Measuring distances between two objects

Hi,
I am trying to measure the distances between a cell body outline and puncta, and I am struggling to make progress. I can outline the cell body manually (IdentifyObjectsManually), and identify my puncta as objects (by inverting the image and then IdentifyPrimaryObjects), but as they are not parent and child objects I can’t seem to then find the distances between each puncta and the cell body.
Does anybody have any advice? I have attached an example image, the puncta are the little black squares (I created this image in ImageJ).

Thanks, Hayley

Hi Hayley,

A few questions:

  • Are you looking for all the red-stained puncta, or just a subset of them? I can’t tell from the image you annotated…
  • Are you looking for the distances from the cell body for just the puncta within the big cell body in the middle of the image? Or are you looking for distances for all puncta, whether they are inside the cell body or not?
  • Are you identifying the cell body as just the central green blob? Or does it include the long projections as well?

Regards,
-Mark

Hi Mark,
Thanks for the speedy reply.
The puncta are the little black squares that can ‘hopefully’ be seen on the image. I used an ImageJ plugin to find overlaps between the red and the green channel, and the black squares mark those points. Normally I identify these in CellProfiler by inverting the image and then thresholding at 1.0 (as the puncta are then saturated pixels).

I am looking for the distance of the puncta from the cell body, or from the center of the body. Ideally, I would determine a centre of the cell body, then measure the distance of each puncta from that spot.

The cell body is the green blob in the middle of the picture, it is a pyramid-ish shape here. I can manually draw this using the IdentifyObjectsManually if necessary.

Thanks for your help!
Hayley

You can use RelateObjects to establish the parent/child relationship between an enclosing object and the objects within it. Within that module, you have the option to calculate parent/child distances, either to the parent boundary, to the parent centroid, or both.

Aside #1: I imagine it’s not too hard to identify the red/green overlap in CellProfiler as well. You can use IdentifyPrimary once to find the red puncta, again to find the green puncta, and then MaskObjects to find the overlapping regions (if any) as a new set of objects…

Aside #2: Similarly, it doesn’t seem to be too hard to identify the cell body automatically, since it’s so bright and large…

Regards,
-Mark

Hi,
I am logging in through a new account as I lost my old password. Thanks for your help with this. I am struggling a bit with the relate objects module, as neither the cell body, nor the puncta are inside each other, so it is difficult to establish the parent child relationship. Is there a way around this? Am I misunderstanding the relate objects module?

Thanks for your help, Hayley

Hi Hayley,

You can use the MaskObjects module to do much the same thing. In fact, I’d recommend it precisely since RelateObjects enforces that an overlapping child object can only be assigned to one parent (since it assumes the parent encloses the children), whereas MaskObjects can assign the same overlapping object to multiple parents

Regards,
-Mark