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FAQ: Frequently Asked Questions
Installing and Updating
Do you have a free trial?
Yes, there is a free 30-day trial.
The software downloads from https://zerenesystems.com/cms/stacker/softwaredownloads .
When first installed, it runs in free trial mode, which provides full functionality for 30 days from first execution. After that, the software will still run but screen images are watermarked and saving images and projects is disabled. At any time, installation of a purchased license key will unlock the software for permanent use.
By default, the technical features in trial mode are identical to those that would continue to be provided by a Personal Edition license key. Advanced features that require a Prosumer Edition or Professional Edition license key are also available, and provide a popup message letting you know that a Pro-only feature has been used.
What are the differences between Personal, Prosumer, and Professional?
There are two classes of differences:
1. how you are permitted to use the product, and
2. what technical features are provided.
Very briefly, Professional Edition is required for uses beyond personal satisfaction and educational instruction. If you're selling many images or using the software as part of your job or to support a business, museum, or funded project, then you need Professional Edition. Professional Edition also provides access to the software's most advanced technical features and extended access to our support staff.
Prosumer Edition is our flagship product for non-professional users. It includes all the technical features from Professional Edition, but at a reduced price for advanced consumers.
Here is a full list of the features that require Prosumer Edition or Professional Edition. (We call these the “advanced Pro-only features” for short.)
- Preserve all metadata, including EXIF, IPTC, and any Lightroom keywords that have been added by the photographer.
- Lightroom plugin.
- Use dust and hot pixels mask while stacking, to avoid defect trails.
- Built-in capability for “slabbing”.
- Option to honor image files' embedded color profiles in Zerene Stacker's own screen displays.
- Ability to overlap I/O with computation for faster operation while stacking.
- Ability to reduce the frequency of screen updates while stacking, for faster operation with deep stacks.
- Additional brush types for retouching.
- Multi-step undo when retouching.
- Additional interpolators for improved handling of very sharp source images.
- Integrated controller for the StackShot automated rail
- Ability to ingest and stack images while they are being shot with a USB-connected camera.
- When retouching, image brightness can be adjusted to facilitate working in unusually dark regions.
- Aligned and brightness-corrected input images can be saved to external files.
- Pixels from each source image that were incorporated into DMap output can be saved as image files.
- Depth map from DMap can be saved as a TIFF file.
Personal Edition is our entry-level product. It contains all the features that many people ever need, plus free trials of the Pro-only features. Trials of Pro-only features cover a 30-day period that starts when each feature is first used. To continue using a Pro-only feature after its trial period has expired, you can upgrade to Prosumer Edition for just the difference in license prices, by contacting email@example.com .
I see some menu items labeled (Pro). What does that mean?
Menu items are labeled (Pro) if you need a Professional Edition or Prosumer Edition license to use them beyond a 30-day trial. Each of these “Pro-only” features has a separate trial period that begins when that feature is used for the first time. After first use, you can keep using the feature for another 30 calendar days. If you don't have a Professional or Prosumer license when the trial period expires, the feature becomes disabled and appears gray in the menu. If you get tired of looking at those grayed-out items, go to Options > Preferences > Look & Feel, and select the option to “Hide unlicensed features after trial period has expired”.
Please see "What are the differences between Personal, Prosumer, and Professional?" for a list of all the Pro-only features.
Can I test Professional and Prosumer options in trial?
Yes, all of the Professional and Prosumer options are available during the free 30-day trial.
In trial, the program's default settings are the same as for Personal and Student Editions.
So, to see exactly how a Prosumer or Professional Edition license key would behave, you'll need to check-mark the following settings explicitly:
- Options > Preferences > Image Saving > “Copy metadata from source images to saved output images”
- Options > Preferences > Color Management > “Use input file profiles for ZS screen displays”
- Options > Preferences > Multiprocessing > “Overlap I/O with computation if possible”
- Options > Preferences > Multiprocessing > “Enable advanced undo”
Are program updates free?
Yes, updates are free. We've been issuing free updates ever since Zerene Stacker was first sold, back in 2009. We have no plans to change that policy. It's so much simpler and more pleasant when everybody can just use the same current version.
Do I have to pay more to get 64-bit mode?
No, it's the same price. Zerene Stacker supports 64-bit mode in all editions including Student and Personal.
I'm upgrading my computer. Do I have to buy a new license?
No, your same license still works, even if you're going from 32-bits to 64-bits. Just download and install the appropriate version for your new computer, and re-install your old license key.
I have both a Mac and a PC. Do I need two licenses?
No, you can mix-and-match however you like, as long as you stay within the total number of computers allowed by the license.
Can I purchase the software on CD?
The software is only available by download, but it's easy to make your own CD. Each download is just a single file that is also suitable for offline installation. Just use any machine that is connected to the Internet to download the version you need. Burn it to CD or thumbdrive on that machine, then carry the CD or thumbdrive to your offline machine and install the software there. Your license key can be transferred the same way. Just write the email to a text file, burn that to CD or thumbdrive, move it to the offline machine, and install the key.
A related issue: when running the software on a machine that is not connected to the Internet, it's best to clear the two checkboxes at Options > Preferences > Updates & Stats. That will prevent the software from attempting to contact zerenesystems.com, which would otherwise produce a warning message when the access failed.
Where can I read the license terms?
We've posted the license terms HERE.
License terms can also be reviewed at any time inside the software, at Help > About Zerene Stacker > “Show license terms”.
How do I download and install the program?
The latest regular release of Zerene Stacker is always posted on our Downloads page. There is one separate file for each type of computer. Choose the appropriate one and download it. For Windows, the downloaded file is a classic Windows installer. Just run it, and it will walk you through the installation process. For Macintosh and Linux, the downloaded file is a self-contained bundle that does not need to be “installed”. Just put it anywhere you like, typically either on your Desktop or in your Applications folder.
The first time you run Zerene Stacker, it will go through a short process of configuring memory allocation based on what type of computer you have and how much physical memory it has installed. After this is done, the program will automatically restart and then you'll be ready to process images.
I bought a license, how do I install it?
