Focus stacking; use focus rail or manually refocus?

[lavery]

i'm getting back into serious macro photography after a few years of being away from it. Lately I've been focus stacking with a Nikon D800, Nikkor 105mm f2.8 macro, on a very solid tripod, with cable release and all exposure settings on manual. I manually refocus in very small increments given the DOF. All post processing is done in Photoshop CS6.

Question: if all of the above parameters are held constant is there a qualitative difference in image quality between manually refocusing and a high quality macro focusing rail? I must say my approach as described above has yielded very, very good results but if a macro rail can take it to another level I will invest in one.

Your thoughts and opinions would be greatly appreciated!

Thank you.

[NikonUser]

I must say my approach as described above has yielded very, very good results but if a macro rail can take it to another level I will invest in one.

Your thoughts and opinions would be greatly appreciated!

Thank you.

The 105 will go only to 1:1; beyond that it is another level.

Please show us your very very good images.

[Chris S.]

Lavery, welcome to the forum!

Much depends on what you mean by "take it to another level." If you seek better results at current magnification, the answer is probably no--turning the focus ring is the preferred method for magnifications up to a certain point. That point is somewhere around 1x, depending on the situation and the photographer. And as NikonUser pointed out, 1x is the highest magnification your macro lens can provide without tubes, bellows, or an additional lens.

If you seek significantly higher magnifications, you will probably want some kind of rail--but you probably also want different optics. (And lots of other things, as well--it's a slippery slope. )

Rik Littlefield covers your question very nicely here: "Is it better to use a focus rail or the ring on my lens?"

Cheers,

--Chris

[lavery]

Chris, thank you for you informative reply! I'm not currently looking for higher magnifications just the best possible images from my current setup and workflow. I think I will look at tools to automate and bring some speed and accuracy to the stacking process though. I will also check out the link you provided. It looks very interesting.

Thanks again.

[Chris S.]

I think I will look at tools to automate and bring some speed and accuracy to the stacking process though.

Lavery, two types of software come to mind for you:

The first is your choice of program specifically designed to assemble a bunch of images into a focus stack. As well you know, Photoshop can do simple focus stacks. But its stacking capabilities are very limited. A dedicated stacking program will often give far superior output and work much more quickly. I use Zerene Stacker for stacking, then take the output (saved as a tif file) to Photoshop for final adjustment. Another dedicated stacking application is Helicon Focus. Both of these products offer free trials. (BTW, the link I provided earlier, discussing methods of focusing, is a portion of the Zerene Systems Website.)

The second is your choice of program for automating image acquisition. ControlMyNikon is a powerful and inexpensive candidate for this. Sending you to the Zerene Systems Website once again, here is a good guide to using ControlMyNikon for focus stacking.

Cheers,

--Chris

--edited typo

[lavery]

Chris, thanks again. I'll be downloading both those tools for preview tonight or tomorrow. I'll try anything to sped up and improve quality of workflow. In PS6, lots of layers, huge files and copious amounts of coffee while I'm aligning and blending them. The unflattened file runs into GB's. I hope these tools have more efficient algorithms. I'll be testing them with some big samples. I hope the trials are time-limited and not on functionality.

Too, I'll be picking up ControlMyNikon. This should really streamline things.

Photography can really be a financial bottomless pit. So many toys.

Regards,

[Chris S.]

In PS6, lots of layers, huge files and copious amounts of coffee while I'm aligning and blending them. The unflattened file runs into GB's. I hope these tools have more efficient algorithms.

You're going to be pleasantly surprised. I routinely do stacks of 1,500 images, with Zerene Stacker never breaking a sweat. Photoshop's basic approach of making a layer and mask for each input image is inherently limited. No dedicated stacking application, so far as I'm aware, goes about it this way.

I hope the trials are time-limited and not on functionality.

I know that Zerene Stacker's trial is fully functional for 30 days. (BTW, when you try this application, you may find the tutorials very helpful.) It's been a long time since I've tested Helicon Focus; poking briefly at their Web site just now, I didn't see a clear statement of the trial terms--just a mention of "demo mode," whatever this may be.

Photography can really be a financial bottomless pit. So many toys.

Truer words were never spoken. My wallet wants to bite my camera. Er, cameras. . . .

--Chris

[lavery]

Chris,

1500 images!? Wow. You must run very high magnification with very minimal DOF (fractions of mm) and/or deep subjects. I'll now stop whining about 50 shots! Maybe you're referring to running several batches of files to constitute the 1500? That's amazing.

I'm looking forward to test driving both processing tools. Can they handle RAW and are they color-managed? Does Zerene have 64 bit version?

[Chris S.]

Lavery,

1500 images!? Wow. You must run very high magnification with very minimal DOF (fractions of mm) and/or deep subjects.

Right you are. I routinely work as high as 100x magnification (where depth of field is around 1/2000 mm), and have a strong interest in deep subjects.

Maybe you're referring to running several batches of files to constitute the 1500?

