The absorption/reflection of the material is probably different.
Dependent on the size of the particles you can apply filters (gaussian, median, ...) of different sizes. Usually you do that to remove noise. If you have bigger particles which decrease the image quality you can segment and filter them or what makes image analysis much simple, improve the acquisition pipeline until you get perfect images.
Uneven illumination can be corrected as follows:
image - gaussianFiltering(sample, large sigma) + mean(image)
Enhancing contrast can be done with CLAHE.
In general image analysis is very image (acquisition system) dependent.