Is it possible to do a "panoramic multidimensional stack" in ImageJ?

Question

I'm doing immunohistochemistry and I have two different signals and want to do cell counting.

My idea was to use a z-stack (20 frames) in two dimensions (marker 1, marker 2). This is no problem for me to do for one image. However, the areas that I am looking at are big and I want to use a high magnification, so I want to combine different images into one very large image, which is also z-stacked in both markers.

Is this possible to do, any tips?

Edit: Also, to note, I don't have a confocal microscope available with a motorized stage, only a regular epifluorescence microscope without the morotized stage.

Thanks, Praz

Answer 1

As long as your images contain substantial overlap (no need for a motorized stage, just make sure two neighboring images share some visual features at their border), you can use the Stitching plugin that ships with Fiji:

• Plugins > Stitching > Grid/Collection stitching
• In the first dialog, choose Type: Unknown position

If your different z levels and color channels are in separate files, you might have to combine them into hyperstacks (Image > Color > Merge Channels...) first before stitching.