Question

I need to see specific points in a CT-scan (I’ve been given a mask representing a segmentation, so I know the coordinate in mm of my features of interest).
This is what I am doing at the moment in ImageJ:

• File/Import/Image Sequence, I select the first dcm file in the folder of the interest, and then I import the stack
• I know my point of interest is at x=10, y=5, z=20 [mm]. So I put the cursor on my image, scroll down the stack with the mouse wheel until I see z=20 in ImageJ window, then move the cursor until I match the other coordinates.

Is there a way to automatically jump to the slice corresponding to the specified location?

Answer 1

Yes. I would either

1. Write a Plugin in Java
2. Write a macro

I’d prefer Java because it provides more options when compared to the macro language.

In Java the code would be

imp.setSlice(20);
int poi=imp.getProcessor().getPixelValue(10,5); //int I assume but could be double

Although this is a very simple Plugin so you could also do the same in the macro language easily