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

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 \

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!