Licenses get installed using copy/paste at Options > Registration while Zerene Stacker is running. Just be sure to include the whole license key including all the equal signs ==== and everything between them. For detailed instructions, see HERE. If you're currently running an expired trial, then pay particular attention to step 5 because a browser window may be covering up part of Zerene Stacker that you need to install the license.
How can I update the program?
Just visit one of those pages and download the appropriate version for your type of computer.
Then install the download as if you were installing the program for the first time.
On Windows, installing the new version will automatically replace the old version.
On Macintosh and Linux, you will have to manually move the old version to trash, and move or rename the new version to replace it. Otherwise both versions will continue to be available, and you will run whichever one you happen to click on. On Mac, when trashing out the old version, do NOT allow any third party uninstaller or cleanup applications like “AppCleaner” to run. In their enthusiasm to eliminate files that they think are not used, they're likely to also delete files you really do need, like your license key and Zerene Stacker configuration files.
Can I have multiple versions installed at the same time?
Yes, this works fine. On Windows, just tell the installer to put the second version in a program folder and Start Menu folder that are different from the first version. On Mac and Linux, the versions are simply distinguished by name and location, which you must specify manually.
There is no limit to the number of versions that you can have installed simultaneously. Each version is self contained and will operate independently except that they share a single folder that contains your license key, program configuration (Options > Preferences settings), and log files.
If you're using the Lightroom plugin, then Lightroom will access whatever version of ZS was last used to create the plugin scripts, at Options > Plugins… > Lightroom.
Do you have a "beta test" channel?
Yes, our beta test channel provides early notification and access to new features as they are developed. The way it works is simple. The latest public beta version is always posted on our Beta Testing Downloads page. Versions that are downloaded from there have build numbers that end in “_beta”. Whenever you're running such a version, you will receive notifications of new updates and announcements for the beta channel, instead of the regular release channel. You can move back and forth between beta and regular release channels whenever you want, just by downloading and installing the appropriate version of Zerene Stacker.
Will Zerene Stacker work with my camera?
Yes. Zerene Stacker will work with any camera. That's because it does not attempt to talk directly with your camera. It just processes the image files that the camera creates. You can tether your camera to a computer so that Zerene Stacker can immediately access the captured images, but in that case it will be some other piece of software that's talking with the camera. Our Tutorials section includes discussion of several commonly used software packages for tethering.
What kinds of image files will Zerene Stacker handle?
The input and output formats are JPEG and TIFF, the latter in either 8- or 16-bit RGB. In general the most reliable TIFF format is uncompressed; some compressed formats such as 16-bit ZIP are not readable. A few other formats such as PNG and BMP can be read but not written.
Does Zerene Stacker handle raw files?
To process any format of raw files, including DNG, takes two separate steps. First you convert the raw files to some standard RGB format, typically TIFF, and then you stack the TIFF files.
For highest quality, we recommend converting raw files to 16-bit TIFF using your favorite raw converter and whatever settings make it work the best. After stacking the 16-bit TIFFs, tell Zerene Stacker to save its output also as 16-bit TIFF.
Because 16-bit TIFF files are lossless and have more bits per pixel than are captured by current cameras, this process retains all of the image quality intrinsic to the raw formats.
Zerene Systems does not provide raw converters. You can download those separately, or use software provided by your camera manufacturer.
If you use Lightroom, then be aware that there's a Lightroom plugin for Zerene Stacker that handles raw conversion automatically. When using Lightroom with the plugin, processing raw files is just a matter of selecting them and doing an Export to Zerene Stacker. See Working with Lightroom for more details about this "Pro-only" feature.
A longer explanation is that no stacking software really works directly with raw files.
The structure of data in a typical raw image file, one value per photosite with color implied by a mosaic Bayer filter pattern, is fundamentally incompatible with the image alignment process that is required for stacking.
Some stacking software from other companies deals with this aspect by accepting raw files at the level of the user interface, then converting them to some RGB format, typically TIFF, in a background process that is easy to overlook and may be difficult to optimize.
Zerene Stacker goes the other route, exposing the conversion process and encouraging users to deal with it as what we think it really is: a key part of the overall workflow that deserves some attention in order to get best results.
How does Zerene Stacker handle color profiles?
By default, whatever color profile is used by the input files is also copied through to output files that are saved as JPEG or TIFF. However, color profile is ignored in Zerene Stacker's own screen displays unless the option is set to “Use input file profiles for ZS screen displays” (at Options > Preferences > Color Management). This advanced Pro-only feature is set off by default in the trial version. As a result, stacks using a wide-gamut profile such as ProPhotoRGB may appear significantly different when displayed by Zerene Stacker than when displayed by Photoshop or similar tool. On some computers Zerene Stacker will also ignore the color profile of your monitor, so that even sRGB images look different than shown in Photoshop. These differences may be worrisome if you don't know what's causing them, but the key thing to remember is that the color profile will be correct in the output file.
Note: there is an optional setting at Options > Preferences > Color Management that can cause color profiles to be omitted from output files. If you're having trouble with profiles, check there to be sure that the Output option is selected to “Copy profile from input”.
How do I save images as TIFF or JPEG?
You need to use File > Save Output Image(s). That will give you a choice of TIFF or JPEG, with options appropriate for each format (compression quality for JPEG, 8- versus 16-bit for TIFF).
It's a common mistake to use File > Save Project and then notice that what gets saved are .zsj and .zsy files that can't be used by anything besides Zerene Stacker. File > Save Project is for tasks like coming back tomorrow to retouch an image that you generated today. It stores images in lossless formats and keeps track of alignment information so that you can resume work immediately, with no expensive computation. See Saving Work In A "Project" for more discussion about that.
If you have used File > Save Project and then left Zerene Stacker, you can quickly recover your work by launching Zerene Stacker again, doing a File > Open Project, and selecting the project folder or the .zsj file inside it. After the project has been re-opened, you can select one or more images in the Output Images panel and use File > Save Output Image(s) to create TIFF or JPEG. (Note: either the project folder or the .zsj file may show as a yellow smiling dog icon, depending on what operating system and program settings you're using. If neither one shows the icon, just select the .zsj file anyway.)
