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Problem/Disturbance at 10x using Wemacro Rail/200mm f4 lens
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skrama



Joined: 17 Aug 2017
Posts: 15
Location: Iowa City, Iowa

PostPosted: Sun Sep 03, 2017 11:09 am    Post subject: Problem/Disturbance at 10x using Wemacro Rail/200mm f4 lens Reply with quote

The photograph is of the stamens of the garden lily flower. I see a lot of camera shake and disturbance in the final photograph composed by Zerene Stacker. The total number of photographs for the stacking 95.

Please help me in understanding the mistakes I have done in this composition.


I took this photograph with Sony a7R II with Canon FD 200mm f4 lens with 10x objective bought from Wemacro and the Wemacro rail. Of course I didnt have any extra stabilization that I see among the tablet-op set-up examples from Charles' post.

Set up:

Heavy desk table (made of solid wood), Wemacro rail. Two flashes at 1/16 power in manual mode. Two 4 LED Promaster light systems on either side of the table at full power. Using the Paul C. Buff transceiver to trigger the flash (one as master and other flash as slave).

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Lou Jost



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PostPosted: Sun Sep 03, 2017 1:03 pm    Post subject: Reply with quote

The wormlike things are dirt on your sensor.

Why would you mix flash and continuous light?
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rjlittlefield
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PostPosted: Sun Sep 03, 2017 1:44 pm    Post subject: Reply with quote

It's unclear exactly what stability issues there are.

As Lou says, the wormlike things are due to dirt on your sensor, turned into "dust trails" by action of the stacking software.

The trails look much different at upper right versus lower left -- short and sharply curved versus long and gently curved. This certainly means that the computation alignment process is having trouble tracking the subject, in addition to whatever physical alignment issues there may be with the rail system.

In general, you should go to Options > Preferences > Alignment and turn off any options that you don't need. With a 10X microscope objective in a rail system, I recommend to turn off Scale and Rotate, leaving X and Y Shift turned on. Brightness can be either off or on, depending on the stability of your lighting and which stacking method you're using.

You mention that "I see a lot of camera shake and disturbance in the final photograph composed by Zerene Stacker." But I don't know what "see" means. I can't tell whether you're looking at the dust trails (as I did), or at some pixel-level detail that I cannot see in this web-sized image.

Can you show us more precisely what you're seeing?

Posting an image that is marked up with arrows and so on would be very helpful.

--Rik
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Charles Krebs



Joined: 01 Aug 2006
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Location: Issaquah, WA USA

PostPosted: Sun Sep 03, 2017 2:58 pm    Post subject: Reply with quote

Quote:
. Two flashes at 1/16 power in manual mode. Two 4 LED Promaster light systems on either side of the table at full power.


A little confused about the lighting... and it could possibly contribute to your problem. What shutter speed was used on the camera? Was the imaging light almost entirely form the flash units or was there a significant contribution from the LED lights?

Here, for example, is a scenario that might cause problems (note I say MIGHT, because at this point I really don't know much about your setup)....
With electronic flash the vast majority of mirrorless cameras first close and then reopen the shutter before the picture is actually recorded . These two mechanical actions (shutter closing and re-opening) will cause a small amount of vibration. This vibration will likely go un-noticed if all of the imaging light is coming from flash units at 1/16 power. But if there is a significant amount of imaging light coming from a continuous light (the LEDs in this case) there is a real possibility that you will also record a slightly blurred image simultaneously with the flash image (due to shutter induced vibration).

It's better to use either nothing but flash for illumination, or nothing but continuous light. If you use continuous light you would want to use a camera mode that offers EFSC (electronic first shutter curtain) or better yet a fully electronic shutter operation.

This doesn't explain the dis-symmetry of the dust "worms" that Rik mentioned which does indicate a different problem.
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skrama



Joined: 17 Aug 2017
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Location: Iowa City, Iowa

PostPosted: Sun Sep 03, 2017 3:34 pm    Post subject: Reply with quote

Thanks Lou. I was hoping to stop any motion with the flash. Hence I used the flash. With the continuous light the camera wanted an ISO of 1250 with the aperture at f=4 with 10x objective mounted in front of it.

With the flash I used ISO 200.

What techniques one use for preventing the motion of the sensor? I used the silent shutter but off-camera flashes dont work with silent shutter on Sony a7R II.

