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Equipment Setup Help Needed

 
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Jwcollect



Joined: 06 Nov 2017
Posts: 15

PostPosted: Thu Nov 23, 2017 9:28 am    Post subject: Equipment Setup Help Needed Reply with quote

Hi,

Happy Thanksgiving everyone.

I recently setup my Nikon D600 with a 100mm macro lenses, a Stackshot and Zerene Stacker. I'm able to do decent stacks but I've left all the settings at their factor settings. Can someone please help me tweak the setting to get better stacks. Also, what's the best setup for my camera.

Thanks
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rjlittlefield
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Joined: 01 Aug 2006
Posts: 18244
Location: Richland, Washington State, USA

PostPosted: Thu Nov 23, 2017 9:58 am    Post subject: Reply with quote

Happy Thanksgiving!

Your question is quite broad and impossible to answer without more information. It's a bit like going to the doctor and asking right off "How can I feel better?", without saying what your ailments are.

I suggest to show some sample images -- both the whole frame and crops to actual pixels -- plus some overview shots that show your setup. Spell out what you mean by "factory settings". We need minimally to know f#, shutter speed, ISO setting, step size, whether your illumination is flash or continuous, and what software methods you've used.

If there are specific things about your images that have you concerned, then tell us what those are.

Also, be aware that this thread is misplaced in the Image Galleries section of the forum. I'll move it to Macro and Micro Technique and Technical Discussions after you've had a chance to see this reply.

--Rik
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Jwcollect



Joined: 06 Nov 2017
Posts: 15

PostPosted: Thu Nov 23, 2017 3:30 pm    Post subject: Reply with quote

Hi,

My camera settings are iso 400, f8, 1/160 with continuous lighting. Im using Stackshot as is when powered up and Zerene Stacker without making any changes from the install. Frankly, Im not sure what to change.



Notice there are double line artifacts on the picture. The picture doesn't seem as sharp and clear as I think it should be.

Thank you
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BugEZ



Joined: 26 Mar 2011
Posts: 642
Location: Loves Park Illinois

PostPosted: Thu Nov 23, 2017 7:35 pm    Post subject: Reply with quote

Your equipment is probably fine.

Not sure what mode you are operating the shutter. A time delay mode where the mirror pops up first, then the shutter is delayed by a few seconds can help reduce shutter vibration. If high speed flash is used, the shutter delay usually is not needed.

With continuous light a longer exposure ~ 0.5 seconds can improve studio shots as the shutter vibration usually settles in a fraction of that time. A 160th exposure may allow some shutter-shake to obscure the subject a bit.

If your rig is very solidly mounted and heavy these vibrations may be small. If the StackShot is supported on a tripod, they probably are important.

In the upper left side it looks like there are some dust trails. This is caused by dust on the sensor. These artifacts away from the subject can be removed by image processing (PhotoShop for example). Sensor cleaning can also fix this. For your next photos. I clean my sensor several times each year.

To help the experts diagnose stacking issues, they will want particulars of the exposure mode, perhaps a photo of your rig. With your excellent equipment I am quite certain you will find success.

Keith
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Aloha
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rjlittlefield
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Joined: 01 Aug 2006
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Location: Richland, Washington State, USA

PostPosted: Thu Nov 23, 2017 7:49 pm    Post subject: Reply with quote

Thank you for the additional information.

Quote:
Frankly, Im not sure what to change.

Quick summary:

- Add light
- Reduce ISO
- Avoid shooting with live view turned on
- Learn how to use DMap, especially how to adjust the contrast threshold slider
- Learn retouching in Zerene, to combine the best bits of DMap and PMax
- Use mirror lockup
- Check alignment of camera and stackshot

Here is a marked-up image followed by some further explanation that may help.



A. The lines of bright dots look like "defect trails" caused by "warm pixels". Warm pixels are when individual photosites on your sensor happen to accumulate stray electrical charge due to leakage faster than their neighbors. The sensor cannot distinguish between charge due to light and charge due to leakage, so those sites end up being seen as bright. Each source image will show single bright spots, which stay at the same position in every image. But as you shift focus, the subject changes size and moves across the frame. In order to stack the images, the software has to adjust the size and position of every frame in order to keep the subject lined up. This causes the bright spots to move across the frame. Then the stacking process sees the spots as details to be maintained, so they end up in the output at every different position that they occupied in the source images, after alignment. The result is that individual bright dots in the source frames turn into lines of dots in the result.

You can minimize the intensity of warm pixels by adding light, so that the light accumulates relatively faster than the stray charge does. Where warm pixels are a problem, flash can be a wonderful solution because it delivers a lot of light in a short amount of time. Shooting in raw format and converting to TIFF or JPEG for processing may help, because raw conversion programs sometimes know where warm pixels occur and can replace those spots with information interpolated from surrounding good pixels.

One reason these pixels are called "warm" is that the rate of leakage depends on temperature. The hotter the sensor, the higher the leakage. The sensor gets warm whenever it runs in live view mode, so when warm pixels are a problem, it's a good idea to run in live view for only the shortest practical amount of time.

