FAQ: Frequently Asked Questions

Purchasing

• What are the differences between Personal and Professional?
• I see some menu items labeled (Pro). What does that mean?
• Do I have to pay more to get 64-bit mode?
• I'm upgrading my computer. Do I have to buy a new license?
• I have both a Mac and a PC. Do I need two licenses?
• Can I purchase the software on CD?

File Formats

• What kinds of image files will Zerene Stacker handle?
• Does Zerene Stacker handle raw files?
• How does Zerene Stacker handle color profiles?
• How do I save images as TIFF or JPEG?
• Why do my output images say they're only 72 dpi?

Shooting Stacks

• Does Zerene Stacker correct for changes in magnification as I focus?
• Does it matter if I shoot the stack in order?

Stacking

• How much memory should I allocate to Zerene Stacker?
• What is the best way to add files?
• My output image has a band of streaks on one side. Why is that?
• My colors changed a little. Why is that?
• How should I set the Alignment options?
• What do the percentages mean for Alignment parameters?
• What is the difference between PMax and DMap?
• How should I choose those DMap Settings?
• How can I detect movement in my stack?
• Can I directly control the order that images are processed?
• Why do my saved output images look washed out?
• What does "Retain full dynamic range" mean?
• What is the PMax setting "Retain UDR Image"?

Retouching

• What are some tips for fast retouching?

Miscellaneous

• Is there some way to turn off the welcome screen?
• Is there some way to control those output names?
• The Zerene Stacker icon -- what is it?
• I need to report a problem. Are there log files I can send you?

Most of the differences are in the licensing terms, which require Professional Edition for uses beyond personal satisfaction.

In addition, in the current release Professional Edition includes several advanced functions, as follows:

• 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.

These features provide increased throughput and convenience; they do not affect output image quality.

As major new features are added, they will generally be available only in Professional (after a free trial period in Personal, of course). If you're eligible for Personal Edition and you don't need the Professional-only features, then we recommend to buy Personal now and upgrade later if desired.

For some hints about how to investigate what's going on, see How can I detect movement in my stack?

There are two reasons that output images can have different colors from the input: brightness adjustment and PMax. “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. Color/brightness/contrast changes can be completely avoided by using the DMap stacking method, with Brightness adjustment turned off at Options > Preferences > Alignment.

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.

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.

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, and it can alter colors somewhat.

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.

As a guideline, the best values for the “radius” parameters at Options > Preferences > DMap Settings depend on two things:

1. how sharp your images are,
2. 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%, then set Estimation Radius = 10 (because 10 times 50% is 5).
• 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, 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.

The easiest way is to “play” the stack as 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.

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 field-of-view and image scale. (By default, ZS processes the stack in order by file name, starting at whichever end has the narrowest 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.

Probably you accidentally put a checkmark on “Retain full 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.

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 full 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 full 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.

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 or dark 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 full dynamic range” on the save.

We have a whole separate page about that; see Tips for Retouching.

On Macintosh no; on Windows, yes. Right-click the launch icon to open Properties and go to the Shortcut tab. Add the parameter -noSplashScreen to the end of the Target line, like this:

    "C:\Program Files\ZereneStacker\zerenstk.exe" -noSplashScreen
    

You've probably noticed that the default names are based on timestamps — 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. Go to Options > Preferences > Image Saving and look at the Template field.

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.

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 support@zerenesystems.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” (note, no space in the name). Click OK. This will open a file explorer window showing the ZereneStacker folder in your user area.
  
  
• 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 disk. Instead it is the one located in your home directory, ~/Library/Preferences. If in doubt, open a Finder window, go to DEVICES and open your root disk, then go to Users, then to your own username, then to Library, then to Preferences, then to ZereneStacker. In the latest “Lion” version of Mac OS X, the Library folder is normally hidden. To see into it, use the simple method shown HERE.

Probably the ZereneStacker folder/directory 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 *ErrorLog20110508090456.txt, where the digits indicate date & time (2011 May 8 at 09:04:56 am). If you did not receive such a popup, then the log file is LastNormalLog.txt.