Any pointers would greatly help me.
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skrama



Joined: 17 Aug 2017
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Location: Iowa City, Iowa

PostPosted: Sun Sep 03, 2017 3:59 pm    Post subject: Reply with quote

rjlittlefield wrote:


It's unclear exactly what stability issues there are.

As Lou says, the wormlike things are due to dirt on your sensor, turned into "dust trails" by action of the stacking software.



I thought that the black worm-like lines are due to the stability of my current system. Thanks for clarifying.

Quote:


The trails look much different at upper right versus lower left -- short and sharply curved versus long and gently curved. This certainly means that the computation alignment process is having trouble tracking the subject, in addition to whatever physical alignment issues there may be with the rail system.

In general, you should go to Options > Preferences > Alignment and turn off any options that you don't need. With a 10X microscope objective in a rail system, I recommend to turn off Scale and Rotate, leaving X and Y Shift turned on. Brightness can be either off or on, depending on the stability of your lighting and which stacking method you're using.



I will try with those options and report back. I will also clean the camera sensor and take new set of shots and update the results.

Quote:


You mention that "I see a lot of camera shake and disturbance in the final photograph composed by Zerene Stacker." But I don't know what "see" means. I can't tell whether you're looking at the dust trails (as I did), or at some pixel-level detail that I cannot see in this web-sized image.

Can you show us more precisely what you're seeing?

Posting an image that is marked up with arrows and so on would be very helpful.

--Rik



Sorry for not being very clear and being vague by using words like see.

The two issues you pointed out. Its not due to the lower size of the final image. I see them in the final image. Also, didnt mean that Zerene Stacker is doing it either. The black worm-like trails and the stamens at 10x dont seem like they are very clear to me. For example at the tip of the stamen, the black bead like structure May be I am expecting too much for a 10x.
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skrama



Joined: 17 Aug 2017
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Location: Iowa City, Iowa

PostPosted: Sun Sep 03, 2017 4:11 pm    Post subject: Reply with quote

Charles Krebs wrote:
Quote:
. Two flashes at 1/16 power in manual mode. Two 4 LED Promaster light systems on either side of the table at full power.


A little confused about the lighting... and it could possibly contribute to your problem. What shutter speed was used on the camera? Was the imaging light almost entirely form the flash units or was there a significant contribution from the LED lights?



I am using the two LED system to fix the starting and ending positions in my focus stacking experiment. Not much light in my basement. Once I fix those, the ISO of 200 and shutter speed of 100 renders the image almost black even with those LEDs. Hence the two light system is only to help me in initial composing of the image.

Quote:


Here, for example, is a scenario that might cause problems (note I say MIGHT, because at this point I really don't know much about your setup)....
With electronic flash the vast majority of mirrorless cameras first close and then reopen the shutter before the picture is actually recorded . These two mechanical actions (shutter closing and re-opening) will cause a small amount of vibration. This vibration will likely go un-noticed if all of the imaging light is coming from flash units at 1/16 power. But if there is a significant amount of imaging light coming from a continuous light (the LEDs in this case) there is a real possibility that you will also record a slightly blurred image simultaneously with the flash image (due to shutter induced vibration).



This hasnt occurred to me and I will check those options and see how to use the camera only using EFSC. I will read/re-read the article in the FAQ regarding the EFSC.

Thanks to you, Rik and Lou for helpful comments.
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Lou Jost



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PostPosted: Sun Sep 03, 2017 5:23 pm    Post subject: Reply with quote

That's a good reason to use the continuous lights. If your shutter synch speed is fast enough, they won't affect the image much. You still may want to turn them off during the exposure because they may still make bright reflections on glossy surfaces, and those will blur due to environmental vibrations.
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Beatsy



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PostPosted: Mon Sep 04, 2017 1:26 am    Post subject: Reply with quote

Could the asymmetry of the dust worms be due to the flower wilting during stacking? I wrap damp paper towel around the end of the stem for botanical specimens and wedge them in a little "vase" made from a cut-down plastic centrifuge tube (the little ones, about an inch long with a snap on cap).
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rjlittlefield
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PostPosted: Tue Sep 05, 2017 9:53 am    Post subject: Reply with quote

Quote:
Could the asymmetry of the dust worms be due to the flower wilting during stacking?

That could definitely be a contributor. If wilting is happening, then turning off Rotation for alignment may end up making the result worse, not better.

