In the developer help document at:
Specifications > Supported Image Formats

There is a list of supported formats to open and save, but I have not yet found the ABBYY recommendations on which format is recommended for some of the most frequent cituations that the ABBYY FlexiCapture Engine product intends to attend.

I have colored fixed forms (response cards, where students fill out answers to alternative questions from a given test). Studying on the subject of image format, I realized that the PDF can do compression and decrease the resolution of the image, which can end up resulting in a poor reading.

I am in doubt whether to use JPEG or PNG, or even TIFF as a third alternative. Using PDF does not seem like a good idea, since I could not do a pre-filtering before processing the files, evaluating the resolution for example, and only allowing to process files that meet the minimum resolution (300 dpi).