Help with stacking in CombineZP

Here you can discuss topics such as focus stacking, stitching and other techniques that relate to the processing of micrographs.
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Help with stacking in CombineZP

#1 Post by MicroMan2 » Tue Dec 29, 2020 8:38 pm

Has anyone used CombineZP for stacking? If so, I have some issues with regarding focus stacking. I was trying to focus stack a quartz photomicrograph with 15 frames. Each frame was focused in 4 degree intervals in my Olympus BH2. Each time I try to do the Macros to perform the stacking functions, artifacts are introduced that detriment the image. I'll post some links so that these artifacts can be seen.
1st frame of stack: ... pITXo2Q0FB

Last frame of stack: ... pITXo2Q0FB

A stack with Pyramid Do Stack/ Pyramid Maximum Contrast/ Pyramid Weighted Average: ... pITXo2Q0FB

A stack with Soft Stack ... pITXo2Q0FB
A stack with Do Stack: ... pITXo2Q0FB
Artifacts include pixels from other frames being used to remove dark edges. Notice at the bottom edge, a mirroring artifact occurs. If anyone is familiar with these stacking flaws, could you provide suggestions to rectify them. Thanks for taking the time to reply.

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Re: Help with stacking in CombineZP

#2 Post by MicroBob » Tue Dec 29, 2020 9:22 pm

You might try PICOLAY, free, supported and under constant development.

Sliding Focus
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Re: Help with stacking in CombineZP

#3 Post by Sliding Focus » Mon Jan 04, 2021 12:58 am

It's been a while, but I've used CombineZP.

As I understand it, the mirroring artifact along one of the edges of the image always occurs, and if you don't want it there then you have to take the image into another program and crop it off. Slightly annoying, but not really a big deal unless you have a lot of images to process.

I'm not familiar with what a quartz crystal should look like under the microscope, so I'm not exactly sure what other parts of your images are artifacts—but it is clear that the various stacking methods produce different results, and that's not unusual. I'm not exactly sure what the best way to address the other artifacts would be, but I wouldn't be surprised if you had to do some manual retouching. Essentially, you can erase portions of the final image to reveal any other layer/image in the stack, allowing you to manually select which layers/images you want to show through in each part of the final image. (Not sure if that makes sense or not—it was confusing to learn, and is difficult to explain concisely.) It's a bit tedious, but it works very well.

Another trick that might work could be to make several short image stacks—e.g. 3 stacks of 5 frames, or 5 stacks of 3 frames—and then make one or more subsequent stacks out of those short stacks until you get the result you want. It took some trial-and-error, but that worked for me for one image that the program couldn't handle when I threw the whole stack at it at once. Contrast and sharpening got boosted a little more than I would have liked, but you can adjust those settings before you make the stacks in order to keep that from happening (or at least to mitigate it). The subject also got distorted a bit, but that was probably unavoidable given the angle at which I positioned it, and so wouldn't necessarily be a concern for your image. Not an ideal solution, but the results were adequate for my purposes (YMMV).

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