Merging objects within a cell into 1 object for measurement

Image Analysis
#1

Hi,
I’m trying to measure the distribution of a bunch of puncta and splotches of the Golgi within the cytoplasm, i.e., compact or spread throughout the cytoplasm. I am able to identify the Cell and to find the Golgi splotches, and to relate the two. My plan was to merge all the Golgi objects within each cell into one object per cell, and measure the area of the bounding ellipsoid.

I seem to be stuck at how to merge the Golgi objects into a single object. I’ve tried a few approaches, but none seem to work very well.

This is what I’ve tried that almost works:
Identify a Tertiary Object using Cell as the larger object and Golgi as the smaller object. This creates a single object that is NotGolgi. Then I repeat the process, using Identify Tertiary Object with Cell as the larger object and NotGolgi as the smaller object.
This almost works, except it includes the perimeter of the cell in the final object, instead of just the internal spots. I’ve tried to fix this by next Shrinking the Cell by 2 pixels and using it to Mask the final object. This almost works, but still leaves a few spots at the perimeter of the cell, and that messes up the measurements.

Is there a better way to turn all of the Golgi objects for each into a single object and measure the area of the bounding ellipsoid (or some similar measure of the spread of the Golgi)?

Thanks,
Seth
Data.zip (3.09 MB)
Pipeline Tert-Tert-Mask G3.cp (20.8 KB)

#2

Hi Seth,

Only one module performs unification of objects, ReassignObjectNumbers, and some creativity is needed to make it work in your case. I’m attaching a pipeline I think does what you want. I’ve stripped out the non-relevant modules (but you can add them back in) and annotated the relavent modules so you can see what the thought process is.

The other issue is the choice of metric for spread. There are several you can chose from from MeasureObjectSizeShape and I’ve added a DisplayDataOnImage so you can see the values in relation to the Golgi objects. The final decision is up to you, but it seems that eccentricity or compactness might what you are looking for. Check out the help for the full definition of these measures.

Regards,
-Mark
2011_03_24.cp (12.9 KB)

#3

Thanks! This looks great. I think you are right that something like Extent or Solidity (these seem similar to me) or Compactness might be appropriate.

Thanks again!
Seth