I turn to my Windows98 machine running an ancient version of Photoshop. In a flattened image, I select a small region and copy its contents. I open a new image automatically sized to the selected region. I paste the copy into the new window and immediately copy the layer and hide the background layer. This gives me the ability to have transparency in the image. I outline the parts I want to keep then create a new layer. In that layer I fill the selection with red and reduce the opacity to 50%. Next I invert the selection and go back to the layer with my image. I delete the extraneous graphics and save the photoshop file. Then I save a gif with transparency optimized for the web. I go back to the source image and note the x, y coordinates of the upper left corner of the selection. I spin to my Linux box with MySQL Query Browser open and I update the database with the x, y coordinates and the new image name.
I’m repeating this process for roughly 160 images. I should be using Amazon’s Mechanical Turk for this.