Many modern cameras allow for automated focus stacking (focus bracketing in Canon speech). Using enfuse and the tools from hugin-tools, it is quite easy to create a nice focus stacked image out of the set of images. These commands came from foto.schwedenstuhl.de.
I use darktable to collect my photos, so the first step is to export the set of images as .tiff files.
In the next step, we use the tool
align_image_stack from hugin-tools to align the images:
align_image_stack -v -m -a Aligned *.tif
Now, we can call
enfuse to create the fused image:
enfuse \ --exposure-weight=0 \ --saturation-weight=0 \ --contrast-weight=1 \ --hard-mask \ --contrast-window-size=9 \ --output=fused.tif \ Aligned*.tif
You can play around with the options, but these were already recommended elsewhere and seem to be a good starting point.
Here is an example. This is the first image of the stack, notice the very shallow focus:
Now, the focus stacked image - you can clearly see that the focus is over the full depth!