You should maybe have a look on ImageJ (
http://rsbweb.nih.gov/ij/). ImageJ associated to hundred of scripts and plugins
will allow you to handle nearly any project in the frame of image analysis/Still and video images processing.
Many of those pluggins are profesional grade java developpement, well documented and easy to use.
Most of them if not all are free, and imageJ too is free, under constant development
The user forum is very useful for finding solutions and very responsive to new problems
(
https://list.nih.gov/archives/imagej.html)
Don't be afraid by the dominant image analysis questions. Many of the scripts or pluggins are very usefull in photography/photomacro and micrography
Among my favorits are:
MosaicJ (
http://bigwww.epfl.ch/thevenaz/mosaicj/) stich together multiple fields in near any shape and picture number with a precision which is difficult to reach by hand
Stackreg (
http://bigwww.epfl.ch/thevenaz/stackreg/) realign precisely pictures taken with slightly different position. Can even realign pictures from the same point of view, taken at slightly different zoom factors.
Extended Depth of field (EDF) (
http://bigwww.epfl.ch/demo/edf/) build a stack of pictures with several level of focus plane and extract a single picture with all "in focus" pixels. A kind of virtually infinite depth of field procedure in photography/macrophotography. For best results, use Stackreg first.
Most of those plugins can be scripted with a simple macro recorder, allowing to organize automated workflows processing
any number of picutures in batch overnight
HTH
Guy