Focus Stack processing example

Posted: 11 years ago Last updated: 11 years ago

This article has been re-written to separate out the instructions for each piece of stacking software;

We're going to walk through how you actually process the images into a composite, once you've shot a stack. As you may not yet have the equipment to put together a well aligned stack I will provide a set of input images here.

This is a zip archive (2.4mb) which includes all of the input images for my "Myrmica rubra" stack from the Bugs -> Ants gallery. These images have been resized down to roughly web size. Note that these input images, and the composite image they produce remain my copyright. They are provided here specifically to allow you to play with stacking software. You may not sell, claim ownership of or commercially use the input images or the composite output. (Sorry about that, I hope you understand!)

So first of all download the zip file linked above. Then unzip the files to a folder on your computer. Remember where you put them!



If you haven't done so already, go and download the trial edition of Zerene stacker and install it.

Zerene is extremely simple to use, I've taken the following basic instructions from the Zerene online documentation;

  • Start the program.
  • Add source images to the list of Input Files. You can do this either with drag-and-drop from Windows Explorer, or with File > Add File(s) in the Zerene Stacker menus.
  • Make a stacked image with Stack > Align and Stack All (PMax).
  • Save the result with File > Save Output Image.

One quick note. Depending on which way you shoot the stack (front to back or back to front) you may end up with alignment 'borders' around the image. If this is the case, try reversing the order of the input images from the file menu and re-stacking, this should remove the borders, or you can trim them off in your favourite image processing software afterwards


Combine ZP

If you haven't done so already, go and download CombineZP and install it. CZP is freeware.

So to start with we will align the images in CZP, so run that up. When first run CZP starts in simple mode, with a limited menu of options available with large buttons. This doesn't give us access to all the features we will need, so to switch to advanced mode, click on the second to right button (which if you hold the mouse over it should show a tooltip which says "Enable menu"). I've put a big red border around the required button in this screenshot:

When you click this the big button menu will change into a normal windows menu with text options 'file', 'macro', 'view', 'stack' and more options available. You can make this view the default by clicking 'File' -> 'Set Options'. Untick 'start in simple mode' and click'OK'. If you don't do this then CZP will start in simple mode each time you run it.

Next we want to To load up the images, so click 'File' -> 'New'. A small file browser window should open. Use this to browse to the location where you unzipped the example files. (Or obviously if you have your own stack of input images available, use those!). Once you've located the files, left click on the first file, then hold the shift key down and left click on the last file. Release the shift key. This will select the range of files you want to process. For now select all of the input images. When they are all selected click the 'Open' button.

CZP will now load up the files. If you are using my example images they should load quite quickly as they have been shrunk to roughly web sized images. If you are loading a lot of full size images then this can take a minute or two.

Once the images are loaded we want to align them, so click 'Macro' -> 'Align and Balance used frames'.

If you are using my shrunken input images on a modern PC this shouldn't take long. When this finishes we want to export the aligned images so that we can stack them in Tufuse as well. (Skip this bit if you are not going to use Tufuse!) So when the alignment finishes, click 'File' -> 'Export Rectangles'. This will open a file browser window. By default, the aligned images will be saved to a sub-folder called 'rectangles' in the location you loaded the input files from. This is a reasonable place to use so click the'Save' button and wait a minute while CZP writes the new files to disk.

Now that is done we can run the stack in CZP. To do so, just click 'Macro' -> 'Pyramoid maximum contrast'. As before if you are using my small input images on a modern computer then this should only take a few seconds and CZP will show you the stacked output image. If you are processing a different stack using full sized images then this can take quite a while!

If the output from the software looks good then we should save it. Before we do that there is a simple trick to remove the alignment borders the software has put around the image. (You should see a weird effect all around the border of the image, this is produced by the software resizing images so they align properly). To do this, hit the "A" key on your keyboard twice. This will move the dashed border on the image inwards to remove the weird stuff around the edge. Now click 'File' -> 'Save rectangle as'. Browse to wherever you would like to save the composite stack and click the 'Save' button to save the file.



Go download the Tufuse pro demo. (Tufuse pro is shareware, you can use the demo for free but it will watermark the output.

As we saved out the aligned images above from CZP it is easy to run this stack in Tufuse as well. (If you did not run CZP then it's worth a shot with Tufuse with unaligned images, see how it goes!)... Run up Tufuse Pro.

Click the 'Add' button. In the file browser which appears, browse to the location where you saved the aligned images. Left click on the first input image. Hold shift. Left click on the last image in the list of input files, and release the shift key. If you saved out the CZP composite output to the same location make sure you do not select that as well! Once you have selected all the input images, click the 'Open' button. Tufuse will open up the files.

Click the 'Configure Settings' button. In the top left of the configuration panel which appears, make sure 'Fusion Mode Presets' is set to 'Focus Blend'. The other default settings should be okay, although these can be tweaked for different results. I am not going to discuss those settings or the advanced software settings at this point. So for now once you have set 'Fusion mode presets' correctly, click the 'OK' button.

The configure settings window should disappear when you click OK. Back on the main Tufuse window click the 'Fuse Images' button. Wait a minute or two while it processes the stack. When it is finished Tufuse will automatically save the output to the same directly the files were loaded from.

So now you've produced three stacks of the same input images in three different software packages. The output should look similar although the Tufuse and Zerene output will still have the alignment borders. You can load up the image into your favourite image processing software (e.g. Photoshop, PaintShop Pro, Gimp etc) and manually crop off the weird bit around the edge.

Welcome to the stacking club!


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