OK, the images are the standard 2dseq files at the end of the Bruker file tree, e.g.,
In order for ImageJ to read these, it needs the BrukerOpener.jar plugin. I assume that you would need the entire file tree in order to parse the parameters correctly in ImageJ. I tried to upload one of these, but this web site does not allow 2dseq files because they are not tiffs, jpegs, etc.
Perhaps I can put a couple of these into DropBox for you? I tried to copy and paste some images here, but no luck.
I think the first thing to do is to try to make these into some kind of stack?
Each 2dseq file contains several slices from front to back of the mouse head showing the various planes of the brain.