Is there some way to save EXIF and other metadata?
Saving EXIF and other metadata is controlled by the setting at Options > Preferences > Image Saving > “Copy metadata from source images to saved output images”. This is a “Pro-only” feature, which means that it's available for long-term use only with Prosumer or Professional licenses. If you're using Prosumer Edition or Professional Edition, then this feature is selected by default. If you have only a lower level license, such as trial, Student, or Personal, then you can run the feature as a 30-day free trial by explicitly selecting it.
Why do my output images say they're only 72 pixels per inch?
First, be reassured that your output images have the same number of pixels as your input images. You haven't lost anything and all your original lovely detail is still there.
The troublesome output images don't actually say 72 ppi. What's happening is that Zerene Stacker has produced an output image that does not have a ppi specification at all, and whatever tool you're using to look at the image has assigned its own default interpretation of “72 ppi”. Ppi is not meaningful for screen images, and for prints ppi is implied by the combination of print size and pixel count. If you really do need some particular setting for ppi inside the image file because that's how a requirement happens to be specified, then just pull the file into Photoshop, do an Image > Image Size… with the checkmark removed on “Resample Image”, then save the result to a new file.
There is an option to preserve the ppi setting, by selecting Options > Preferences > Image Saving > “Copy metadata from source images to saved output images”, before doing File > Save Output Image(s). This Pro-only option will also save all other EXIF metadata such as camera & lens type, exposure settings, GPS location, and so on. Note that “Copy metadata…” is automatically selected by default when you are running the Lightroom plug-in, so if you're running the trial version with default settings, you may notice a difference between going through Lightroom and launching Zerene Stacker separately.
Does Zerene Stacker help me to shoot a stack?
In most cases, no. Typically you'll shoot a stack either by controlling focus manually, or by using a camera control device such as CamRanger, or by tethering your camera and using a program like ControlMyNikon or ControlMyCanon. In all those cases, Zerene Stacker does not participate in the capture process. The only time that Zerene Stacker gets involved in controlling the shooting of a stack is when you're using a StackShot rail and you've chosen to use Zerene Stacker's own Stackshot control panel for that.
Does Zerene Stacker correct for changes in magnification as I focus?
Yes, it surely does. This question is often asked by people who are worried about focusing by using the big ring on their macro lens. In that case it's clear that magnification changes along with focus. But it turns out that there are magnification changes almost all the time due to perspective, no matter how you focus. The software doesn't care what the cause is for magnification changes; it just corrects for all of them.
Does it matter if I shoot the stack in order?
For DMap, it's definitely best if the frames are processed in order, either front-to-back or back-to-front. If they're out of order, then the result may still look OK at first glance but it's almost certainly degraded. Often there will be obvious artifacts like nasty halos.
PMax itself does not care about order, but going from one end straight to the other is still the safe way to get good alignment. Sometimes when source frames are processed out of order, enough error accumulates in the alignment process that two frames, focused at nearly the same depth but far apart in the stack order, end up aligned slightly differently. When that happens, you get artifacts like “echoes”.
Does it matter if I work front-to-back or back-to-front?
Front-to-back versus back-to-front makes no difference in most cases. The visibility methods currently used by Zerene Stacker are symmetric with respect to depth order. They produce the same image quality and artifacts no matter which way the stack is processed. The default behavior is to start processing at the narrow end of the stack, meaning whichever end appears to have a smaller FOV based on comparing first and last frames. That choice reduces or eliminates edge streaking and in some cases can slightly improve the quality of alignment. Options are provided to process the stack in a specific order if desired, but those are to control framing, not image quality.
One exception occurs if your subject is liable to move away while you're shooting. In that case you should start at whichever end you consider most important, so that if the subject does leave you may still have something useful to work with.
Do I need a focus rail?
If you're shooting very small subjects such as details of insects and flowers, then a high precision screw-driven focus rail is very helpful and sometimes required.
However, you don't need a focus rail for many applications, and in fact for larger subjects you'll probably get better results by stepping focus with the ring on your lens. See HERE for more discussion on that point.
Lenses with auto-focus capability can usually be controlled very precisely by software if you tether your camera to a computer. See the Tutorials Index for suggestions regarding software to do that.
How do I figure out what aperture setting and step size to use?
There are several good ways to figure out what aperture setting and step size to use.
If you're going to be shooting a lot of stacks under similar conditions, then one very good method has four major steps:
- Decide what magnification you want to shoot at. Even with the same lens, the best aperture setting will be different at 1:1 than it is for a landscape.
- At the selected magnification, shoot a series of pictures that vary the aperture setting over its entire range. Look closely at the pictures and find the one that has the most depth of field while still retaining the sharpness you need, in the plane of best focus. Whatever aperture setting took that picture, that's the one you want.
- At the selected magnification and aperture setting, experiment with different step sizes to find the largest step size that gives a clean result with no focus banding.
- Write down what you found, and use your notes to guide further work under similar circumstances.
The above procedure is very reliable and automatically incorporates your own criteria and the requirements of your own application. Both of those can make large differences in determining which aperture setting and step size are best for what you're doing. However, this experimental method obviously takes a fair amount of effort.
As a shortcut, you can skip steps 3 and 4, and rely instead on the tables that we've provided HERE. They basically rely on computation to determine for you a step size that will prevent focus banding, once you have determined the magnification and aperture setting that you want to work at. Similar tables that provide focus distances for landscape and other large scale work can be found HERE.
By the way, it turns out that the classic tables and formulas for DOF are not so good for focus stacking with modern cameras and display software. They worked OK for shooting single pictures with film and prints, but now the numbers that they produce are often too large. If you rely on the old values, you're very likely to see focus banding when you zoom in to look at “actual pixels” and full camera resolution.
How much memory should I allocate to Zerene Stacker?