Another possibility -- the one I had in mind -- is that, with this asymmetric composition, change in appearance with focus might be misleading the alignment algorithm into thinking that the subject had moved even though it really had not. In that case turning off Rotation is a good thing to do because it will give the software one less degree of freedom to do the wrong thing.

When working with subjects that may wilt, I find it helpful to shoot an extra "check" frame, after the main stack and back at the start of focus, so that I can at least detect without question whether the subject moved while the stack was being shot.

--Rik
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skrama



Joined: 17 Aug 2017
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Location: Iowa City, Iowa

PostPosted: Tue Sep 05, 2017 10:55 am    Post subject: Reply with quote

rjlittlefield wrote:
Quote:
Could the asymmetry of the dust worms be due to the flower wilting during stacking?

That could definitely be a contributor. If wilting is happening, then turning off Rotation for alignment may end up making the result worse, not better.

Another possibility -- the one I had in mind -- is that, with this asymmetric composition, change in appearance with focus might be misleading the alignment algorithm into thinking that the subject had moved even though it really had not. In that case turning off Rotation is a good thing to do because it will give the software one less degree of freedom to do the wrong thing.

When working with subjects that may wilt, I find it helpful to shoot an extra "check" frame, after the main stack and back at the start of focus, so that I can at least detect without question whether the subject moved while the stack was being shot.

--Rik


Rik,

The flower wasn't wilting as it was a fresh flower from the plant.

Secondly, with scale and rotation turning off, it made the result worse. The image is in my home computer. I will update the post with image.

One other thing when I first started this thread is "stability". My Wemacro rail is just sitting on the table without any hooks/bolts/screws to secure it. So, the movement forward during the stacking may be causing the camera/sensor move a little. Do you think that can be a possibility? I will stabilizing mechanism soon, similar to either Charles or yours or Chris S', etc.

Again, many thanks to everyone for chiming in and helping me in understanding the nuances of this whole "micro/macro" world.
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rjlittlefield
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PostPosted: Tue Sep 05, 2017 1:57 pm    Post subject: Reply with quote

Have you looked at the stack using the techniques described at https://zerenesystems.com/cms/stacker/docs/faqlist#how_can_i_detect_movement_in_my_stack ?

Playing the stack like a filmstrip should at least clarify what the motion looks like. If it's slow and gradual, then a gradually deforming subject is the way to bet. If there are sudden big jumps, then sideways movement of the rail is probably the culprit.

--Rik
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Chris S.
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PostPosted: Wed Sep 06, 2017 12:29 am    Post subject: Reply with quote

skrama wrote:

I am using the two LED system to fix the starting and ending positions in my focus stacking experiment. Not much light in my basement. Once I fix those, the ISO of 200 and shutter speed of 100 renders the image almost black even with those LEDs.
(Boldface added)

"Almost black" could be part of your problem. If the image isn't completely black, those LEDs--or other room lighting--are contributing to your exposure. I'd suggest turning the LED's off, and possibly other room lighting, until you get a completely black image when flash is not used.

Also, you mention Paul C. Buff transceivers. Are you also using his flashes? If so, his flashes such as Alien Bees and White Lightning have longer flash durations under partial power than at full; by 1/16 power, the durations are pretty long, and could easily provide time for vibration to be an issue. (Buff's Einsteins can be set for the opposite behavior, of course).

Do be aware that flash can can actually induce vibration in some subjects, by rapidly heating the subject, which causes the air around the subject to heat, whereupon the heat-excited air particles "kick" the subject. But for many macro photographers, flash is a near-magical eliminator of vibration.

You mentioned building a solid rig, which is a good idea. When your camera system and subject holding system are mechanically coupled by a single, solidly-attached base, vibration-free work is much easier to do.

Quote:
. . .the stamens at 10x don't seem like they are very clear to me. For example at the tip of the stamen, the black bead like structure May be I am expecting too much for a 10x.

Another issue may be applying here. Are the features you mention fully illuminated from a wide range of angles (ideally, from every portion of their "sky")? If not, you may be running into "utilized aperture" problems, which rob detail.

