Image stitching and Data Integrity

Hello all,

My lab is having a couple of issues with the stitching function of ImageJ/Fiji software. I would like to stitch a range of about 3-5 image segments of a C. Elegans to facilitate data extraction; however, I do not know how to control for changes in pixelation and consequent distortion and changes to the parameters of the original images. I have tried grid/collection stitcher and bigstitcher but both seem to alter the image (or perhaps I’m not using them correctly). From the fused image, I would like to extract fluorescence intensity, among other things, but I am afraid that once stitched the data would be different. I have been informed that controlling for these changes is easy; however, I am new to the software.

What do I need to do to fix this issue?

I have attached a couple of images for reference.

MAX_ABC252 tir1OE BIGb411 control 5_(1, 1).tif (3.8 MB)
MAX_ABC252 tir1OE BIGb411 control 5_(2, 2) .tif (3.8 MB)
MAX_ABC252 tir1OE BIGb411 control 5_(3, 3) .tif (3.8 MB)

Control BIGb411 ABC252 tir1OE Worm 2 Fused.tif (14.5 MB)