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Andrena helvola and a few questions

 
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Jonas



Joined: 25 Feb 2017
Posts: 11

PostPosted: Fri May 11, 2018 3:05 am    Post subject: Andrena helvola and a few questions Reply with quote

I have a good 30 stacks under my belt and I feel that I am starting to get the hang of atleast some aspects of the wonderous world of high magnification photography, but some things still cause me a lot of problems. These things include, but are not limited to:

"useless details"; with most of my stacks, I notice that I like lower resolution images better than the full resolution output from my camera (6k x 4k). This troubles me as rescaling images to lower pixel sizes surely mean a loss of detail.

Areas of high contrast; in the process of stacking, I notice that dark areas tend to have their contrast increased to the point of complete detail loss - even when stacking with RAW files converted to TIFF. This happens even when I stack with Dmap. This is noticable in the shadow under one of the antennae in the attached photo.

"scruffy" fine detail; fine hairs and other sharp structures tend to be a little blurred in my initial images and this slight blurredness is made worse when I stack the images and I have to (over)sharpen or otherwise post process the details to get a somewhat decent look. This issue is particularly noticable in white hairs. I feel that my images are never as "crisp" as many of the excellent photos that are shared here.

Smooth surfaces are never truly smooth; there always seem to be some level of detail in areas that - atleast under a dissection microscope - appear to be smooth. This gives the final image a somewhat "dirty" look. I realize that there is quite alot of actual dirt in this image, but I still feel like some of the areas could look "smoother". A noise-reduction issue, maybe?



Where to go from here? I am looking for my next equipment upgrade, but I can't figure out if the jump to microscope objectives is "worth it". Are there other aspects of my setup that require more urgent upgrades?

I hope you will take the time to answer a couple of these "problems" - any and all feedback is greatly appreciated.

This image was taken with a Nikon d7100, Tokina 100mm 2.6 macro pro, Raynox msn-202 and the R1C1 flash-system. Light is diffused with some opaque plastic combined with oven tray liner; one flash firing from the left and one from above the specimen.
The stack was processed with slabmaker and Zerene; retouched dmap with details from Pmax. I did some levels adjustments, noise reduction, color correction (so much chromatic aberration with my camera), some detail work (Topaz Detail) and finally I sharpened it with some highpass -> soft light filters. I fear that may have gone a little over board with the sharpening, but I find it really hard to judge this as I tend to go "blind" to this after working with the stack too long - this goes for contrast and detail work aswell.

100% crop (1024x1024):



This second photo was made in roughly the same way, but is cropped a little harder.

100% crop:


Thank you for your time!
-Jonas
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Jonas



Joined: 25 Feb 2017
Posts: 11

PostPosted: Fri May 11, 2018 12:04 pm    Post subject: Reply with quote

Here's the link to the full resolution (and less contrasty) images:
#1: https://flic.kr/p/274fJGX
#2: https://flic.kr/p/274g2nk

-Jonas
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Jonas



Joined: 25 Feb 2017
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PostPosted: Sat May 12, 2018 10:33 am    Post subject: Reply with quote

After spending some time away from the pictures I can now see that atleast the second stack is hideously overworked and oversharpened. The sharpening on the first stack looks better, but I think I went too hard on the details with Topaz.
I suspect that the complete lack of replies to my thread stems from the fact that the answers may already be on here, so I am going to do some searching and hopefully find what I am looking for in existing threads.

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

PostPosted: Sat May 12, 2018 11:07 am    Post subject: Re: Andrena helvola and a few questions Reply with quote

Well, in my case the lack of reply just means that I've been busy with other tasks during the, um, 32 hours since you posted.

I can answer a couple of your questions.

Quote:
Areas of high contrast; in the process of stacking, I notice that dark areas tend to have their contrast increased to the point of complete detail loss - even when stacking with RAW files converted to TIFF. This happens even when I stack with Dmap. This is noticable in the shadow under one of the antennae in the attached photo.

