Help with Zerene Stacker

A forum to ask questions, post setups, and generally discuss anything having to do with photomacrography and photomicroscopy.

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ayyappanm
Posts: 7
Joined: Tue Dec 29, 2020 10:05 am

Help with Zerene Stacker

Post by ayyappanm »

Zerene Stacker is unable to stack the images which has fine hairy structures. Both the stacking modes fail. This is the first time I'm encountering this in Zerene Stacker and unable to determine what is going wrong.
Screen Shot 2021-01-09 at 1.14.19 PM.jpg
Any advise is greatly appreciated.

Thanks.

rjlittlefield
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Re: Help with Zerene Stacker

Post by rjlittlefield »

I notice three things that seem relevant:

1. In the right-hand image, the front structure is very high contrast and is surrounded by a discolored edge. This suggests an extreme value of "brightness" adjustment, caused by having some source frames that are very different from other source frames.

2. In the left-hand image, which I assume is one frame of the source images, I see no trace of the structure that is front in the right-hand image.

3. Assuming that left is one source frame and right is PMax output, then the output looks properly stacked except for suffering from an extreme case of "inversion halo" that darkens background areas around the very bright and high contrast foreground structure. The extreme inversion halo probably is due to the contrast issue mentioned in point 1.

My first thought is to wonder if you have accidentally loaded into Zerene Stacker some frames that do not belong to the same stack. I suggest to step through your source images, one by one, to confirm that they all do go together.

If there is no error in loading source images, then I suggest to remove the checkmark on Options > Preferences > Alignment > Brightness. This will remove the brightness adjustment that I'm pretty sure is causing the discolored edge and strong inversion halo around the front structure.

Let us know what you find, please.

--Rik

ayyappanm
Posts: 7
Joined: Tue Dec 29, 2020 10:05 am

Re: Help with Zerene Stacker

Post by ayyappanm »

Hi Rik,

Turning off Brightness under Options > Preferences > Alignment did the trick. :D

Thanks for your input.

rjlittlefield
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Re: Help with Zerene Stacker

Post by rjlittlefield »

Great!

Can we see the final image, please? I am very curious what this subject looks like (and what it is, for that matter).

Also it would be great to get some information about magnification, step size, number of frames, and so on.

--Rik

ayyappanm
Posts: 7
Joined: Tue Dec 29, 2020 10:05 am

Re: Help with Zerene Stacker

Post by ayyappanm »

I'm taking photo of seeds having interesting shapes. The subject I was having challenge in staking is Cornflower a.k.a Bachelor's Button seed.

The final image came out very good. Also, I like to hear your thoughts on the fuzziness around the hairy portion of the seed. Do you think if that can still be minimized further? If so, how?

My Equipment
Amscope 4x Infinity Objective, mounted in front of Canon Telephoto 100-300mm Zoom lens focussed at infinity & focal length set to 135mm.
Stackshot controller with step size 5 micrometer.
I take approx 300-500 pics of portions of the seed & stitch them using photoshop.

Please feel free to share your thoughts or any improvement tips.

Cornflower a.k.a Bachelor's Button seed
Centaurea_cyanus-seed-06.jpg
Popcorn Kernel
popcorn-seed-05-insta.jpg
PepperCorn
peppercorn-01-insta.jpg

rjlittlefield
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Re: Help with Zerene Stacker

Post by rjlittlefield »

Thank you for the additional information. These images look great.
ayyappanm wrote:
Sat Jan 09, 2021 9:35 pm
I like to hear your thoughts on the fuzziness around the hairy portion of the seed. Do you think if that can still be minimized further? If so, how?
I assume that by "fuzziness" you refer to areas like I have marked here, where it seems like we should be seeing pure black background between the hairs of the pappus.

2021-01-09_20-52-54.jpg

Usually there is no way to address those during the stacking process. The difficulty occurs when those areas are never seen as black by the camera, because they are always covered by some out-of-focus parts of the pappus. The software has no way to know that those areas "should" be black, so it colors them consistent with what it has seen. There is more written about this issue at https://www.photomacrography.net/forum/ ... ht=#102557 .

In some cases it is feasible to retouch those areas to be black, using the advanced masking and painting tools of software like Photoshop. In fewer cases, this can be facilitated by some outputs from Stack Selected or slabbing, carefully chosen to help separate focused detail from out-of-focus surround. But all this is never simple, so at some point you have to decide whether the added quality is worth the added effort.

--Rik

klevin
Posts: 61
Joined: Fri Dec 14, 2012 5:28 pm
Location: SW New Hampshire, USA

Re: Help with Zerene Stacker

Post by klevin »

Love these pictures.

How did you hold the subjects?

ayyappanm
Posts: 7
Joined: Tue Dec 29, 2020 10:05 am

Re: Help with Zerene Stacker

Post by ayyappanm »

rjlittlefield wrote:
Sat Jan 09, 2021 10:27 pm

I assume that by "fuzziness" you refer to areas like I have marked here, where it seems like we should be seeing pure black background between the hairs of the pappus.
Yes Rik.

ayyappanm
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Joined: Tue Dec 29, 2020 10:05 am

Re: Help with Zerene Stacker

Post by ayyappanm »

klevin wrote:
Sun Jan 10, 2021 3:53 pm
Love these pictures.

How did you hold the subjects?
Hi klevin,

* I'll take an insect pin (size 05 or 03 depending on size of of the seed).
* I'll paint the pin black using water color [this helps to avoid reflection + allows me to quickly remove the pin from the final photo during post processing, as my background is also black].
* Using a magifying glass, I determine how the seed can be placed for photographing. Once I decide, I'll glue the seed to the pin using Elmer glue.[/list]

When stacking lower part of the seed, I consider the end position as the point where the pin starts to get into focus. That way, upon stacking, the pin is always blurred and out of focus, which makes post processing simpler and faster.
IMG_20210110_175904_compress26_resize_88.jpg
IMG_20210110_175901_compress83_resize_82.jpg
Thanks.

klevin
Posts: 61
Joined: Fri Dec 14, 2012 5:28 pm
Location: SW New Hampshire, USA

Re: Help with Zerene Stacker

Post by klevin »

Very clever! Thank you for answering.

joshmacro
Posts: 30
Joined: Thu Apr 23, 2020 5:25 pm
Location: New York

Re: Help with Zerene Stacker

Post by joshmacro »

ayyappanm wrote:
Sun Jan 10, 2021 5:25 pm
* I'll paint the pin black using water color [this helps to avoid reflection + allows me to quickly remove the pin from the final photo during post processing, as my background is also black.
Compelling photos ayyappanm. You can also take thin black nails and glue the flat head of the nail to the back of your subject. Then you can stick the sharp side of the nail into a small piece of wood or other type of material. This would create an "L" shape and isolate your subject even more from the background. Just something I have used in the past.

physicsmajor
Posts: 73
Joined: Sun May 10, 2020 12:56 pm

Re: Help with Zerene Stacker

Post by physicsmajor »

Re: fuzziness around fine suspended structures like these hairlike projections

While it won't remove this effect completely (as noted it's due to the optical system), the best method I have found to minimize this is using slabbing leveraging Zerene's PMax algorithm. The PMax algorithm tends to create an inverse halo around bright structures which is slightly darker than the background would otherwise be. This artifact can be made to serve you and at least in part clean up the 'haze' in these areas.

When dealing with minerals that have fine structures like this I often will do a slabbing pass with PMax and then combine the slabs with DMap. If there are DMap artifacts I then touch up from the slabbed PMax images, which frequently look better in these regions than any source image.

If you haven't tried this approach, give it a shot! The improvement is subtle but I do notice it.

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