PAT DAVID

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January 22, 2013

8 MIN READ

FOCUS STACKING MACRO PHOTOS

(ENFUSE)
I recently got a new camera to update my aging (gracefully!)
Olympus E-P1. Deciding to stay with the µ4⁄3rds (or µ43rds, or micro
four-thirds - I just wanted to play with some HTML entity codes), I
found a really tasty new Olympus OM-D E-M5 waiting for me for
Christmas! In deciding which kit lens to go ahead and get with it, the
Olympus M.ZUIKO DIGITAL ED 12-50mm F3.5-6.3 EZ was a no
brainer. Water-resistant (to match the camera), and a neat macro
function!

This article is about focus stacking, for exposure blending, see here:
Automatic Exposure Blending with Enfuse (HDR-ish)

Well, I couldn’t help but snap a couple of macro shots of my trusty

Warhammer 40k Space Marine to play with this newfangled lens.

The problem, if you haven’t done macro photography before, is that

the depth of �eld will become razor-thin. You can alleviate it a bit by
closing down the aperture a bit, but at some point you’ll hit
di�raction limits (and reduced sharpness).

Focus Stacking
So, what if you want a deeper depth of �eld in your shots? Well,
there’s a neat technique called “Focus Stacking” where you will take
multiple images, with the only thing that varies between them is the
focal point. Look again at the lead image, and speci�cally notice how
the focus plane shi�s along the length of the gun body.

Basically, compose and capture an image with the focus at one

point, then focus a little further into your image, repeat as o�en as
needed to have the range you want all in focus.
Focus stepping across my subject.

The problem, of course, is that you now have multiple images, all
with di�erent focus planes. How can you combine them all into one
image where the di�erent in-focus areas are all combined?

Well, we’re going to use the open source Enfuse to do this dirty work
for us. First, though, we need to make sure the images are properly
aligned �rst…

Hugin Align Images

Well, Enfuse will work best if the images that are going to be
combined are all as perfectly aligned as possible. To do this, we’re
going to use align_image_stack from Hugin.

Hugin is a really useful tool to have installed if you haven’t already.

To follow along with any of this, you’ll need to install it anyway - so
go do that now. Once installed, you can invoke the
align_image_stack script from the bin/ directory of wherever you
installed Hugin. It will look something like this (on Windows at the
moment, so this is what the Windows command will look like on my
machine):

C:\Program Files\Hugin\bin\align_image_stack -m -a OUT FILE1 FILE2 FILE3

Don’t Panic. To follow along, basically, put all of your focus stacked
images into a single directory. Open a command prompt, and
navigate to that directory.

Assuming your Hugin installed in the same place as mine, you can
run the command as I show above. The -m switch will optimize the
�eld of view for all images except the �rst. The -a OUT will pre�x all
the output �les as OUT…tif, and FILE1 FILE2 etc… are the names of
each of your focus stacked images you are starting with.

When it’s done, you’ll have a few new images in your directory
named OUT000#.tif. These are your newly aligned output images,
and will be what we work with from here on out.

Enter Enfuse
At this point you’ve got your images aligned perfectly (hopefully),
and now all that is le� is to mask each image so only the sharpest,
in-focus portions show through. This is exactly what we are going to
get Enfuse to do for us.

Enfuse can be run from the command line (the same bin/ directory
where align_image_stacks was located) as part of a Hugin
installation, or there is a GUI called EnfuseGUI that will expose all
the options along with fast previews.

The EnfuseGUI interface.

I’ll cover both here just to be thorough.

From the manual for Enfuse, there is a section that speci�cally

addresses focus stacking. In particular, they refer to a bare-bones call
for Enfuse to stack the images:

enfuse \
--exposure-weight=0 \
--saturation-weight=0 \
--contrast-weight=1 \
--hard-mask \
... \
--output=output.tif \
input-<0000-9999>.tif

The same options entered in EnfuseGUI are located at “Fusion

options”:

Base focus stacking

parameters in EnfuseGUI.

Exposure and Saturation weighting should be set to 0, while

Contrast weighting should be set to 1 and Force hard blend masks
should be checked. These options will not be changed as you dial in
your focus stacking parameters.
You can actually go ahead and run it at this point to see what your
output will look like. It should run reasonably quick, and you can
investigate the results. The nice thing about EnfuseGUI is that you
can generate a fast preview of the results using the Preview button
instead of a full run (this is very useful while you tweak parameters
to see what type of e�ect they’ll have).

EnfuseGUI preview of base focus stacking parameters.

If you’re happy with these results, then stop here. That’s it! Quick,
relatively painless, and you’re happy with the results. Go have a
beer! (Seriously, many people will be �ne with these results, and
don’t have to head any further).

If you’re curious whats happening behind-the-scenes, you can pass

the option: –save-masks to have Enfuse save each of the masks that it
creates. Below, for example, are the masks that were generated for
the above image. You can clearly see the in-focus plane in white in
these masks:

Masks generated by Enfuse (white areas in-focus).