If contrasts and/or colors change even with DMap, then the problem must be due to brightness "correction" during alignment. What brightness correction actually means is to adjust scale and gamma so that the mean and variance of the luminance channel is the same for each image, after alignment. This does a pretty good job of correcting for actual exposure differences, say due to flash inconsistencies or less than completely stable continuous illumination. But it can also create problems where none existed otherwise, particularly if the first or last frame in the stack has a significantly different overall appearance from the frames in the middle.

I suggest to remove the checkmark at Options > Preferences > Alignment > Brightness and see if the problem with DMap goes away.

PMax is a different story. The stacking algorithm used by PMax tends to increase contrast as an unavoidable side effect. The only cure for that problem is adjust contrast in post-processing, having been sure to pre-process or stack in such a way as to not clip desired darks or lights before that.

If you're shooting raw and processing to TIFF, then it is simple to adjust the raw development parameters so as to leave a comfortable margin at both ends of the histogram.

Otherwise, another useful technique is to save the output image as 16-bit TIFF, with "Retain extended dynamic range" selected during the save. That will brighten and cut contrast as necessary to be sure that no pixels get clipped at black/white, and then you can apply levels & curves adjustment to taste in post-processing.

Quote:
Smooth surfaces are never truly smooth; there always seem to be some level of detail in areas that - atleast under a dissection microscope - appear to be smooth. This gives the final image a somewhat "dirty" look. I realize that there is quite alot of actual dirt in this image, but I still feel like some of the areas could look "smoother". A noise-reduction issue, maybe?

You're probably aware that PMax can accumulate noise, but DMap will not.

If you're seeing this problem even with DMap, then the best bet is that you're seeing real detail that the dissection scope did not reveal, perhaps because of different illumination, perhaps because of actual resolution, perhaps because pixel-peeping an image almost always reveals details that the eye overlooks when viewing through a scope, or perhaps because digital sharpening has made apparent detail that went overlooked in the original source images.

The best way I know to debug this issue is to carefully study your source images. Be sure to run them through the same processing steps, especially sharpening, that you're applying to the stacked output.

I hope this helps!

--Rik
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Jonas



Joined: 25 Feb 2017
Posts: 11

PostPosted: Sat May 12, 2018 12:28 pm    Post subject: Reply with quote

Thank you very much for your reply, Rik.
I have to apologize for my comment regarding the lack of replies. The activity of people on this board is so high and questions seem get answered rather quickly, so I assumed that the silence was a hint from the "hive mind" Smile I hope I have not appeared ungrateful.

I will try running problematic stacks without the brightness correction and take care that every image is exposed similarly beforehand. These projects are the first that I have run using tiffs converted from RAW-files, and I am not sure I would do it again - not untill I have invested in a stationary PC with more processing power and RAM than this decade old laptop, atleast.

I suspect that the "noise" I am seeing has been exasterbated by the detail work done in Topaz - I get carried away by the desired effect on wanted details and tend to forget that the process amplifies noise and subtle differences aswell.
The pixel-peeping is definitely an issue and it has caused me many sleepless nights. And it seems to only get worse!


Since I posted my questions, a new one has surfaced, that you may be able to help med with aswell:
My lens should have an optimal aperture around f5.6, but when I shoot with the msn-202 mounted, everything is pretty much a blur. I can see where the "sharpest" regions are supposed to be in the photo, but nothing is really sharp. I have done some not very scientific tests and found that I can stop down to f11-ish without seeing much diffraction diffusion, but I would like to test it properly.
So my question is: is it expected that my 100mm lens + msn-202 is not sharp at all at 5.6 (or lower for that matter) and that whatever effect is responsible for it does not disappear untill I stop down to around f8? This has bothered me for quite a while Smile


Thanks again for your reply!
-jonas
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rjlittlefield
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PostPosted: Sat May 12, 2018 5:32 pm    Post subject: Reply with quote

Jonas wrote:
I have to apologize for my comment regarding the lack of replies. The activity of people on this board is so high and questions seem get answered rather quickly, so I assumed that the silence was a hint from the "hive mind" Smile

No worries -- I know we set such a high standard that sometimes it's hard to keep up to it ourselves! Rolling Eyes Laughing

Quote:
These projects are the first that I have run using tiffs converted from RAW-files, and I am not sure I would do it again - not untill I have invested in a stationary PC with more processing power and RAM than this decade old laptop, atleast.

