I try to align images but cellprofiler is very time-consuming and not that accurate

I do multiplex staining on a same slide and then try to align them.
There is a reported pipeline to do co-registrationAlignment - Batch.cppipe (80.6 KB)
But there is a problem that my image size is big(about 600 mb).It takes time and the whole software will be crashed when I load images and start program.
Is there any solution to this?Can imagej or other software solve this problem?
I really need help!!!
There are my two rescaled images that are just part of my original photos.
334311-4e-BCL6_001|nullxnull 334311-4e-H|nullxnull

Good day,

assuming that there is neither a scale nor a rotational difference between both of your sample images, I get the following translational parameters:

Image 1 (redish stain) must be shifted down by 69 pixels and to the left by 1 pixel, relative to their initial centered positions. These values are obtained by cross-correlation.

If the images differ in other aspects than shifts, then you need to use more involved matching techniques.



I am totally a novice.I will try it later.Thank you soooo much for your advice !!!

I tried TrakEM2 to align the photos but it can’t detect any cross-correlation.
Could you share some details about cross-correlation.Is it a automatic module?
Thank you!!! Herbie!
You have helped me a lot.