 Enfuse Expert Options
If you’re still here, I am going to assume that you are less than
satis�ed with the results.

If you pay careful attention to high-contrast edges in your image,

you may notice some faint “ghosting” on either side. On the dark
side of a high contrast edge, you may notice a faint, light seam, and
vice-versa on the light side. There may also be some slight
“smearing” in areas that obscure some details.

One of the options that I �nd to produce slightly better results are to
use the L* channel of LAB colorspace as the grayscale projector to
Enfuse (don’t worry about the technical stu� - basically use the L*
channel in LAB to create the masks as opposed to averaging).

Using L* from LAB to create

masks

If you notice some haloing e�ects around high contrast edges, you
can mitigate them a bit by increasing the size of the box Enfuse uses
to evaluate contrast detection. The option to adjust this box size is:
–contrast-window-size=X Where X ≥ 3. The documentation points out
that values larger than 5 might produce blurry images, but I would
experiment with values all the way up to 9 to see how it e�ects your
�nal output.

There is another good option to tweak your �nal output, and that is
to enable the Laplacian Edge Detection algorithm. Laplacian Edge
Detection can be enabled by passing a positive value to: –contrast-

edge-scale=X Where X typically ranges between 0.1 - 0.5 (pixels), and

0.3 is suggested as a good starting point.

Unfortunately, due to a bug in EnfuseGUI, the GUI won’t accept

values that are commonly used for the correct parameter. The GUI
only accepts integer values, with no way to pass a decimal value (0.3
for instance).

No problem! We can just switch gears here at this point and fall back
to the trusty command line. So at this point, besides the base
parameters, I am going to add in contrast-edge-scale to enable the
Laplacian Edge Detection algorithm:

enfuse \
--exposure-weight=0 \
--saturation-weight=0 \
--contrast-weight=1 \
--hard-mask \
<span style="color:#00FF00;">--gray-projector=l-star \</span>
<span style="color:#00FF00;">--contrast-edge-scale=0.3 \</span>
--output=output.tif \
input-<0000-9999>.tif

You can compare the results of adding in the l-star option and using
the Laplacian edge detection at 0.3 pixels below:

Base stacking parameters detail (mouseover for contrast-edge-scale=0.3)

 In Summary
Whew! That was a lot of information. Let me summarize the steps
here. Assuming you have all of your stack images in the same
directory:

1. Use Hugin's align_image_stack to make sure all of your images

are perfectly aligned. align_image_stack -m -a OUT FILE1 FILE2 FILE3

2. Try Enfuse with the base focus stacking parameters to see if you
are happy with the results. enfuse --exposure-weight=0 --saturation-

weight=0 --contrast-weight=1 --hard-mask --output=base.tif OUT*.tif

3. You can also try a di�erent type of grayscale conversion, I've

found the L* channel from LAB to be pretty good overall (
--gray-projector=l-star ). enfuse --exposure-weight=0 --saturation-

weight=0 --contrast-weight=1 --hard-mask --gray-projector=l-star

--output=base.tif OUT*.tif

4. If there are halos around high contrast edges, you can try
increasing the contrast-window-size a bit. ( --contrast-window-
size=5 ). enfuse --exposure-weight=0 --saturation-weight=0 --contrast-

weight=1 --hard-mask --contrast-window-size=5 --output=base.tif OUT*.tif

5. If details are smeared, try using Laplacian Edge Detection

 instead. (Adding --contrast-edge-scale=0.3 to the base
command), and possibly removing --contrast-window-
size. enfuse --exposure-weight=0 --saturation-weight=0 --contrast-

weight=1 --hard-mask --contrast-edge-scale=0.3 --output=base.tif

OUT*.tif Modify the value between 0.1 and 0.5 to see which result
is best for you.

Thoughts

If you want a truly sharp macro shot with a large, smooth depth of
�eld, you’ll be taking a lot of photos. Seriously. I’ve seen 100+ images
used for a single macro shot. Look at these:

Red eyes by Gilles San Martin, on Flickr. 52 image stack.

Xylotrechus arvicola by Gilles San Martin, on Flickr. 55 image stack.

Try keeping an overlap between each of your shots. It’ll avoid any
seams in the �nal result. Remember, Garbage in - Garbage out.

The documentation o�ers a good tip as well - if the in-focus to out-

of-focus transition is too sharp, try taking another image at the
transition area with a larger aperture to allow a smoother, more
natural fallo� to occur.

Thats it! Hopefully this will be helpful to somebody, somewhere! If

you found this walkthrough helpful in any way, please feel free to
share it with others

Some References

• The Enfuse documentation (section on Focus Stacking)

• How to obtain a greater depth of �eld in macro photography -
EDU PÉREZ (Internet Archive)
• EnfuseGUI

FILED UNDER: PHOTOGRAPHY, TUTORIAL, GIMP, FOCUS STACKING, ENFUSE, HUGIN,

MACRO

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