Stackreg not aligning images

I’m new to using FIJI and I’m trying to use stackreg to align some black and white images I have of nerves.

I have downloaded stackreg and turboreg as per the website instructions, but when I run stackreg the program just progressively shifts the images to the left. This happens in every type of alignment I try to run on stackreg.

Does anyone have any ways to troubleshoot? Thank you in advanced!


Are you just aligning images in a stack then? Perhaps these tools could work for you in this case: Linear Stack Alignment with SIFT or Register Virtual Stack Slices

You can check out all the tools for Registration here:


Thank you for your reply. I have just tried Stack Aligment with SIFT and I am experiencing there same problem. The results cause the image to just gradually go over to the left hand corner. Register Virtual Stack slice says the image I put into input doesn’t exist?

Any help? Thanks again


Perhaps you can share a dataset with us to test ourselves - just use a link to a file sharing site - such as Dropbox, etc. Perhaps it’s best to get our hands on the data too to better help you.

Too - and share EXACTLY what you did try step-by-step… so we can try to recreate the issue you are seeing.