Understood. Shooting raw may be the path to absolute best quality, but sometimes it can be so expensive that it gets in the way of any result at all! JPEG's that are carefully illuminated and exposed to avoid clipping can do excellent work too and are much less expensive to work with.

Quote:
My lens should have an optimal aperture around f5.6, but when I shoot with the msn-202 mounted, everything is pretty much a blur. I can see where the "sharpest" regions are supposed to be in the photo, but nothing is really sharp. I have done some not very scientific tests and found that I can stop down to f11-ish without seeing much diffraction diffusion, but I would like to test it properly.
So my question is: is it expected that my 100mm lens + msn-202 is not sharp at all at 5.6 (or lower for that matter) and that whatever effect is responsible for it does not disappear untill I stop down to around f8?

Yes, that's to be expected. The reason is that while you're attending to the f/5.6 which refers to the 100 mm lens, the "heavy lifting" is actually being done by the msn-202, which at only 37 mm focal length is then being asked to work at only f/2.1 (37 mm focal length, divided by aperture size 100mm/5.6). I expect you can easily imagine that the msn-202 is sharper at f/4.1 (=37/(100/11)) than it is at f/2.1.

If you're thinking in terms of diffraction, and imagining that at f/5.6 and 2.7X, you must be running at effective f/20.7 because Feff = Fnominal*(mag+1), then be aware that formula does not apply when you're using closeup lenses. Instead, you do the calculation of Feff using the rear lens alone, even though the added lens provides more magnification. Assuming that your rear lens is set at infinity focus and f/11, then your effective aperture is only f/11, just on the edge of diffraction for the D7100 at 24 megapixels on an APS-C sensor.

--Rik
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ChrisR
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PostPosted: Sun May 13, 2018 1:54 am    Post subject: Reply with quote

The detail in the "hairs" around the eye in the full image is good, whereas (on my screen ) it doesn't look super sharp when compressed to 1024 wide. I think that's just the way compression makes things look. Some subjects work the other way.
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Jonas



Joined: 25 Feb 2017
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PostPosted: Sun May 13, 2018 7:57 am    Post subject: Reply with quote

rjlittlefield wrote:

Yes, that's to be expected. The reason is that while you're attending to the f/5.6 which refers to the 100 mm lens, the "heavy lifting" is actually being done by the msn-202, which at only 37 mm focal length is then being asked to work at only f/2.1 (37 mm focal length, divided by aperture size 100mm/5.6). I expect you can easily imagine that the msn-202 is sharper at f/4.1 (=37/(100/11)) than it is at f/2.1.

Thank you for this! This takes care of a major headache Smile I take it that I still have to consider a change in effective aperture from mounting the combination (lens+raynox) on my extension tubes (68mm)?

@ChrisR: Thank you for your reply. There are enough factors affecting the look and feel of the final photo to make my head spin - I am truly grateful that this forum exists (and is managed by such a competent team)!

-Jonas
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mawyatt



Joined: 22 Aug 2013
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PostPosted: Sun May 13, 2018 8:35 am    Post subject: Reply with quote

Jonas wrote:
These projects are the first that I have run using tiffs converted from RAW-files, and I am not sure I would do it again - not untill I have invested in a stationary PC with more processing power and RAM than this decade old laptop, atleast.


Jonas,

Certain Nikon cameras can produce TIFFs files directly. This saves the headache of converting from RAW to TIFF in post. I know the D500, D800 & D850 do. Zerene can accept these in camera generated TIFFs without issue I've found.

