MacroStop.

com

Retouching Stacks
RETOUCHING STACKED PHOTOS
Most, if not all, stacked photos require retouching for the simple
reason that focus stacking is a sampling method, much like CDs
and DVDs. Sampling, by definition is lossy in that some data is
sampled and the rest is left out. This is particularly true when it
comes to focus stacking digital images. If you want a perfect im-
age, just stick with the traditional one-shot photos and don’t bother
with focus-stacking.
Of course, traditional one-shot photography has problems of its
own, like you have one focus plane and one point that draws the
eye, leaving the rest to be less in focus. With a stacked image,
there is no reason to have any particular point of view other than
one you choose or, equally, there can be several areas of prime
focus in a stacked image.
I am not trying to sell you on stacked images, but just pointing out
that focus-stacking has its merits, and not just liabilities, such as
the various artifacts that can appear due to the fact that sampled
images are lossy, by definition. This article is aimed at helping to
cut the losses in sampling that stacked photos provide by their
very nature.
Stacking Software
I have published a number of books and many articles on the
technique of focus stacking, so I will only be touching lightly on it
here. And I am not going to review, like I have in the past, all the
focus-stacking software. However, I will tell you about the stacking
software that I use and why. It is called Zerene Stacker and you
can read more about it here.
http://zerenesystems.com/cms/stacker
I have bought and tried all of the stacking software I am aware
of, plus also the free stuff. For my work, Zerene Stacker gives me
more of what I need than any other software. Aside from impecca-
ble support, there are two main reasons what I use Zerene Stack-
er, one is their alternate method of stacking (called PMax), which
is not matched for detail resolution by any other software, and I
have tried. And second, their method of retouching is unmatched,
superior to any other methods that I have found.
I am a systems programmer with 45 years of experience and
founded the second-oldest software company still on the Internet
(Matrix Software), the oldest being a little company called Micro-
soft. I have written, used, and marketed software for many years.
Zerene Stacker is one of the finest pieces of software that I have
ever had the pleasure to use. This is the best recommendation
that I can offer.
Artifacts
When I first started out, I did not like the idea of retouching
stacked photos and didn’t retouch. It was like a protest, against
what I can’t remember. My resulting stacked photos eventual-
ly pointed out to me that retouching was an integral part of focus
stacking, and not just an option. Once I realized this, the ease (or
lack of) dictated what software I had to use. And it gets worse.
Not only do we need to retouch within the focus-stacking soft-
ware, but after that is done, certain persistent artifacts require a
trip to Photoshop for some post-graduate retouching. So keep
in mind that focus stacking itself is very slow, but the retouching
in post-production is ever so much slower. If you don’t like the
idea of this kind of dedication, I suggest you not consider focus
stacking. For myself, learning to stack focus and retouch was
totally remedial for me, a perfect way to learn patience, and a
relatively fun way at that.
In this article I have pointed out the basic retouching procedure
with illustrations. Now let’s get down to the nitty-gritty a bit. Let’s
say that you shot a stack of images, imported them to Light-
room, converted them to .TIFF files and sent them to Zerene
Stacker, where they were processed into a resulting single im-
age. And now you look at that image, probably still in Zerene
Stacker.
Instead of a seamless photo like we are used to in traditional
one-shot photography, we have a photo riddled with all kinds of
flaws. What’s the point of even producing such a flawed image
in the first place. This is the refrain from many who cannot ap-
preciate stacked photos. Why bother!
Well, there are those of us who see something more than just
a flawed photo in a stacked image, perhaps the sometimes
three-dimensional quality or the ability to stack focus in just cer-
tain areas of the photo, leaving the rest to bokeh – blurred. You
tell me. For myself, I like stacked photos, obviously, but as I
have become more experienced I use stacking judicially, where
I feel it adds to the beauty of the image.
I see little point in just stacking an image until it looks like, well,
a traditional photograph, but just more in focus, although that is
somewhat appealing as well. If I have time, I will illustrate some
of the different methods of stacking photos, but for now: what do
we do with all these artifacts that deface our stacked photos?
First it is necessary to understand what kinds of artifacts we
have.
Take a moment and work through the next several pages care-
fully. They show some of the common types of artifacts we
come across. Look at each artifact, and there are many more I
didn’t bother to point out in the enclosed images. Let them reg-
ister in your mind and let’s learn how to fix them. Some of them
can be fixed in the stacking software, some have to be Pho-
toshopped, and some can never be fixed. Those that can’t be
fixed are probably the fault not of the stacking software, but of
what is called “Operator Error;” that would be you and me.
NOTE:
In the next many illustrated pages, I am going to attempt to walk
you through the basic process I use when stacking photos, the