The memory requirement is determined by image size as measured by pixel count. The recommended setting is at least 100 MB for each 1 megapixel, so 12 megapixel images need 1200 MB, 24 megapixel images need 2400 MB, and so on. Somewhat smaller settings can be used, down to a minimum of roughly 75 MB for each 1 megapixel, but this may make stacking run a little slower. Larger settings, up to about 200 MB for each 1 megapixel, may make some operations run faster.
Note that the memory requirement depends on pixel count and not on input file size or number of frames in the stack. There is no significant difference in memory requirement between processing JPEG and TIFF images, and the memory requirement does not increase with deeper stacks.
In most cases it is counterproductive to allocate much more memory than described above, because this will just cause more contention with other processes in your computer.
What is the best way to add files?
Drag-and-drop is usually the quickest and easiest method. You don't have to use Add Files at all. Just open another window showing your operating system's file chooser, either Windows Explorer or Macintosh Finder. Select files there, then press and hold the mouse button while dragging the selected files onto the Input Files panel of Zerene Stacker. Release the mouse button to drop the files into Zerene Stacker. This method is more powerful and flexible than Add Files because you can use all the display options provided by your operating system, including tables of thumbnails or popping up another image viewer if you need to take a closer look at some image before deciding to add it to Zerene Stacker.
My output image has a band of streaks on one side. Why is that?
Streaked edges usually happen when some source images are centered differently from others. The streaks appear in areas that are outside the frame of at least one image.
What happens is that the software picks one frame, either the first or last, to use as a master. Then each succeeding frame essentially gets registered against the first using a rotate/shift/scale approach based on comparing the image content. If it happens that a later frame ends up not covering the whole area covered by the first frame, then the software fills in the missing edge strips with copies of the closest available pixel. As a result, any detail that appears along the edge of the frame gets smeared from wherever registration puts it clear out to the edge of the frame. That produces streaks like the ones you see. Sometimes the streaks do not propagate clear through to the output because they are overwhelmed by stronger real detail in other frames. But when the filled-in streaks are the strongest available “detail”, then they propagate to the output and produce the effect you see.
Streaked edges are common for stacks that are shot handheld. They can also happen with a focus rail if the camera is pointed a little bit to the left or right, or tipped up or down, or if the rail is mounted on a tripod that sags when the camera is moved. Shooting through some stereo microscopes can also produce this effect, because with those scopes the camera is essentially shooting what one eye sees, and that's pointed a little bit left or right to produce the stereo effect.
Streaked edges can also occur when the subject moves slightly within the frame, such as a flower that slowly wilts while the stack is being shot. From the standpoint of the software, there's really no difference between the subject moving around the frame, and the frame moving around the subject.
For some hints about how to investigate what's going on, see How can I detect movement in my stack?
Edge streaks can also be caused by forcing a stack to be processed starting at the “wide” end, meaning whichever end of the stack has the widest field of view. In this case the streaks are likely to appear on all four edges, and may extend from the edge of the image to the edge of the narrowest field of view. With standard settings, Zerene Stacker automatically determines which is the narrow end of the stack and starts there, which completely prevents edge streaks with a well aligned stack. However, it can be forced to start at either end by de-selecting Options > Preferences > “Automatic order”. Normally we recommend to leave “Automatic order” selected, and set things up when the stack is shot so that everything you care about is contained even within the narrowest frame. See the tutorial HERE for more information on that point.
My output images have worm trails! Why is that?
That description sounds like what we call “dust trails” or “hot pixel trails”, depending on whether the trails are darker or lighter than their surroundings.
If you carefully check your source images, you will find that in each of them there are a few individual spots, one spot for each trail in your output.
Those spots will occur at exactly the same pixel coordinates in each source image.
The reason that trails appear during the stacking process is this: Due to magnification changes, jitter, or systematic drift in your focus stepping setup, the subject moves slightly left/right/up/down in each frame. Essentially the subject is moving around with respect to the spots. In order to make a clean rendering, the focus stacking process must correct for the subject movement, so the subject stays in the same place for each frame. But then the spots appear to move around with respect to the subject. To the focus stacking algorithms, the spots look just like sharp detail that should be retained, and so in the final image you see each spot in every position that it ever occupied with respect to the subject. In combination with the human eye's great ability to pick out linear structures, this causes each spot to become a collection of spots that looks like a straight line, a wiggly trail, or something in between, depending on exactly how the jitter and drift behaved in the first place.
In general, these sorts of artifacts can be called “defect trails”, because they are trails of small defects in the original images. The most common form is “dust trails” due to dust on the sensor, producing dark trails on light backgrounds. Light spots, typically very small, are caused by “warm pixels”, in which individual photosites on the camera sensor accumulate charge due to electrical leakage in addition to light exposure.
The best cure for these problems is to prevent them in the first place. Fixing the problem after the stack has been shot inevitably means guessing about what the pixel values should have been, that were hidden by the spots. So, it's best to clean your sensor and keep it that way. Warm pixels get worse with long exposures and higher temperatures, so the best way to avoid them is to use short exposures by adding light, typically flash. It also helps to avoid Live View mode during actual shooting, if possible, because continuous use of the sensor during Live View causes the sensor to get warmer.
If you cannot avoid dust or warm pixels in the first place, then the second-best approach is to remove them before stacking, using some technique equivalent to batch mode dust removal. This can be done using tools such as Lightroom or Photoshop. You can find a lot of information about this by searching the internet for words like “remove dust from multiple pictures”. Alternatively, it often works great to paint over the trails by retouching, either inside Zerene Stacker using Edit > Retouching, or outside Zerene Stacker using something like Photoshop's healing brush or clone tool.
My colors changed a little. Why is that?
There are three common reasons that saved output images can have different colors from the input: 1) brightness adjustment, 2) PMax, and 3) “Retain extended dynamic range” when saving. “Brightness adjustment” refers to Zerene Stacker's attempt to correct for uneven exposure between various input images. That feature is turned on by default, but you can turn it off by un-checking Brightness at Options > Preferences > Alignment. “PMax” refers to the PMax stacking method, which often makes slight changes in brightness, contrast, and saturation as a side effect of doing its focus stacking. This behavior is an unavoidable side effect of PMax and should be considered as one of the tradeoffs of PMax versus DMap. “Retain extended dynamic range” when saving causes the range of internal pixel values to be compressed if necessary to fit within the 0-255 range of image files. Internally the range can exceed 0-255 as a result of PMax, brightness adjustment, or even just pixel interpolation during alignment.
