Using segmentation results to isolate grey-scale objects in 3D stack

Hello everyone,

My question has two parts…

Firstly, I was wondering if anyone knew a way of selecting the outlines of segmented objects (similar to the wand tool) automatically in an image stack?

Secondly, is it possible to use the results of such an operation and apply it to another volume? What I want to do is to have the outlines of the objects I have segmented and isolate the corresponding grey-scale values in the original image sequence I segmented.

Any suggestions?

Have a look at the 3D image suite:

It also has an ROI Manager for 3D objects which probably could be applied to another stack:

Follow the instructions to segment your objects in 3D.

Hi Bio7

Thanks for the answer, its not that I have a problem with segmenting in 3D, I already have an image stack which I’ve segmented. What I want to do is to use the segmentation results to to isolate the pixels I have segmented. I’ve attached a workflow below to better illustrate what I would like to do. I can do this for single images within my image stack using the wand (tracing) tool but this is really time consuming (it takes a while to select all the features within a single image let alone in several 100 of separate images!). Any thoughts?

Hi Jonny,

Maybe you just want to use your thresholded data as a mask. The idea is then to multiply your thresholed iamge by the original image. Here a macro to do this :

run("Dot Blot (7K)");
run("Duplicate...", "title=copy");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Divide...", "value=255");
imageCalculator("Multiply create", "Dot_Blot.jpg","copy");

You can do the same in 3D of course, hope this helps.



Hi @Jonny251990,
another idea could be to pass by the “clear outside” function.
Today I’ve no time to create a fake example to show you how, but generally I think that you can in any z-stack combine the Rois present in the specific z-stack with the OR command in the ROI manager then use clear outside from Edit->Clear Outside menu

Hoping to be helpful,
see you
Emanuele Martini

Hi Everyone,

Thanks for the useful advice, I’ll have a go at implementing your ideas and let you know how it goes,