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Focus stacking with CombineZP
September 26, 2014
Forum Posts: 188
Member Since:
February 19, 2014

Focus stacking with CombineZP

I hope it's not just me, but I find I need to do focus stacking when I use objectives of 10x and larger.
I have tried several stacking programmes and I find the best one for my use is CombineZP by Allan Hadley.


This is not a tutorial on how to use CombineZP. There are just too many features to try and explain what they do. The Help file in the programme does a good job of  explaining the use and options for the various stacking methods.

By default the programme is set up to do focus stacking. There are six predefined macros  you can use for focus stacking. You can run one at a time or all of them at once.
When the "All Methods" macro is used, the programme automatically aligns and balances the images.

My preference is to run all the macros at once with the "All methods" macro and select and save the best image.

I tried my hand once again at making a crystal slide. This time I used some brown sugar. I used a well slide and the sample ended up being rather thick and the images actually focused at three or four different levels.
It is not the best specimen, but it sure is a good test for focus stacking

 I took five photos with a polarizing microscope at crossed polars. The photos were captured as 5600 x 3800 JPEG images and passed directly to CombineZP "All methods" to produce these six photos.
The six stacked images were balanced and sharpened in Lightroom using image masking.
Each photo is the output from one of the predefined focus stacking macros.
Pyramid Do Stack produces results that are similar to DO Stack
, but may produce better results.


Pyramid Maximum Contrast may lose some detail though what detail is preserved will be sharper.


Pyramid Weighted Average produces a softer result but  include more detail.


Soft Stack is similar to Do Stack but may work better in some cases.


Do Stack may produce better results with some stacks, especially if edges are less sharply defined.


Weighted Average this method may be better than Do Stack when crossing bristles etc. cause problems.


The differences in some instances are subtle and your opinion may vary, but frequently my choice is Pyramid Maximum Contrast.

Microscope:                     Labomed LB-592
Canon 5D MkII
Camera adapter:            
LM 2x
Capture software:         
Canon Utilities
Post processing:             
Adobe Lightroom
Objective used:                20x


The descriptions of each macro is from the CombineZP Help file.

A horse named Splenda Splenda-horse_Av-1.jpg
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