regarding the second part of your question, you could use the MeasureAreaSizeShape module to measure these objects and then FilterObjects to apply a filter based on those measurements. Since your objects are so different in shape, I think that it should be pretty easy to discard them, perhaps by using the Width or Eccentricity features. If you want to explore what values different types of objects have, DisplayDataOnImage can be very handy. If a single measurement can’t discriminate between your true objects vs background, you could use CalculateMath to calculate a length / width ratio, which would almost certainly be different for true objects vs noise.

A couple of other things I would check:

  • Can you discard these objects when you create them by adjusting your size filters? (Does adjusting the upper bound for “Typical diameter of objects, in pixel units” eliminate these objects?). That would be the easiest fix!
  • I would make sure that you are using the most stringent / highest threshold that you can use without sacrificing true objects. If you can change thresholding methods and then get rid of the noise, that would be a nice easy way to get around this issue!
  • Another option might be to get rid of the noise using CorrectIlluminationCalculate and CorrectIlluminationApply? Then you wouldn’t need to do the measure + filter objects step

These are just a few ideas, hope they’re helpful!