ImageJ Fiji Grid Stitching image output issue

Hello,

New to ImageJ Fiji and I have this question as to why my images have these shadow squares (see image):

I stitch these images using Fiji grid stitch row by row plugin and all of them have theses shadow squares and I have checked the source images and none are that dark or have these shadows.

Did you check the absolute grey values in the input images? It might very well be that the capturing software or hardware has adjusted the exposure time, camera gain or the illumination intensity to best suit those areas individually.

You want to record with constant exposure time, gain and illumination intensity for the best results. And make sure the illumination is even across the entire field of view.