post-processing end of it. I use Adobe Lightroom, Zerene Stacker,
and Adobe Photoshop.
If you studied the basic flow in the enclosed illustrated images you
got the idea that, basically, retouching involves using the DMap
image on the right side of the screen, and any other image in the
stack of the left side of the screen to be sampled from. In other
words, DMap is the final image, and all other images are source
material for us to copy from into the final image. And while we can
use any image in the stack as a source to copy from, the best
(and most often used) image is the PMax image that we created
at the time we did the DMap image.
Next, take time to watch these short videos from Zerene Stacker’s
creator, Rik Littlefield, because he is more experience than am I
in retouching. If you are not ready to invest the time to digest his
method of retouching, you will limp along until you do. I did just
that, and lived to regret it. Here they are:
Beginning:
http://zerenesystems.com/cms/stacker/docs/videotutorials/re-
touching001/index
Advanced:
http://zerenesystems.com/cms/stacker/docs/videotutorials/re-
touching002/index
The images in the advanced tutorial were shot by yours truly, who
sent them to Rik Littlefield for guidance, which he gave through
this tutorial.
As you can see, retouching within Zerene Stacker is a process of
painting in from PMax (or the actual separate photo layers) some
part into or onto the final result, which is usually DMap. It is a little
more difficult than Paint-by-Numbers, but still pretty easy, at least
in the broad strokes. Of course, it can get just as nasty as you
want to, trying to solve the hard cases, which often are better re-
solved through better camera technique.
Halos
One of the most common, aggravating, and hard to fix retouching
problems are what are called “halos,” and usually (at least for me)
dark halos at that. It can be a heavy outline surrounding leaves,
flowers, or what-have-you. If you generate, as I suggest, both
PMax and DMap images with each stack, then DMap is used as
the final result-image (right-hand side of screen). DMap most often
does not have halos, but PMax most often (even usually) does.
So, use DMap as your base and be very careful when copying/
painting from Pmax not to copy the halos.
Sometimes, instead of using PMax, I use the individual layers
themselves, since the halos don’t occur there, but are an artifact
of stacking itself. This can involve some very careful painting on
my part. Some stacked images become so painful that it may be
easier to abandon them, instead of spending hours retouching
them.
And finally, if that does work and the halos are still there, I take
the final image into Photoshop and use the Clone Tool to very
carefully remove the halo by cloning just above the shadow-ha-
lo and painting down and over the halo to the very edge of what
leaf or flower is being haloed. You may want to expand the Pho-
toshop image until it is very large, to make it easier. And shaky
hands are not a virtue in this procedure. If that does not do it, I
abandon the image.
Failed Crossing
Another very common problem is where two edges overlap or
meet. In the stacked image, they don’t meet, but come close
and then get all fuzzy. This is due to the two objects being too
far apart to stack nicely. The answer here is found in one of two
places. Looking at the original layers does not usually help, be-
cause there is no correct layer to be found. The place to look
is in PMax, which more often than not has a better result or at
least closer than DMap. If that fails, then careful cloning in Pho-
toshop is the only alternative, and it happens a lot. I have be-
come, by necessity, pretty good at straightening out fuzzy cor-
ners, if that makes sense.
Transparent Overlays
Another common problem is when there is bleed-through of one
image on another. For example, an area (leaf, stem, etc.) that
should be under another area is not or is partially transparent,
etc. Looking to PMax to solve this is usually not helpful. The an-
swer is to look through the image layers and find the layer that
shows the proper overlapping and carefully paint that out. This
is where the problem should be fixed, not in Photoshop. Photo-
shop does not have the information to be much good.
Summary
Hopefully, you get the general idea. Identify the artifacts, fix
them in Zerene Stacker, or fix them (last resort) in Photoshop.
My rule of thumb is that if it bugs me in the final result, I should
fix it. It pays to develop better technique on the shooting end of
things, as opposed to hours spent retouching, or worse, trying
to retouch. It is enough to make you want to give up stacking…
sometimes.
For those who are on the fence, please see my article on using
really highly-corrected lenses instead of stacking. While expen-
sive, it is really worthwhile:
The New Zeiss APO Lenses for Close-up Work
http://spiritgrooves.libsyn.com/the-new-zeiss-apo-lenses-for-close-
up-work
Post-Processing Images
I don’t want to spend a great deal of time on how to post-process,
as in “develop” digital negatives, such as stacked TIFF images or
even raw files. But I will mention a couple of things I do regularly.
Lightroom Plug-in for Zerene Stacker
Note: Zerene Stacker has a Lightroom plug-in that comes with
its professional version, so this may interest some users. With
this plug-in, one can select a stack from Lightroom and send it to
Zerene Stacker and have it returned, finished, to Lightroom. I don’t
use this often because I tend to process a lot of stacks in batches.
You can read about this plug-in here:

Trim the Branches

http://zerenesystems.com/cms/stacker/docs/workingwithlightroom
What I mean here is to remove parts of your photo that take-away
from the composition. The Lightroom tool for doing this, the “Spot
Removal Tool” is, for my purposes about worthless. As they say,
that tool and a ticket will get you a ride on the bus. I use it for
spots, but not as a cloning tool. IMO, it sucks.

Instead I go to Photoshop, where I use the “Quick-Selection Tool”

or the Rectangular Marquee Tool” to define an area I want to re-
move and delete it using the “Content-Aware” feature, which IMO
is one of Photoshop’s finest moments.

The Next Pages

In the next pages, some of thje concepts discussed above will be

illustrated, so take time go over them so that they are clear. Fol-
lowing this next section I will offer a few extra comments.

You can find many more free e-books, articles, and video tutorials
on photography and focus-stacking at MacroSpot.com.

In addition, there are some 26 video tutorials on these subjects on

YouTube.com at the following link (scroll down until you reach the
photography area.

https://www.youtube.com/channel/UC3cL8v4fkupc9lRtugPkkWQ

MIchael Erlewine
Michael@Erlewine.net
The previous image, corrected
in Zerene Stacker and further
in Phoshop with the CLONE
TOOL and Content-Aware.
Some Final Comments on Photography
Because I do a good amount of focus stacking, I accumulate a lot
of images that have to be stored, backed up, and generally cared
for. There are many ways to keep track of files, but I find myself
using Adobe Lightroom. Lightroom is a non-destructive working
environment, simply meaning that no matter what you do within
Lightroom, no matter the number or kind of changes you make to
a photo, the original photo remains untouched. It sits on your hard
drive and is only accessed by Lightroom in a read-only fashion.
Lightroom never writes to that file, so it remains pristine, just as it
came out of the camera.
Adobe Lightroom has two general ways of keeping track of the
changes you make, i.e. whatever adjustments you make to the
original file. And this next part is very important and includes a
warning, so please note:
The first way (and most common) to record development adjust-
ments is for Adobe Lightroom to create an internal catalog that au-
tomatically includes whatever changes you make to your photo.
The second way Lightroom keeps track of adjustments is that ev-
ery time you make a change to a photo, Lightroom writes a small
file called a sidecar file (.XMP) and stores it on the hard drive next
to where the original image is. And here is a key point:
By default, when you first start using Lightroom, it creates a cata-
log, but does not write the sidecar files UNLESS you turn on that
feature. If you do turn it on, Adobe will create both of these ways
of storing your adjustment, a catalog and a sidecar file for each
image. And here is the warning:
The catalog method of monitoring adjustments is great AS LONG
AS the catalog does not get corrupted and you do not move your
original files to some other place. If the catalog file gets corrupted,
you can be in for a world of hurt and are in danger of losing hours,
weeks, or years of hard work, everything you have done in terms
of developing your digital negatives.
Sometimes the corrupted file can be salvaged, but quite often it
cannot. Of course, if you back-up Lightroom each time you close
it, you can revert to the previous back-up, etc. Otherwise, the re-
sult is that suddenly you have your original files still untouched,
but everything you have to do make those files beautiful and us-
able is lost. You have to start all over again or at least redo all files
(develop them) since your last backup.
However, if you turn on the switch to also always write embedded
sidecar files, then all of your adjustment are safely stored along
with our originals and can be reimported with very little loss.
Note: When you choose to store your adjustments in sidecar
(.XMP) files, there is some data that is not stored in the .XMP files,
and they are: the Edit History for each file, any virtual copies (du-
