Stacking Software

Here you can discuss topics such as focus stacking, stitching and other techniques that relate to the processing of micrographs.
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MichaelG.
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Re: Stacking Software

#31 Post by MichaelG. » Sun Dec 23, 2018 9:03 am

janvangastel wrote:A stacking program much used by astrophotographists is autostakkert. It's free and works very well. Maybe worth trying. https://www.autostakkert.com/
Unfortunately, the meaning of the term 'stacking' differs between Astro and Micro work.

In photomicrography, it involves stacking focus [Z-axis] layers to improve the depth-of-field.
In AstroPhotography, it is mostly about alignment in X and Y axes, and noise reduction.

MichaelG.
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Edit: Here is an good introduction
http://zerenesystems.com/cms/stacker
Too many 'projects'

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janvangastel
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Re: Stacking Software

#32 Post by janvangastel » Sun Dec 23, 2018 11:18 am

OK, I didn't know that. Thank you.

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coominya
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Re: Stacking Software

#33 Post by coominya » Tue Jan 22, 2019 1:06 pm

I can use my new camera itself, though I must admit I haven't composed any as yet, nor been near the microscope in weeks :oops: The Olympus M5 camera I bought has consumed my spare time as I have always been a photography buff but haven't had a decent camera in a couple of decades. Catching up for lost time making stop-go movies and shooting wildlife etc.

Anyway this article explains the process inbuilt in the camera. I suppose in a few years everyone may be employing this technology, especially since the speed of the capture is lightening fast and the focus points precisely measured.

https://learnandsupport.getolympus.com/ ... -with-om-d

Quote: The focus stacking feature will shoot 8 photos at the focus positions you set and then merge them into one jpeg file at full resolution. Achieving good results will take some experimenting since so many variables are at play - subject size, distance from subject, lens choice, aperture setting, and focus differential. All eight photos are recorded plus the final stacked image.

Hobbyst46
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Re: Stacking Software

#34 Post by Hobbyst46 » Tue Jan 22, 2019 1:52 pm

coominya wrote: Quote: The focus stacking feature will shoot 8 photos at the focus positions you set and then merge them into one jpeg file at full resolution. Achieving good results will take some experimenting since so many variables are at play - subject size, distance from subject, lens choice, aperture setting, and focus differential. All eight photos are recorded plus the final stacked image.
From this quote I understand that the camera stacks a set of photos that cover a depth of focus range, and were obtained by automatically spaced focusing with the camera itself. This is not identical to stacking photos created by spaced focusing with the microscope, since the microscope image is optimal when the camera and eyepieces are parfocal. So I am not sure that in-camera automatic shooting-stacking can replace the integration of microscope focusing with shooting, then stacking.
Zeiss Standard GFL+Canon EOS-M10, Olympus VMZ stereo

MicroBob
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Re: Stacking Software

#35 Post by MicroBob » Tue Jan 22, 2019 5:46 pm

Hi Doron,
in theory this is right, but I think that in practice stacking by camera lens focus change will work very well.
It won't be too difficult to compare the results so I would give it a try if I had a camera with stacking function.

Bob

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coominya
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Re: Stacking Software

#36 Post by coominya » Tue Jan 22, 2019 10:49 pm

I didn't realize it when I posted the comment above, but the only way it works is with the camera's auto-focus lens attached. Hence it is probably of limited value in microscopy.

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RobBerdan
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Re: Stacking Software

#37 Post by RobBerdan » Mon Jan 20, 2020 5:10 am

HI I tested all three programs I use Photoshop regularly, Helicon was better and both support RAW files. Zerene was Ok, but did not support RAW images. https://www.canadiannaturephotographer. ... cking.html

jb89
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Re: Stacking Software

#38 Post by jb89 » Tue Feb 18, 2020 3:39 am

I also just tried Helicon Focus and I love it.

I can just set my camera to take a video while I lower or raise my stage and then import it and a minute or two later have a fantastically stacked image(useful for me but maybe not photographically excellent).

It's very little effort for an end result that works well for me and I'd definitely recommend it

BramHuntingNematodes
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Re: Stacking Software

#39 Post by BramHuntingNematodes » Tue Feb 18, 2020 3:05 pm

Wow... PICOLAY is still processing an 8 image stack from when I last posted on this thread. It says it's on step 3206 and it is still counting. I don't think it's going to work for me. Is this normal behavior for this program?
I have used the program a little bit, and although I'm not overly familiar with it I have gotten it to stall on some endless loop a few times. There are many optimization algorithms which may fail to produce an answer even outside of programming error, and this is a common problem with data processing in general. My advice would be that if something is taking much longer than expected, kill the process and try again with tweaked settings. If nothing else, Picolay does a good(excessive?) job of recording your progress.

MicroBob
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Re: Stacking Software

#40 Post by MicroBob » Tue Feb 18, 2020 5:57 pm

Hi together,
I have used Picolay for a couple of years now and it never got stuck, even with over 100 20 megapixel images. I use a faster notebook with i5 2,9 GHz processor and 8GB ram. When you experience a problem with PICOLAY you can contact the very helpful developer, Heribert Czypionka. The program is not idiot proof, it is possible to check boxes that do something you don't actually want. In my experience the end resolution is limited not by that of the single images but by the width of focus gap between them. So usually you don't loose anything when you reduce the resolution by 50% linear beforehand to get quicker calculation times on slow computers.

Bob

BramHuntingNematodes
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Re: Stacking Software

#41 Post by BramHuntingNematodes » Tue Feb 18, 2020 6:25 pm

I have a similarly spec'd computer, but admit I don't recall it getting stuck since installing the update released on Feb. 6 . Maybe trying the process again with the new version?

MicroBob
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Re: Stacking Software

#42 Post by MicroBob » Tue Feb 18, 2020 7:22 pm

You could make a test with a couple of small images like 1024 pixel and the least amount of boxes ticked.
My PICOLAY version is from september 2019. Perhaps a software bug was introduced since then?

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