--Chris S.
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skrama



Joined: 17 Aug 2017
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Location: Iowa City, Iowa

PostPosted: Wed Sep 06, 2017 8:01 am    Post subject: Reply with quote

Chris S. wrote:
skrama wrote:

I am using the two LED system to fix the starting and ending positions in my focus stacking experiment. Not much light in my basement. Once I fix those, the ISO of 200 and shutter speed of 100 renders the image almost black even with those LEDs.
(Boldface added)

"Almost black" could be part of your problem. If the image isn't completely black, those LEDs--or other room lighting--are contributing to your exposure. I'd suggest turning the LED's off, and possibly other room lighting, until you get a completely black image when flash is not used.



Tried a couple of experiments yesterday. I am posting the images here. The first image is a result of 68 images stacked from ZS. I didn't use any flash this time, just the two LED systems. With auto ISO, at Ts=1/100, f=4, the ISO obtained by a7R ii was 2000, so I fixed the ISO at 2000. I turned on the Silent Shutter option on a7R ii. The first image is with Scale and Rotation turned "off" and the second image is both Scale and Rotation turned "on" with everything else left the way the software comes with.

Quote:


Also, you mention Paul C. Buff transceivers. Are you also using his flashes? If so, his flashes such as Alien Bees and White Lightning have longer flash durations under partial power than at full; by 1/16 power, the durations are pretty long, and could easily provide time for vibration to be an issue. (Buff's Einsteins can be set for the opposite behavior, of course).

Do be aware that flash can can actually induce vibration in some subjects, by rapidly heating the subject, which causes the air around the subject to heat, whereupon the heat-excited air particles "kick" the subject. But for many macro photographers, flash is a near-magical eliminator of vibration.



I am using his transceiver and receiver but using Phottix Mitros and Yongnuo 568-EX II both at 1/16 power and firing them with transceiver. I do have PCB AlienBees (one) and Einstein (two in #).

Quote:


You mentioned building a solid rig, which is a good idea. When your camera system and subject holding system are mechanically coupled by a single, solidly-attached base, vibration-free work is much easier to do.

Quote:
. . .the stamens at 10x don't seem like they are very clear to me. For example at the tip of the stamen, the black bead like structure May be I am expecting too much for a 10x.

Another issue may be applying here. Are the features you mention fully illuminated from a wide range of angles (ideally, from every portion of their "sky")? If not, you may be running into "utilized aperture" problems, which rob detail.

--Chris S.


I am going to contact the person whom you mentioned in your set-up thread. But also looking at locally to see if anyone can do it here.




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Charles Krebs



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PostPosted: Wed Sep 06, 2017 11:54 am    Post subject: Reply with quote

Quote:
. With auto ISO, at Ts=1/100, f=4, the ISO obtained by a7R ii was 2000, so I fixed the ISO at 2000. I turned on the Silent Shutter option on a7R ii.


I don't understand why you would want to use ISO 2000 with a subject like this. If you are at 1/100 sec at ISO 2000, then you would be somewhere around 1/4 second at ISO 100. Even with an excellent camera like the a7R II your image quality would be better at ISO 100-200. And importantly, noise "build-up" in PMax stacking mode should be far less.

The f-stop setting on the lens really doesn't do much of anything as long as it is large enough to avoid vignetting. With a fully electronic shutter, a shutter speed of 1/4 second is perfectly fine... as long as there is no external ("environmental") source of vibration. (And if that were the case you should be using high speed flash for your lighting).

A good thing to do is to set up on a subject and focus so that you can see some very small specular highlights. Magnify those on the rear LCD screen as much as the camera allows. Observe the specular highlight and see if it "jiggles" at all (it should not during the actual exposure). Gently "tap" the camera or lens and see how long it takes for the system to settle down. While the electronic shutter should not cause any vibration problems, the mechanical movement of the rail as it steps to the next position could. You want to be sure you set sufficient "settle" time on your stacking controller. Be aware of anything that might cause "environmental" vibrations... walking around, moderate to loud music, fans, air conditioners. Even an operating clothes washer or dryer in another part of a frame house can sometimes be an issue.


On that first image...
Quote:
The flower wasn't wilting as it was a fresh flower from the plant.

Did you carefully check the source images as Rik suggested? "Wilting" or slight changes in shape of plant matter is a very significant issue for large stacks. Even when I take special care (as Beatsy suggested) it still occurs during a significant number of large stacks. It may be barely noticeable unless you check for it.
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Last edited by Charles Krebs on Wed Sep 06, 2017 3:33 pm; edited 1 time in total
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