These sorts of color/brightness/contrast changes in the saved images can be completely avoided by using the DMap stacking method, with Brightness adjustment turned off at Options > Preferences > Alignment, and “Retain extended dynamic range” turned off at Options > Preferences > Image Saving or in the file save dialog.
In some unusual cases, color changes can also result from issues in the handling of color profiles of the image files and/or monitor. See the discussion above, at How does Zerene Stacker handle color profiles?
Why do my images look noisy as soon as I load them into Zerene Stacker?
Sometimes images look fine in Photoshop, Lightroom, or some other image viewer, but suddenly look noisy when you load them into Zerene Stacker. If you look closer, you discover that the noise appears when the images are viewed at some reduced scale like “Fit window”, but at 100% the images look the same in Zerene Stacker as they do in the other programs.
The reason this happens is that the other programs “anti-alias” their screen displays by averaging together lots of image pixels to make each screen pixel, and Zerene Stacker doesn't bother to do that.
The effect can be worrisome when you first notice it. However, the screen display appearance does not affect the quality of output image files, so once you realize what's going on, the worry goes away.
How should I set the Alignment options?
The best settings at Options > Preferences > Alignment depend on what you're doing.
The default settings are to correct for every common issue:
- scale changes due to perspective and focusing;
- X- and Y-shifts due to handholding, or due to jitter or misalignment of a focus rail;
- rotation due to handholding; and
- brightness changes typically due to flash variation.
However, in many cases one or more of those issues is ruled out by hardware when the stack is shot. If you're using a focus rail or a microscope, then it's unlikely that there's any rotation to deal with. If you're using continuous illumination instead of flash, then it's probably quite consistent from frame to frame. In some microscopy work, none of these issues are important.
The basic guideline is to turn off any alignment option that you don't need. That will make the alignment process go faster. In some cases, particularly at high magnification such as through a microscope, turning off unnecessary options will also give a better result image. This issue is discussed in a lot more detail in the forum thread at http://www.photomacrography.net/forum/viewtopic.php?p=79878#79878.
What do the percentages mean for Alignment parameters?
The percentages at Options > Preferences > Alignment are limits and are measured with respect to the master frame. Most of the time they can be left at the default values, which are fairly large. Once in a while, typically with handheld work, it's necessary to increase the limits to allow correct alignment. Rarely, it's also necessary to reduce the limits to keep the software from wandering off and latching onto some bogus alignment. Typically this happens only if the image contains some strong repeating pattern like a regular grid.
What is the difference between PMax and DMap?
PMax is a “pyramid” method. It is very good at finding and preserving detail even in low contrast or slightly blurred areas. It's also very good at handling overlapping structures like mats of hair and crisscrossing bristles, nicely avoiding the loss-of-detail halos typical of other stacking programs. But PMax tends to increase noise and contrast, it can alter colors somewhat, and it's liable to produce fuzzy “inversion halos” around strongly contrasting objects.
DMap is a “depth map” method. It does a better job keeping the original smoothness and colors, but it's not as good at finding and preserving detail.
The two methods complement each other. Some types of subjects look good when they are processed automatically by PMax, but not by DMap. Other subjects are just the opposite. For particularly challenging subjects like bugs and flowers shot through microscope objectives, neither method is ideal by itself. In that case the best results are obtained by using human judgment and the retouching tool to combine the best aspects of both algorithms.
For further discussion of these issues, see “DMap versus PMax” on the Zerene Stacker: How To Use It page.
How should I choose those DMap Settings?
First, note that there's a tutorial specifically on “How To Use DMap”. Visit the Tutorials index page to find that.
But as a quick guideline, the best values for the “radius” parameters at Options > Preferences > DMap Settings depend on two things:
- how sharp your images are,
- whether there's any side-to-side movement of the subject after alignment is done.
There are basically three cases:
- If there's no movement and your images are sharp when viewed at 100% scale (actual pixels), then set Estimation Radius = 5.
- If there's no movement but your images are blurred when viewed at 100% scale, then reduce the scale until the image does look sharp, and set Estimation Radius to 5 increased in proportion to the scale factor. For example if your images look sharp at 50% (that is, reduced by 2X), then set Estimation Radius = 10 (because 5 times 2 is 10). Similarly if your images look sharp only at 33% (reduced by 3X), then set Estimation Radius = 15 (because 5*3=15); at 25% (4X), set ER = 20; at 20% (5X), set ER = 25; and so on. (Math geeks: compute ER=5/scale, where scale=0.25 for 25% and so on.)
- If your stack has subject movement, then try setting Estimation Radius to between 1/100 and 1/200 of your image width in pixels, for example around 20-40 if your images are 4K pixels wide.
In any case, set Smoothing Radius to half the value of Estimation Radius.
When DMap pauses for you to Set Contrast Selection, you're supposed to move the slider until out-of-focus background goes black in the preview image, while your subject retains most of its natural colors. What you're doing is using your human judgment to mark “can't tell” regions where you want the program to emphasize smoothness rather than getting misled by pixel noise that might look like detail but isn't.
When you use the slider, you are actually setting two numbers: the percentile which says what fraction of pixels ended up getting shown as “black in preview” (that is, contrast of details is below threshold), and the level which describes the strength of detail at the break between “black in preview” and normal colors. The numeric value of level is not meaningful to a human, beyond the understanding that the values will be larger in areas that show sharp detail with high contrast, and smaller in areas where there is less detail to be seen.
Usually it is best to set the slider interactively on every stack. However, for batch operations where you have a bunch of stacks with similar appearance, you can checkmark the option to “Use preset contrast threshold”. That prevents the slider and preview image from being shown, so that multiple DMap operations can be done with no user interaction. In that case, you must also select to either use the value of Level that was left over from the last interactive setting of the slider, or compute a new threshold for each stack based on specified Percentile and the image contents of that stack.
