Zerene Stacker

Welcome to my basic Zerene Stacker guide.

Zerene Stacker for me is a relatively recent piece of software. I spent a few years using and getting to know Helicon Focus, until early in 2013 I found myself struggling with a few difficult specimens. In my searches on the internet, I came across Zerene Stacker. I’d heard of it before, but not given it a second thought as I was happy with Helicon.

I downloaded the trial and gave it a go. There was some improvement in the tricky parts of the stacks I was using, though I found the interface to be a little clunky.


 Benefits of Zerene Stacker

Comparing between Zerene, Helicon, and manual methods, the main advantages of Zerene are:

  • Minimalist interface (less confusing?)
  • Slightly cheaper than Helicon
  • Results seem to be fairly similar to Helicon, if not a little better (though this depends on settings and subject)

Zerenes drawbacks:

  • The program itself is written in a weird Java system. I found that on my laptop, it struggled to get enough processing resources (IE, Memory) to run stably. Helicon has an edge here. (Note that on my new computer, with more than enough power, this isn’t an issue)

*NOTE* The above is just my basic opinion based on using both stacking programs, other users may have different opinions.

I’ll be using Zerene Stacker 64bit. You can view the programs website, and download a trial, from the following link:

Zerene Stacker website link


For this guide, you can either use your own stack of images, or use a set that I have made available here: Click here to download the zip file.

All screenshots in this guide use this set, featuring a dung beetle. Note that this is a 50mb zip file!

Regardless of which images you intend to use, it’s easiest if you keep all the images in a single folder (so that you can use “select all” in future steps).


Starting up / adding files

Once Zerene has been installed, open the main program. You’ll be presented with the following blank screen.

The default Zerene Screen, visible when you first start the program.

The default Zerene Screen, visible when you first start the program.

To load the images you want to process, go to File -> add files

Add files

To add images to the stack, click “file” and then “add files”

Navigate to the folder your source images are stored in, and select all the images

This box will open, navigate to and select the files you want to add

This box will open, navigate to and select the files you want to add

Once the images are selected, click “add”. After a brief pause, the images will appear as a list on the left, and the first image in the stack will be previewed to the right, as seen below.

The screen once the images are loaded.

The screen once the images are loaded.


Processing the stack

Once you have your source images loaded, you’re ready to process the stack. Zerene has several different options and ways to work, but there are 3 basic options which are a good place to start:

The 3 basic options, Pmax, Dmap, and "Both"

The 3 basic options, Pmax, Dmap, and “Both”

  • PMax – Pyramid method
    (Best for complex subjects, increases contrast)
  • Dmap – Depth map
    (Best for simple subjects)
  • Both – process with both methods, generating both PMax and DMap outputs
    (Best for if you have time to retouch afterwards)

For this tutorial, choose “Align & Stack all (Both)”.

What you will then see is the progress as Zerene first processes the “Pyramid” method, followed by the “Depth map” method.

Intermediate output for the Pyramid (pmax) method. Source image on the left, output on the right.

Intermediate output for the Pyramid (pmax) method. Source image on the left, output on the right.

Depth map intermediate processing output. Source image on the left, output on the right.

Depth map intermediate processing output. Source image on the left, output on the right.

Note that once the “PMax” method has completed, and “Depth map” is underway, you will be prompted to set the “Contrast threshold” for the Depth map output. Move the slider to the left and right to calibrate the contrast for the depth map. What you want is the slider to be as far to the left as possible, whilst maintaining the detail of your subject. In essence you are telling Zerene what parts of your image are “background noise”. (This is most effective if you photographed your subject raised away from the background)

Contrast slider to the left. note how much of the background is included in the output image (the image on the right)

Contrast slider to the left. note how much of the background is included in the output image (the image on the right)

Depth map contrast 2

Here I’ve moved the slider to the right a little. Note that the background has been removed a little. The parts of the background still included were due to the camera not being completely perpendicular to the subject.

Once you have set the contrast threshold, Zerene will finish processing the depth map output file. We are now ready to perform any retouching (if necessary).


Retouching

Zerene has a simple but powerful retouching feature. It allows you to tweak your output using any source image in the current project, as well as any output images. Because we produced both Pmax and Dmap outputs in the last section, we can retouch one output using the other as the source.

In the example below, you can see that the dmap output (right side) is blurry inbetween the hairs on the leg of the beetle. The Pmax output (left) however has avoided this.

Up close comparison of the differences in Pmax (left) and Dmap (right) outputs

Up close comparison of the differences in Pmax (left) and Dmap (right) outputs

Select the Dmap output in the output window in the bottom left of the screen. Then go to “Edit-Start retouching”. After a brief pause, Zerene will load the output on the right hand side, with the source image on the left.

To start retouching, go to Edit->start retouching

To start retouching, select the output you want to edit, and then go to Edit->start retouching

Next, select the pmax output from the output window. You’ll notice that the “source image” window gets updated, and now shows the PMax output.

Now you can use the mouse cursor to move over your output images. As you do so, you’ll notice that the cursor is duplicated over the source image as well. Find an area that is not in focus on your output, and click. You’ll see that the output image is “painted over” using the source file (In this case the PMax output). You can adjust the size of the “brush” to cover larger or smaller areas. Remember you can also zoom the window using the “scale” box at the bottom of the Zerene window.

Perform any retouch tweaks you want, and when you are happy go to “edit-> Commit retouching”

To store your edits go to "Edit->commit retouching"

To store your edits go to “Edit->commit retouching”


Saving

Once you are happy with your outputs, you can select the output images you want to save in the lower left hand window, and then go to “File – Save output images”. This will provide you with window allowing you to choose where to save the images to, file names, and a few image format/quality options.

Select your final output images and then go to "File->save output image(s)"

Select your final output images and then go to “File->save output image(s)”

Save dialogue

Save dialogue


This is the end of the tutorial. I appreciate it’s a very basic guide, but hopefully it’s enough to get started. Please do get in contact if you have any questions!


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