Analyzing Images For Scientific Research

I am a lab assistant at Norther Arizona University's Ecosystem Science research lab with the task of analyzing thousands of images in photoshop.

The goal is to calculate the amount of living, green plant matter within a specific circular area.

I am hoping for advice on how I can streamline this process.

Any help would be greatly appreciated! Thank you .Here is a link to a video a made detailing my problem.



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As you can see below, the image is a t-shirt shape made up of several images like a collage/mosaic (ignore the fact that the same image is repeated, they will eventually be different images).

I have achieved this by applying clipping masks to the different image layers over the top of the t-shirt image. What I now want to do is individually save all of these images so that they can be used as buttons in Adobe Flash. This is the part I am having trouble with.

I have tried using the slice tool which does work however the saved slices are all square shaped when obviously each individual image is not always a square/rectangle. Even saving them as a .png with a transparent background, I still can't use them as when they are brought into Flash, the whole square area becomes clickable as a button which I don't always want.

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