Defect trails tend to form straight lines that point to the geometric center of the focus stepping process. Ideally that will be the center of the image. But I've added blue lines to extend your defect trails, and it's clear that they point pretty far off center. A common cause for this effect is to have the camera pointed slightly off to one side, with respect to the axis of the StackShot.

B. The fuzzy dark streaks at upper left are probably more defect trails, but this time due to a spot on the lens or possibly dust on the sensor. Again there will be a single blurred dot on each frame, which is turned into a trail by the stacking process. Note that the dark blurred lines point to the same location as the lines of bright dots.

C. The generally high level of noise even in smooth background results from a combination of 1) having your ISO too high, so that individual source images are noisy, plus 2) using the PMax stacking method, which tends to accumulate noise because it tends to confuse noise with detail at the pixel level.

D. The dark blue halos surrounding some of your yellow petals are due to incomplete elimination of out-of-focus information by the PMax stacking method. Those can be made to go away if you use the DMap stacking method. But note that DMap has a control called the "contrast threshold slider", which you must operate properly in order to get good results. Study the tutorial "How To Use DMap", which is linked off the main Tutorials index page on the Zerene website. The proper setting of the slider will make all of the nearly uniform out-of-focus background go "black in preview", except for a very narrow band right next to your focused subject.

Quote:
The picture doesn't seem as sharp and clear as I think it should be.

There are several possible reasons for this. First, take a good look at your individual source images to be sure that they are as sharp and clear as you think they should be. This is a place where mirror lockup can help a lot. Using the DMap stacking method instead of PMax can also help, because sometimes with setups like yours there is a bit of movement of subject features, due to changes in perspective, that Zerene Stacker cannot completely correct for, and the PMax stacking method can turn that bit of movement into a bit of blur. DMap mostly selects pixels from single frames, so it can give a cleaner rendition when uncompensated movement is a problem.

But note that DMap has its own challenges. Where your subject has strong front/back overlaps, such as between the lip and the rear petals and sepals of your orchids, PMax will probably do a better job of rendering everything sharp and without halos. So, you get the best results by rendering twice, once with DMap and once with PMax, then using Zerene Stacker's retouching tool to combine the best bits of both. Again, this is addressed in the How To Use DMap tutorial, plus the retouching tutorials also linked on the Tutorials index page.

--Rik
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Jwcollect



Joined: 06 Nov 2017
Posts: 15

PostPosted: Fri Nov 24, 2017 3:29 am    Post subject: Reply with quote

I'm shooting in aperture mode.

Thank you for the advice and help, I have a lot to learn.

Thanks
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rjlittlefield
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Joined: 01 Aug 2006
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Location: Richland, Washington State, USA

PostPosted: Fri Nov 24, 2017 9:54 am    Post subject: Reply with quote

Jwcollect wrote:
I'm shooting in aperture mode.

For stacking, it's best to shoot in manual mode. Any mode that involves automatic exposure stands the risk that the camera will make different choices from one frame to another. The software tries to compensate for such differences, but it cannot do a perfect job. In the worst case, you end up with light/dark bands in your stacked output. This is most likely to occur with DMap, again because it works by selecting pixel values from typically only one frame at a time. PMax is mostly invulnerable to light/dark banding due to exposure changes, but as mentioned above, PMax has other downsides. Uniform exposure, the same for every frame, is the best practice.

--Rik
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Jwcollect



Joined: 06 Nov 2017
Posts: 15

PostPosted: Sat Nov 25, 2017 7:41 am    Post subject: Reply with quote

I've made several changes to my setup including attaching my camera directly to the Stackshot. I shot this in manual mode at 1/60th, iso 100, f8, added light and reduced the step. I definitely have to clean the sensor. It was 76 steps, used DMAP and contrast 35. What is the mottling in the background especially near the bottom. Also there is a dark line or halo around the bottom leaf of the left orchid, does that have to do with the contrast I set?

Thank you



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rjlittlefield
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PostPosted: Sat Nov 25, 2017 9:48 am    Post subject: Reply with quote

The mottling is due to exposure variation between frames, combined with a contrast threshold setting that is too low.

I cannot get my eye on the dark line or halo that you mention, but yes, a defect that's described like that is probably due to contrast threshold setting also.

Again, for a scene like this with focused subject surrounded by nearly uniform background, the proper setting for contrast threshold makes the entire background go black in preview, except for a narrow band right next to the subject. Like this:



The setting that you used was notably too low:



Note that the percentile number is the fraction of total pixels that are painted black in preview. With a scene like this, the number should be about equal to the fraction of frame occupied by featureless background, around 58% in this example.

With a much lower setting, such as 35%, a lot of background is not marked black in preview. That leaves it open to mottling due to essentially random frame selection. No focused detail means no useful information about which frame to use, so the decisions get driven by pixel noise.

--Rik

Edit: fixed typo & formatting


Last edited by rjlittlefield on Sat Nov 25, 2017 10:27 am; edited 1 time in total
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Jwcollect



Joined: 06 Nov 2017
Posts: 15

PostPosted: Sat Nov 25, 2017 10:20 am    Post subject: Reply with quote

Thanks Rik.
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