imageJ -- image transformations and stitching of these three photos -- possible?

Sample image and/or code

Hi folks,

I am attempting to stitch 3 photos together based on the overlapping blue chalk lines in each photo. Unfortunately the subject (insect infested tree bark) is at a different distance from the camera in each photo. As you can see, the pixel to cm ratio is known for each photo so I was hoping there is a way to transform them to all be the same size and then stitch them together based on over lapping blue lines?

Any geniuses out there feeling generous?

My best,


Hi Ken,
I would suggest to first of all use the scale bar information to scale the images so that they all have the same scale ((Image->Scale…).

You could then try to use one of the stitching plugins to combine the image. I had a quick go using pairwise stitching in Fiji-ImageJ (Plugins -> Stitching -> Pairwise stitching). The result wasn’t that great, but you might be able to improve on it working from the original images.

There is also another plugin MosaicJ (, which I have used for similar tasks in the past. It allows you to manually pre-arrange your images and does various transformations of the images if necessary/selected.

Finally, if everything else fails, you could do it completely manually by increasing the canvas size of one of the images and then copy and paste the other images in the appropriate place. If necessary, you can first rotate the images so that they match each other. A quick attempt using your provided image resulted in the image below.

Hope this helps,


1 Like


Thank you so much for your reply I will give this a shot. One follow up question I have is do you know if there is a way to transform an image based on the curvature of the object to flatten it? i.e. a tree trunk. I have wire-wrap with 1.27 cm wide squares around all my imaged experimental beech trees incase I could figure this out.

Screen Shot 2020-11-14 at 2.23.05 AM

My best,


IMG_8598.tif (3.4 MB)

Sorry Ken, not something I have tried before. Perhaps the Spline Deformation Generator available as part of the ‘Transform’ plugins might be useful (
Good luck,