How to crop and stitch multiple images

I have dozens of images that are images of the same object. Meaning, each of these images is a section topograph of the same object. Each of the images is of a bright arc against a dark background. Imagine a rainbow against a blue sky. Imagine you take many hundreds of images of the rainbow, but each of the images is only a slice of the overall rainbow. So, you may have a blue streak in your first image. Then the next image is also a blue streak, but this second streak lies just above the first. Then the third image is also blue, but it is the image of the layer just above streak 1 and streak 2. That is what I mean by section topograph. You take images of individual SECTIONS of the rainbow. Let’s say when you come to the 50th image, it’s not blue anymore but red. And there will be dozens of images with red streaks, but each is taken at different sections of the rainbow. And then you have green, orange, violet and other colors of the rainbow. My job is to stitch all these sectional images together so that I can reproduce the original rainbow. But each of these images has a streak with a blue background against it (the blue is the sky). I want just the streak, but not the blue background. So, I want to stitch together all the individual streaks (blue, green, red, violet, etc) but eliminate as much of the background blue sky as possible. Somebody told me something about Fiji interpolation plugin, but I don’t think the interpolation plugin can achieve this. What can I do to achieve this? When I crop an individual image of a section topograph of the rainbow color, I cannot avoid including a bit of the background sky because the rainbow is an arc whereas the cropping facility in Fiji is a square, so each crop includes a bit of the sky. I want to stitch the hundreds of images together WITHOUT there being any sky in between the individual arcs. I just want to recreate the rainbow. If there is sky around the overall rainbow, that OK. But I don’t want any sky around the INDIVIDUAL arcs. And finally I want to produce a 3-D image of this rainbow. I don’t know if you understand what I’m. trying to say. Can anyone help?

Hi @Tigve,

Welcome to the forum.

If you post some example images to the form, it will probably help us understand your problem better.

That being said, your problem sounds like it could be broken up into several smaller problems. It’s hard to know exactly what you

“Stitching” : try BigStitcher.

Segmentation - identify which pixels belong to the “rainbow” vs those that belong to the “sky”.

All images are rectangles in imagej. You can either “mask” away the sky such that the non-rainbow parts are some default value (Black, say). Or the more complicated alternative is to transform the arc into a rectangle.

I know this isn’t much help, but if you post some example images, I’m sure someone will be able to give you more useful advice,