I have a 4-axis motorized microscope that takes images of an insect in a 2D raster pattern, and repeats this multiple times while rotating it. Through software like Microsoft ICE, I stitch the images taken in the raster pattern into a single image, with the idea of then using 50+ of these stitched images to create a 3D model of the insect. For instance, here are 20 stitched images of a stink bug. Each image was created using 35 individual images.
The problem is that I have to run the 2D stitching for each set of images, and this is just too labor intensive for larger datasets. Ideally, I would be able to just select a list of folders and stitch the images contained in each folder --- something like microsoft ICE but with batch capability. I've looked far and wide... does anything come to mind?