How to merge different stacks together in ImageJ?

merge alignment imagej stack
Daniele Piccolo picture Daniele Piccolo · Sep 19, 2013 · Viewed 40.7k times · Source

I'm trying to find out a way to merge two stacks together. For example I'm taking some 60X images about the soma of a neuron and then I'll take another stack at 60X for the basal dendrite. Then how can I combine them together?

Answer

ctrueden picture ctrueden · Sep 26, 2013

Combining stacks

Probably what you want is to create a composite image, with each image stack forming one of the channels in a combined multichannel image. You can do this using the Merge Channels command:

Merge Channels

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.

Alternately, if what you mean is to merge each plane in some mathematical way (though I am guessing not), the Image Calculator command can combine two stacks using various operations:

Image Calculator

Image registration/alignment

I am also guessing your images will need to be coregistered first, especially since you tagged this question with alignment.

The Fiji distribution of ImageJ has several nice tools for that, including:

See the Fiji wiki for other options, too.

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