Suppose, for example, that you're doing product photography. If your collection of stacks consists of various colors of shoes photographed against a uniform background, then it's probably best to select Percentile because the shoes may have very different appearances but all will cover about the same fraction of the frame. But if you're photographing an assortment of diamond and silver jewelry, say rings, bracelets, and necklaces, then it would be best to select Level because different pieces of jewelry would cover much different fractions of the frame but have similar appearance of detail in whatever region they did cover.
Note: If DMap does not pause for you to Set Contrast Selection, then go to Options > Preferences > DMap settings and remove the checkmark on “Use preset contrast threshold”. The software is distributed with that option not checked, but sometimes it gets checked by accident and then the lack of pause can be very confusing!
What is "slabbing" ?
Slabbing is a technique for making it easier to work with stacks that contain large numbers of images. The concept of slabbing is that you split your stacking into two big steps. In the first step you might reduce say 200 original source images to 30 intermediate images, by stacking sets of 10-15 photos each, with some overlap between sets. Then in the second step you stack the 30 intermediate images, the “slab outputs”, to produce an image with the full stack combined.
When you retouch with slabbing, typically you only have to reach back to the intermediate images, instead of all the way back to each of the original source images. In the example, that means retouching from a set of only 30 images instead of 200.
Slabbing can also be very helpful if you need to explore a variety of settings for the DMap parameters. In this scenario you would generate the slab outputs using the PMax stacking method, then stack the slabs using DMap. The gain here is much faster computation for the stacking, because DMap only needs to work with the much smaller number of slab outputs, instead of all the original source images individually.
For more information about slabbing, see HERE.
Should I sharpen before or after running Zerene Stacker?
In many cases it doesn't matter. If you have a good sharpening tool that can identify and sharpen real detail while leaving pixel noise largely unchanged, then you may get better results by running it before Zerene Stacker. That's because it improves the “signal-to-noise ratio”, which helps Zerene Stacker to make better decisions. But with sharpening filters that do not have that level of discrimination, you'll get similar results either way and it's quicker and safer to just sharpen the final result. If you do sharpen before stacking, be sure not to oversharpen because fixing that problem would require reprocessing the whole stack.
The same reasoning applies to noise reduction. If you can reduce noise while preserving real detail, then that improves the signal-to-noise ratio and it's a good thing to do before running Zerene Stacker. Just don't overdo it, again because fixing that problem would require reprocessing the whole stack.
How can I detect movement in my stack?
The easiest way is to “play” the stack as if it were a filmstrip. To do this, just press-and-drag within the list of input files. File selection will track the cursor, while the image shown in the source window will update to match. This makes it easy to quickly find any portion of the stack that you are interested in, and at the same time makes it easy to joggle between two or three frames to identify the exact frame where some problem turns up.
If you have already processed the stack, then you can also put a checkmark on “Show as adjusted” in the input files panel. This will show the source images as they ended up after alignment. This makes it much easier to spot movement of the subject. Of course if you are interested in seeing how stable and well aligned your setup is, you will want to leave “show as adjusted” unchecked so that you're seeing the source images before alignment.
By default, processing the stack also generates a set of highly compressed preview-quality images that can be played more quickly than the original high quality source images. For this reason, it's usually better to put off “playing” your stack until after it's been processed once, unless you have some reason up front to suspect that subject movement may be an issue.
Why did the software reverse the order of my images?
Normally Zerene Stacker starts processing at whichever end of the stack has the narrower field of view. This is to minimize or prevent edge streaking, which otherwise may appear in edge regions that are not covered by some source image. The narrow end of the stack can be either foreground or background, depending on exactly what lens you're using and how you're doing the focus stepping. The software determines which end is narrower by comparing images in the first and last frames. Sometimes in microscopy the decision looks essentially random because it depends on the arrangement of objects in the image and how they appear to change size as they go into and out of focus.
You can stop Zerene from automatically setting the order by going to Options > Preferences > Alignment and removing the checkmark on “Automatic order”. Then you can switch the order, if desired, by using File > “Reverse order”.
Can I directly control the order that images are processed?
Sure. First, go to Options > Preferences > Alignment and remove the checkmark on “Automatic order”. This will prevent Zerene Stacker from rearranging the stack based on its analysis of which end has a narrower field of view.
If you need to set the order very precisely, then you may also have to add the images one at a time or in small groups, using drag-and-drop or Add File(s) multiple times. Each time you drop files into the Input Files panel or click the Add button inside the Add File(s) dialog, ZS will sort the newly added files by name.
By removing the checkmark on “Automatic order” and adding files one at a time, you can set exactly any order that you want.
Why do my saved output images look washed out?
Probably you accidentally put a checkmark on “Retain extended dynamic range” while saving the image. Remove that checkmark at Options > Preferences > Image Saving, or when you save your next image, and the problem will go away.
What does "Retain extended dynamic range" mean?
As background, you need to know that the PMax stacking method often causes contrast to increase, pushing darks darker and brights brighter. If your source images are already high contrast, then the increase can internally push pixel values to “darker than black” or “brighter than white”. Such values cannot be saved in ordinary image files. By default, Zerene Stacker clips these pixels to exactly black or white when the file is saved, thus throwing away some information you might like to keep. Placing a checkmark on “Retain extended dynamic range” essentially does a “levels adjustment” that reduces contrast and possibly brightens the image, exactly enough to occupy the full range of allowed pixel values, 0-255 in an 8-bit image. This preserves all the computed pixel values so that you can apply your own levels or curves adjustment in Photoshop or any similar tool to get whatever appearance you like best. When using “Retain extended dynamic range”, it's also a good idea to use 16-bit TIFF output, so as to preserve good gradation that might be lost if the extra dynamic range were compressed into 8 bits.
Note that in previous versions of Zerene Stacker, this option was named “Retain full dynamic range”. It has been renamed to more accurately reflect its function.
What is the PMax setting "Retain UDR Image"?