plicates) of an image and their adjustments, the Pick-Flag, all col-
lections and groupings, and any disabled edits. This is unfortu-
nate, especially the “Pick” and duplicate copies.
However, the above data is kept in the Lightroom Catalog. The
bottom line here is to turn ON the option “Automatically write
changes into XMP,” which can be found in the Catalog Settings
form, under the Metadata Tab, the 3rd option from the top. Check
edits. This is unfortunate, especially the “Pick” and duplicate
copies.
However, the above data is kept in the Lightroom Catalog. The
bottom line here is to turn ON the option “Automatically write
changes into XMP,” which can be found in the Catalog Set-
tings form, under the Metadata Tab, the 3rd option from the
top. Check the box that says “Automatically write changes into
XMP.”
DNG Files
This is one other suggestion I would make about storing digital
negatives. Adobe has their own method of storing digital nega-
tives called “.DNG” files, which basically mean just that, digital
negatives. Unlike raw negatives with their accompanying side-
car files, .DNG files store the adjustments (sidecars) within the
.DNG file itself. Adobe has released .DNG to the public domain,
but they still may in the future have some control over it. Their
claim that as the more and more different raw formats prolifer-
ate, over time, we may lose the ability to read some of the file
formats, thus the advantage of using the .DNG files. They have
a point.
I can see it both ways. For myself (and some of the photogra-
phers I admire), I am sticking with the raw files and foregoing
converting them to Adobe’s .DNG format. I use Nikons and I am
sure that there will always be some converter available to con-
vert what I have into .DNG files or whatever has a grip on the
market at that point in time.
So, I store my raw Nikon .NEF files along with the sidecar .XMP
files in the same directory. The only caveat is that, of course,
when I move images to another drive, I have to be sure to take
the .XMP files with them.
Files like .Tiff .JPG, .Gif, .PNG, and .BMP don’t have sidecars of
adjustment. They are “baked” in, meaning what you see is what
you get. While raw files can be further developed, the above
files are fixed in what is called a delivery format – finished. A
raw file is still flexible and can be output in any of the above,
baked-in, formats.
Marking Files Within Lightroom
Since I take a great many photos, I have to have some way to
keep track of them. So far, it seems I am not a great keyword-er,
meaning I tend not to keep up with that. I know I should do bet-
ter. Here is what I do.
Of course I look over any new batch of photos once I input them
into Lightroom. I mark them with colors as follows:
Yellow: Something is wrong with the photo. Ignore it.
Blue: This is a keeper, but needs to be developed further. When
I am in the mood, I scan Lightroom for the blue-bordered im-
ages, finish developing the blue ones, and mark them with five
stars when done.
Red: Saving this for a future category.
Purple: Marks a special category
Green: Family and related photos.
As for the Star Ratings, I use them, but not very intelligently. Ba-
sically I use them for emphasis.
I do use the Pick to mark ones that I want to export, so import-
ant images for me have a blue border and are marked with the
white Pick AND five stars.
Color Space
I have Lightroom and Photoshop set to work in the ProPhoto
RGB color space, and not Adobe RGB or sRGB. When I output
an image for use on the web or online, I output it in the standard
sRGB format at maximum quality, because most web browser
cannot read Adobe RGB color, and none that I know of can han-
dle ProPhoto RGB, although I wish they would. Actually, Pro-
Photo has such a large gamut that I know of no monitors that
support it, and some say there never will be one.
Cameras
I have owned and use many cameras, from tiny point-and-shoot
cameras all the way up to the big Nikons and even medium-for-
mat cameras. I am a Nikon user and have always been one. I
know there are many other cameras and I have owned (or still
own) cameras by Sony, Panasonic, Kodak, BlackMagic, and
