Z stack 3d reconstruction

1. What is Z stacks?
2. How do I merge stacks in ImageJ?
3. How do I merge Z stacks in Fiji?

What is Z stacks?

Z-stack imaging is a compilation of photographs taken at a set interval between the first and last planes of focus of a pollen grain. These images are combined into a brief "Real-time" video that allows users to explore the pollen grain at any plane of focus without the use of a microscope.

How do I merge stacks in ImageJ?

Combining stacks

Just open each image stack separately, then run Image > Stack > Merge Channels..., assigning each image stack to the desired channel. The result will be a composite of each respective plane.

How do I merge Z stacks in Fiji?

Merge the stacks using the menu command Image › Color › RGB merge. Assign the duplicate stack as red and the original stack as green. For Red-Green anaglyphs, set blue to be none. For red-cyan anaglyphs, set the blue channel to be the same as green.