Consistent approach to saving images used for image and signal processing in microscopy?

I wish I had known how much work I created for myself by using images from different programs, different ppi, different RGB, CMYK, grayscale, and dimensions.  A little standardization in my approach would have made getting the data much easier. A word to the “wise”.

My images were from so many sources, so many were pixelated, low contrast, warped, screenshots from publications, and general inconsistent in quality, and made by different microscopes, and different microscopic techniques.  A polyglot for sure.