UDR stands for Unrestricted Dynamic Range. As discussed in the previous FAQ, the PMax stacking method often causes contrast to increase, pushing darks darker and brights brighter. To compensate for this effect, the last step of the PMax method is a type of HDR (High Dynamic Range) local adjustment of contrast & brightness that preserves detail in overly light regions while pushing those regions back into standard bounds. By selecting the option to “Retain UDR Image”, you can preserve the image as it stood just before the HDR step. This allows you to run your own HDR methods outside Zerene Stacker, say in Photoshop. When you select “Retain UDR Image”, each run of PMax produces two Output Images, one of them with “UDR” in its name. To finish processing that image outside Zerene Stacker, you should save it as 16-bit TIFF using “Retain extended dynamic range” on the save.
What is the PMax setting "Grit Suppression"?
As mentioned in other FAQs, the PMax method tends to accumulate noise. That's because in general it is relentless about preserving the sharpest detail at all size scales, but at the very finest scale it has trouble distinguishing between focused detail and pixel noise. The “grit suppression” option, which is selected by default, makes a small sacrifice in saving fine detail, in exchange for the benefit of getting significantly less noise in the final image. The simplest way to understand its significance is to render with PMax twice — once with and once without grit suppression selected — and then compare the results when zoomed in to 100% actual pixels.
Are there settings to make stacks process faster?
Yes, there are several. First, turn off functionality you don't care about. This applies especially to “Cache unaligned screen images” and “Cache aligned screen images”, found at Options > Preferences > Caching & Undo. If you seldom or never want to detect movement by playing a stack as if it were a filmstrip, then remove the checkmark on “Cache unaligned screen images”. If you don't plan on retouching from source or you're prepared for frame selection to be sluggish, then remove the checkmark on “Cache aligned screen images”. Un-checking Options > Preferences > Alignment > Rotation and Brightness can help too, if your setup does not allow rotation and has stable illumination. On Mac, try un-checking the External TIFF Reader at Options > Preferences > Preprocessing; if you still get correct results, you'll get them a little faster. Also, note that there's an option at Preferences > Multiprocessing, to “Overlap I/O with computation if possible”. If you're using trial, or a Personal or Student Edition license, then that option is turned off by default. You can turn it on by explicitly selecting it and answering “Yes” to the question about “start trial?” For other options and details, see the discussion at http://www.photomacrography.net/forum/viewtopic.php?p=141699#141699.
Why does the program complain that my images are different sizes?
There are several possible causes for the error message that “Image <filename> is a different size from the first image.”
- In a vertical setup, if the camera is set to auto-rotate, then sometimes the camera will switch randomly between landscape and portrait orientations. In this case the images are different “sizes” because their widths and heights don't match, even though the total number of pixels is the same. The best fix is to set the camera so as to turn off the auto-rotate option. However, stacks that have this difficulty often can be processed by setting Zerene Stacker so that Options > Preferences > Preprocessing > “Ignore EXIF orientation” is checkmarked.
- If a stack is preprocessed as HDR, combining multiple camera frames to produce HDR source frames that are then fed to Zerene Stacker, then the HDR process often produces outputs that are slightly different sizes. This happens because of the HDR process's own alignment procedure, combined with image noise or slight jitter in the stack acquisition. In this case the best fix is to set Options > Preferences > Preprocessing > “Image Pre-cropping” to be the size of the smallest image produced by the HDR process. Often this will be the same size as the original camera images, but with some HDR software it may be smaller.
- If a stack is shot as raw, then very rarely, some raw conversion software will make slight changes in the image size apparently at random. Again, a good fix is to set Options > Preferences > Preprocessing > “Image Pre-cropping” to be the size of the smallest image produced by raw conversion. As an alternative, try turning off distortion correction in your raw converter. Lens distortion can change with focus, prompting the raw converter to output slightly different image sizes.
When do Options > Preferences values get saved and reloaded?
Whenever the program exits, it writes current preferences to a configuration file, named “zerenstk.cfg”. The next time the program is launched, it reads those saved preferences from zerenstk.cfg . All preference values that relate to stacking, file formats, etc. are also written to each project file (*.zsj) that is created or updated by File > Save Project. Whenever a project is reloaded by File > Open Project, all the preferences of that project also become the current preferences of the program. So, when the program exits after reloading a project, the preferences that are saved to zerenstk.cfg will be the values belonging to that project, not whatever preferences were set before the project was reloaded. Preferences can also be explicitly saved and restored, independent of any project, by using the “Save preferences…” and “Load preferences…” buttons in the Options > Preferences panel.
Most of the time, you can just ignore all these details and the program will do what you expect it to do.
However, there are a few situations where the program's handling of preferences can produce unpleasant confusion. Perhaps the most common one is when you've been doing some stacking, then you reload an old project for whatever reason, then you start a new project without realizing that the old project had different preference settings and now you're using those again!
If you frequently change preferences and reload old projects, then it's probably good to get in the habit of explicitly saving and loading preferences by using the buttons in the Preferences panel.
What are some tips for fast retouching?
We have a whole separate page about that; see Tips for Retouching.
What are the different brush types for retouching?
To understand about the additional retouching brush types, it is best to start with the default “Details” brush that is provided by all editions.
That brush is discussed in some detail at http://www.photomacrography.net/forum/viewtopic.php?p=85715#85715 . Very briefly summarizing, the Details brush is optimized for retouching between two areas that may have different overall brightness, notably between original source and PMax output, or between PMax and DMap outputs. It is sort of like Photoshop's clone tool, but with adaptive hardness that causes it to have soft edges where there is not much detail in the subject, and progressively harder edges where fine detail is present. In addition it automatically corrects for brightness differences between source and target, so in most cases it automatically does a “seamless” retouch that could be very difficult to do with Photoshop's clone tool.
In most cases, this default brush is the best one to use, but it does have downsides in certain circumstances. First, there is always some potential for the default brush to slightly change colors and contrasts, even when brushing from original source into a DMap output. But the most obvious limitation is that if you want to change the overall lightness of an area, for example to retouch darkness into a bright area, the default Details brush won't do that.