so on. I am not too fond of Nikon lenses, but I am very fond of
Nikon Cameras.
I have owned a number of mirrorless cameras, and try as I
might, could never get comfortable with any of them. I sent most
of them back. I am not a snob when it comes to cameras; I just
have a professional need for these large megapixel (and very
heavy) cameras.
I very much believe that while any camera will take pictures and
that good pictures can result from them, this is not for me. I ac-
tually use the features of these large full-frame camera bodies
and don’t mind carting them around, heavy as they may be. I
just don’t think of my discomfort when it comes to photograph-
ing.
I also feel this about cameras, tripods, and above all about lens-
es. To me fine lenses are at the tip of the top of photographic
equipment. I have spent more time studying and using lenses
than I have any other aspect of photography.
The Process
When asked why I take photographs, the answer is simple, but
perhaps hard to understand. I am in love with the process itself
of photographing, and I don’t mean the mechanical process, but
rather the psychological process of peering through a lens at pris-
tine micro worlds – the clarity of that. I am a close-up and macro
nature photographer, and I mostly photograph plants and whatev-
er critters I come across.
I gave up hunting for photographs and critters long ago. You
could say I am a photographer of found objects, whatever I come
across, which boils down to the old concept that beauty is in the
eye of the beholder. It takes one to know one, and it takes one to
see a good image and photograph it. When I see something that
sparks beauty in my mind, I try to photograph that beauty.
I am a confirmed follower of the term “inscape” that the great poet
Gerard Manley Hopkins coined, which refers to whatever in na-
ture (and the world) that catches our attention, flags us down,
and leads us inward to the beauty of the mind itself. When I pho-
tograph, I basically make myself available to nature and wait for
inscapes to occur, for some sign to catch my eye, melt my hard
heart, and take me inside to the natural nature of my own mind.
That is true rest. That is the essence of the process of photogra-
phy for me.
Close-up and macro photography are very time consuming and
the very process slows me down to a crawl, which is where I need
to be once in a while to keep sane. If I add my interest in focus
stacking to the mix, where I may take upward of 100 images of the
same flower at slightly different focal points and then merge them
into a singe image, I really am moving at a snail’s pace through
time, slowing down enough to surrender my speed and allow my-
self to rest in the nature of the mind itself. That is the reward for
me of photography. Of course, if I take enough time, the photo-
graphs sometimes improve as well.
Developing the Digital Negative
When I first got into digital photography, the idea of developing the
digital negative did not make much sense to me. Of course at the
time I was taking .JPG images with their “baked in” color, so there
was not a whole lot of developing possible. Delivery-format for-
mats like .JPG are like that. They are pretty much beyond devel-
oping.
However, with the advent of the raw format, the possibilities of
developing dawned on me. Raw format really is flexible. We can
push and pull it in many ways. We can develop it and the raw for-
mat actually is a digital negative. Once I tried raw, I never went
back, and when I come across my old .JPG-format photos my
heart always sinks a bit because I know that I cannot do much in
the way of development with those photos. What you see is what
you get for all time.
Who knows what amazing photo-developing techniques may
arise in the future. If we shoot in raw, we may be able to extract
even greater resolution and flexibility. For that same reason I tend
to save all of my layers of my stacked photos, although the disk
space required is enormous. I have already seen improvements
is restacking old photo stacks and in the better development tools
made available in Lightroom since I started.

I encourage you to shoot raw. You will not regret it later.

The Author