Best,
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rjlittlefield
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PostPosted: Sun May 13, 2018 2:06 pm    Post subject: Reply with quote

Jonas wrote:
I take it that I still have to consider a change in effective aperture from mounting the combination (lens+raynox) on my extension tubes (68mm)?

Correct, but there may be a catch there too. It depends on exactly what equipment you have. With a modern Nikon camera, lens, and tubes, quite possibly the f-number that is shown on your camera is already the effective aperture, corrected for close focus and/or extension tubes. To check, put your lens on extension tubes, extend it for closest possible focus, then check to see what is the largest f-number that you can set. If the reported f-number is the same as what's printed on your lens, then you'll need to do the correction manually. But if the reported f-number is significantly larger (that is, a smaller aperture), then most likely it is already the effective f-number, corrected for whatever the camera and lens can know about.

If you add an external stop, for example by sticking a microscope objective on the front of the lens instead of that msn-202, then the effective aperture will be smaller than the camera thinks it is.

And if you were using Canon instead of Nikon, then I would say that yes, unconditionally, you need to do the correction manually because Canon DSLRs never do it automatically.

Complications on complications...

mawyatt wrote:
Certain Nikon cameras can produce TIFFs files directly. This saves the headache of converting from RAW to TIFF in post.

True, but there are TIFFs and then there are TIFFs. Typically when you convert from RAW to TIFF in post, intending to stack, you would choose to make 16-bit TIFF so as to preserve the full dynamic range. But Nikon cameras, as far as I know, only shoot 8-bit TIFF, which makes them no better than JPEG in that regard.

--Rik
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mawyatt



Joined: 22 Aug 2013
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Location: Clearwater

PostPosted: Sun May 13, 2018 3:08 pm    Post subject: Reply with quote

rjlittlefield wrote:

mawyatt wrote:
Certain Nikon cameras can produce TIFFs files directly. This saves the headache of converting from RAW to TIFF in post.

True, but there are TIFFs and then there are TIFFs. Typically when you convert from RAW to TIFF in post, intending to stack, you would choose to make 16-bit TIFF so as to preserve the full dynamic range. But Nikon cameras, as far as I know, only shoot 8-bit TIFF, which makes them no better than JPEG in that regard.

--Rik


Rik,

We looked at this some time ago and found that Nikon was doing something with their camera internal generated TIFFs. I recall a comparison between internal and external TIFFs created from RAW that showed the internal TIFFs were as good as the externals for the particular subject being evaluated. I don't remember the exact time nor details though.

Edit: Found the threads.

https://www.photomacrography.net/forum/viewtopic.php?t=35006&start=60

https://www.photomacrography.net/forum/viewtopic.php?t=35277&postdays=0&postorder=asc&highlight=nikon+tiff&start=0

Best,
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rjlittlefield
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PostPosted: Sun May 13, 2018 5:05 pm    Post subject: Reply with quote

Mke, I definitely do remember those earlier discussions. But with respect, my impression is that what they mostly showed was that you never did figure out how to properly post-process your raw files, and in the end you gave up trying to figure it out because the in-camera TIFFs were giving a good result for what you were doing.

In the thread here, Jonas has specifically raised the issue of high contrast causing dark parts of his subject to lose detail.

Improved detail in dark regions, without blowing out the brights, is one area where shooting raw, properly tuning the development parameters, and using a 16-bit workflow can make big improvements.

I appreciate that for your particular work the in-camera TIFFs look like a great choice.

But I want to be clear about the issues so that Jonas can make an informed decision for his own work.

--Rik
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Jonas



Joined: 25 Feb 2017
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PostPosted: Mon May 14, 2018 3:39 pm    Post subject: Reply with quote

Rik and Mike,

The idea of avoiding a fairly time-consuming conversion is certainly alluring, but sadly my camera does not have this feature. Thank you both for your insight, though.

- Jonas
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