Hi folks, I’m a neurobiologist and I study axons. I put tissue sections on slides and image them on a confocal microscope. I get image stacks from the confocal, but my axons don’t nicely fit into one section. Sometimes I’ll have to take an image stack from 3 different, but sequential tissue sections. This creates a problem because now I want to combine those image stacks and put them into registration, but there is little to no overlap between those image stacks for the computer to put them together in a program. Do you folks know of any method or software I can use to combine these stacks into one stack that matches? I’ve attached a summary of my problem to this as a PNG file. Note that the Z-dimension is really important here. I have experience with Image J (FIJI), Vaa3D, and I just downloaded a trial of DragonFly. In an ideal situation, I could put all of my image stacks on a “canvass” and translate them in all dimensions until (3D) until all three stacks are in registration. Does anyone have any advice for me?