Answers to both questions: For counting Fusarium, try ImageJ http://rsb.info.nih.gov/ij/ It was written with NIH money to do exactly what you are looking for, and is freely available.
As for using Photoshop to estimate vegetation cover, no, not directly, since it becomes really awful for more than one or two samples, but I do have an R package that will estimate percentage green (or any other color) in a series of images, based on the calibration values from a training image that you set up manually. It's not super- sophisticated, but works well for automating green-cover analysis in hundreds of images taken against a dark soil background. It also does a decent job of discriminating between live and dead, although not as good as between soil and live green vegetation. Sarah -- Sarah Goslee http://www.functionaldiversity.org