Instead, to do that job of retouching darkness into a bright area, you need to use the (Pro) Pixels brush. The Pixels brush is almost identical to Photoshop's clone tool. It has fixed hardness, adjustable by slider, and all it does is to copy pixel values from source to target.
The Darken and Lighten brushes are like the Pixels brush, except that they only copy pixel values if that copy will make the target get darker or lighter, respectively. This is occasionally handy when retouching small isolated features such as the bristles of an insect.
Do you have a user forum?
There is no forum dedicated to just Zerene Stacker. Instead, for most users we recommend going to photomacrography.net, a strictly non-commercial web forum that covers all aspects of the photography of small things. Many of our users and the principal developer of Zerene Stacker are active participants there, and we prefer to keep our efforts concentrated in one place. Photomacrography.net has a well-earned reputation for in-depth technical information, combined with astounding images created by world-class photographers who are happy to discuss tips, techniques, and tools from all sources. On the other hand, if you're working entirely with subjects that too large to discuss at photomacrography.net, then the best source of information is to email firstname.lastname@example.org. We'll be happy to either answer your questions ourselves or point you to other resources as appropriate.
How does Zerene Stacker work with Lightroom?
We have a separate document for that: see Working With Lightroom.
Are there any keyboard shortcuts?
There are several keyboard and mouse shortcuts for selecting images and for adjusting image scale and brush size. Those are described HERE.
Recent versions of Zerene Stacker also have keyboard shortcuts for some common operations such as opening and saving files. These are identified in the menu system, as usual for whatever type of computer you are using.
Is there some way to turn off the welcome screen?
Yes. Just go to Options > Preferences > Look & Feel, scroll down until you can see the option to “Suppress splash screen on launch”, put a checkmark on that option, and exit from Zerene Stacker. Your next launch should be quiet.
Is there some way to control those output names?
You've probably noticed that the default names are based on timestamps, for example “2018-12-01_16.48.14” means 2018 December 01 at 4:48 PM plus 14 seconds (local time zone). Names like that are good for uniqueness but not necessarily what you want for readability. You can construct your own templates to include source image numbers, processing options, and so on. This feature is documented at Options > Preferences > Image Saving; look at the Template field.
How can I find and remove orphaned files?
The underlying issue here is that if Zerene Stacker crashes or is aborted by the operating system while it has image files loaded, then the project and any temporary image files it was working on will be retained on disk and may consume significant space. These items are likely to be located in a folder of temporary files where they won't be obvious. Especially on Windows, orphaned projects and image files may be retained for long periods, since the operating system does not clean up temporary files very often.
To find orphaned projects, simply search your disk for folders (directories) whose name begins with “unnamedZSproj”. The full name will be something like “unnamedZSproj20090707122911640”, where the trailing digits are a timestamp (year, month, day, etc). Remove these folders and all their contents.
If you're using the Lightroom plug-in, and Zerene Stacker crashes or is aborted, then the plug-in's temporary image files will also be orphaned. These files can be located by searching your disk for folders whose name begins with “Lightroom_Export_to_ZereneStacker”. Again, the full name will be something like “Lightroom_Export_to_ZereneStacker_20140128223721”, where the trailing digits are a timestamp. Remove these folders and all their contents.
On Windows, in both cases you will have to select the option to “include hidden files and folders” so that the Windows Explorer Search function will find projects in the %TEMP% folder where they are normally placed.
The Zerene Stacker icon -- what is it?
The “smiling dog” image is the wing pattern of a California Dogface butterfly, Zerene eurydice. See HERE for an explanation of how the name “Zerene” came to be used for the software also.
I need to report a problem. Are there log files I can send you?
Yes, a log file is automatically saved for each execution that encounters an unexpected problem. One log file is also saved for the last normal execution. All you need to do is locate these files in the ZereneStacker application directory as described below, then attach them to an email sent to email@example.com. The logs are ordinary text files that you can look at with any text editor if you have any concerns about their content. As an alternative to attaching the file, the content can also be copy/pasted into the body of your email.
To locate log and configuration files, proceed as follows:
- On Windows, do a Start > Run on the Windows taskbar. In the little window that pops up, specify to Open: “%APPDATA%\ZereneStacker” (omit the quotes, and no space in the name). Click OK. This will open a file explorer window showing the ZereneStacker folder in your user area.
On Windows 10, usually it is not possible to open the Start > Run dialog. Instead, you can open a File Explorer window, then in that window's address bar, type in %APPDATA%\ZereneStacker and hit the Enter key. Searching Windows for %APPDATA%\ZereneStacker will also work.
On some systems, it is also necessary to set the folder view options to “Show hidden files, folders, and drives”. See for example http://www.windows10themes.net/guides/how-to-view-the-appdata-folder-in-windows-10/
- On Mac OS X, use Finder to navigate to your home directory, and from there to your home directory's Library/Preferences/ZereneStacker.
Note that the required directory is not in the /Library/Preferences that hangs off the root of your computer's disk. Instead it is the one located in your own home directory, ~/Library/Preferences. In modern versions of Mac OS X (“Lion” and later), your own Library folder is normally hidden in Finder. To see into it, simply click the Go menu in Finder, then press and hold the Option (Alt) key to add Library to the list of available folders (as shown HERE). Continue holding the Option key while you click on Library to view its contents, then double-click to open the Preferences folder and then the ZereneStacker folder.
Probably the ZereneStacker folder will contain several log files. To identify the proper one, consider the circumstances: If you received a popup diagnostic that said “Uh-oh – something went wrong and caused an internal error”, then the file is named something like ErrorLog<timestamp>.txt or AutoErrorLog<timestamp>.txt, where <timestamp> is a string of digits that indicate date & time. For example the file may be named ErrorLog20110508090456.txt, for a problem that occurred on 2011 May 8 at 09:04:56 am. If you did not receive such a popup, then the log file is LastNormalLog.txt.
Are there more FAQs?
No, this is the end of the list.
The blank space after here is just a matter of page formatting — it lets most browsers display every linked FAQ at top of page, even if it's near the end of the list.