There are lots of ways to process infrared imagery to analyze plant health. Here are a few:
Infragram.org
(more coming soon)
Image Sequencer
A pure JavaScript sequential image processing system, inspired by storyboards
Image Sequencer is different from other image processing systems in that it's non-destructive: instead of modifying the original image, it creates a new image at each step in a sequence.
See the Image Sequencer page for more.
- Demo: https://publiclab.github.io/image-sequencer/
- Source code: https://github.com/publiclab/image-sequencer/
Photo monitoring plugin
@nedhorning has developed a plugin for ImageJ (aka Fiji, on the Mac) which can do a lot of powerful infrared compositing work, including batch conversion and image alignment.
Python
For those who use the webcam and have a Python interpreter, there are some image processing codes available at Python Webcam Codes.