This weekend I managed to start playing around with focus stacking, using Zerene Stacker. I seem to be getting mixed results from the final output images. There are however quite a few variables to play with, modifying depth of field through aperture size both on the camera and the microscope, varying number of images in a stack, light conditions, etc. The images above show the preliminary results. They were all imaged using the same aperture settings, about mid setting on the microscope and 6.3f on the camera. Each set of images contains the final stacked image on the right and two of many (40-50) images used to create the final stack, giving some sense of the obstacle of a reduced depth of field. These images were taken at roughly ~200x, ~1000x, and ~2000x magnification. It's neat to compare these images to those taken with the SEM in the gigapan below:
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