For any measurements, you need to transform the 3D images form Z-stacks and visualize them in 2D. for measurements, you can use built-in tools or ImageJ with the transformed images.

I am not aware of what system you have, but i suppose these could be some settings for the measurements in the non-transformed 3D images.

Another way is to simply extract the stack which you want to measure, and use it for the measurements with any software.

@abhijeetsingh

If I convert Z stack images in 2D, is it possible to get dimensions of mitochondria?

"Another way is to simply extract the stack which you want to measure, and use it for the measurements with any software."

Which software are you referring here?

For the complete dimensions (l;b;h) you could use different axis to extract the dimension information and transformation, but I assume you are mainly interested in length.

If you extract a single interesting slice from the stack, you can use image analysis software which could be build-in in microscope software or use open-source software like ImageJ/Fiji, Bio7 etc.

Using Fiji/ImageJ is ideal for such measures. If you think 2D projection results in information loss, or selecting the "ideal plane" is also not the best, and if you want the full 3D detail, you can try to do reconstructions and measure "volumes". Also a plugin in ImageJ.