I mean anything about lighting, perspective or ....
The analysis is going to employ on some fine aggregates (smaller than 0.075 micrometers), and the change in the color is the matter of great importance.
You do not give away which type of "geomaterials" you are considering and which features you want to extract, thus only some generalized considerations can be given:
Be aware that lighting is the very first stage of image processing: lighting such that the features of interest become 'prominent' greatly helps.
There is no "universal lighting" - each task may require its own light setup.
OK - for all situations one basic rule applies: have "sufficient" light to keep noise low and allow for high contrast.
About noise in Imaging: image sensors sport - amongst other sources of "noise" - some basic (thermal or dark) noise. If you have low light conditions, this noise is high with respect to your "Image signal". With higher light conditions, this ratio improves as this noise is virtually constant while the amplitude of the image signal increases with lighting. So this is merely some mathematical topic.
What I somehow missed were the other topics.
I assume "3D" is not really an issue
Seems you want to take microscopic Images. Thus - aside from lighting - precise control of focus will be important to get the best images possible.
It is important to tell what geomaterial do you intend for imaging.
For noise reductions, you can acquire images several times in the same condition of camera, and average their pixel values.
I suggest that take several images from each situation and intensity, and compare their corresponding results, and then set your system with that situation and intensity in which provide best results and go ahead for your next experiments.