Stacking Microscope Images for Greater Depth of Field

One challenge I have encountered with microscope photography is the very limited depth of field. Only a very thin slice of the subject matter (whether that is coffee grinds or paramecium) can be in focus at a time.

For relatively still subjects, I have found photo stacking (sometimes called z-stacking or focus blending) can effectively increase the depth of field.

I downloaded a trial version of Photoshop and used the instructions found in the article “Focus Stacking comparing Photoshop, Helicon Focus and Zerene”. I took 9 photos of decaf coffee grinds taken at different focus depths, and blended them in Photoshop. Here is the result:

Photo stacked image of coffee grinds

As a comparison, below is the first of the nine photos used. Only the highest part of the coffee grinds are in focus with everything below progressively blurred out.

Top-most photo used in the photo stacking experiment

This initial experiment used only 9 photos. I’ve seen examples online of dozens of images blended together to create incredible images.