Images combining in Fiji


I have an image of the neuron which consists of 3 images stacks. Each of the 3 stacks represented different parts of the neuron. As a result, after tracking all of the parts of the neuron, I should receive a 3d image of the entire neuron.

But I don’t know how to combine all of the 3 traced images into 1.

I have tried “Concatenate” option, but it didn’t work. Because each of the stacks is not a continuation of the previous one. Rather, each stack is a separate image that displays the successive parts of a single neuron.

And if I will trace each of the stacks separately, is it possible to combine it afterwards?

I would appreciate any suggestion.

Hi @Veronika,

Welcome to the forum.

I think the jargon that you’re looking for is “image stitching.” This wiki page has some helpful information about that task and talks about the “Grid/Collection Stitching” plugin for ImageJ.

The same authors of that plugin made a new, updated one called BigStitcher, which is quite nice, and worth trying, imo.

Post back if you have any other questions, or run into trouble with any stitching plugins.

Thank you for the help!