If you have suggestions for a better way to estimate the vegetation cover for photos like the one I've used as an example here, I'd love to hear about it. Email me, or add comments below.
Step 6- Copy and paste the selected parts of the image into a new layer and turn off the background layer. You should only see the areas that were selected. Use the erase tool to erase any areas that should not be included in the pixel count (for me, these were areas in shadow that were picked up, as well as weeds that I didn't want to count).
Step 7- Open the histogram box and make sure you're looking at 'Expanded View'. You should see a box below the histogram with data including a pixel count. Toggle between Source: Entire Image (for the pixel count for the original image), and Source: Selected Layer (for the cutout of the selected vegetation). Divide the latter by the former and you'll get the proportion of the original image that was selected in steps 3-6. Add to your spreadsheet and you're done.