There are lots of ways to process infrared imagery to analyze plant health. Here are a few:

Infragram.org

(more coming soon)

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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/

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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.

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Python

For those who use the webcam and have a Python interpreter, there are some image processing codes available at Python Webcam Codes.