Can I merge Z-slices in QuPath (IHC-DAB)?

Hello everyone, I need to do some measurements in QuPath and it would be great to merge the Z-slices, I mean, overlap all the z-planes in a single plane, showing all the information in every slice. Is this possible with native QuPath tools? Or do I need a script?

I’ve been thinking that it may go wrong because I could merge in-focus and out-of-focus points in the same spot, so it will be visually comfortable because I got all the information, but it is challenging for the software to deal with blurry and sharp objects in the same spot.


Hi @Renato, there’s nothing in QuPath currently to do this. I don’t think I’ve ever encountered an IHC-DAB z-stack, so it’s not something I’ve ever worked on. As you say, it’s a tricky thing to solve that could go wrong in different ways.

You can send part of your image to ImageJ and explore the Image → Stacks → Z Project… command there to see how it impacts the image.

1 Like

Focus stacking of transmitted (or reflected) light images is a bit tricky.
There is no ‘standard’ in ImageJ that could do this.

If your images are not to big (not GB sized virtual slides) and if you can open the images in ImageJ you can try

1 Like