On my computer, Zerene Stacker routinely stacks 1,000 or 2,000 images without blinking, and with no need for me to separate them into batches. But for my own ease in retouching, I often do what you describe, approaching visually-difficult stacks by adding an extra step, commonly called "slabbing," which aggregates source images into larger overlapping groups. This approach also lets me combign the advantages of two different stacking algorithms (DMap and PMax). But slabbing is an advanced topic, and based on your work as so-far described, I think you can safely ignore it for now. If you get to the point where slabbing matters to you, check out SlabberJockey (a simple slabbing utility I wrote for my own use, and share at no cost) and Bugslabber (a more sophisticated slabbing utility written by Bill Eldridge, available for a tiny donation to a science charity, on the honor system).

I'm looking forward to test driving both processing tools. Can they handle RAW and are they color-managed? Does Zerene have 64 bit version?

Zerene Stacker definitely has a 64-bit version, which is what I use. I don't know about Helicon focus.

Zerene Stacker has a pass-through approach to color profiles, which I appreciate. It doesn't change your color profile at all--it preserves it for your pixel editing software (such as Photoshop). Some color profiles may not display with perfect accuracy in Zerene Stacker, but this is no problem. I retouch in Zerene Stacker (paint in input layers for spots where the stacking algorithms did a less-perfect job than my eye). But I do color management later, in Photoshop. I don't know about Helicon focus.

Raw handling: This, I think, is an area of widespread misunderstanding, which sadly tends to drag developers of stacking software in a useless direction. The simple--and misleading, to my mind--answer is that Zerene Stacker does not at present accept raw input images, and Helicon Focus does. But let's think about this for a moment--and perhaps dope-slap Helicon for pandering to popular stupidity. Helicon Focus uses default values to convert raw for its use. But if you're OK with default values, why the devil did you bother shooting raw in the first place? Default conversions rob you of the advantages of the raw format. Better to shoot carefully in Tiff or high-quality jpeg.

On the other hand, raw can be very useful, for photographers who understand raw formats, and don't mind tweaking raw conversion for optimal output using a dedicated raw converter. (For Nikon, at present, the best raw conversions come from Nikon Capture NX-2 or Nikon Capture NX-D--despite their clunky, buggy interfaces.)

For my stacks, I often shoot raw plus jpeg. If the subject appears to be within the dynamic range of jpeg, I tweak exposure to record the best possible jpegs, which I then stack and save as a tiff. But if the subject appears to exceed the dynamic range of the jpeg format, I expose for a high-quality raw file, and during raw conversion, adjust the exposure to within the range that a tiff or jpeg file can handle. Then I convert the raw files to tiff or jpeg, stack with Zerene Stacker, save the stacked image as tiff, and tweak in Photoshop.

So to be blunt, I consider Helicon Focus "auto-default" treatment of raw files to be useless. It eliminates any benefit of shooting raw.

Cheers,

--Chris

[lavery]

Hi Chris,

You must do this professionally. I'm curious what hardware/software you use to get 1/2000mm focusing resolution...that's amazing. Certainly ControlMyNikon can't do this can it? Maybe I'm missing something fundamental. Also what's the resolution of each image? You must have a NAS box with TB's of storage!

On the RAW thing maybe I will revisit RAW converters. My workflow has me shooting in NEF (Nikon RAW), bringing it into Lightroom as a DNG and then doing all post production in LR/PS6. My monitors are color-calibrated. You're probably gagging at this point.

I'm very new to this forum and it seems a little out of my league but fascinating. Very arcane stuff. Can you recommend others?

[Chris S.]

I'm curious what hardware/software you use to get 1/2000mm focusing resolution...that's amazing.

You can check out my setup here: Another macro rig (the "Bratcam"). The Bratcam has evolved, so to get the whole picture, make sure to visit the boldfaced links I've added to that post, which describe updates.

Certainly ControlMyNikon can't do this can it?

You're right--ControlMyNikon can't do this. I do use ControlMyNikon for tethering (providing remote control of camera settings, live view and and image review on the computer screen, and saving the images to the computer's hard drive. For focus-stacking movement and camera shutter actuation, I use a Cognisys StackShot controller. This controller is made for exactly this sort of job, so it's very easy to operate. Optionally, Zerene Stacker has features that provide a very nice computer interface for the StackShot controller. It doesn't take much computer horsepower to do these jobs, so I use a rather old laptop on the Bratcam. Since my computers are networked, it's easy to transfer the images to a more powerful machine for stacking and post-processing.

Also what's the resolution of each image?

At present, I have a Nikon D7100 camera body dedicated to the Bratcam. I chose this body because it places 24 megapixels in the DX (APS-C) sensor format, the size of which is a good match to the high-quality image circle of the microscope objectives I commonly use. Since I do have other lenses whose high-quality image circles cover the sensor of a full-frame DSLR, I've sometimes mounted a FF Nikon. FF for me, right now, is the 12.1mp Nikon D700. At some point, I may pick up a 36MP D810--and the day after I do, Nikon will surely announce a 54mp D-whatever.

You must have a NAS box with TB's of storage!

I actually do it a bit differently from the NAS approach. My stacking & post computer has nine hot-swap bays, which allow me to pop hard drives in and out like bread in a toaster. This makes it easy to keep a large library of drives, and take some of them to another location as off-site backups.

On the RAW thing maybe I will revisit RAW converters. My workflow has me shooting in NEF (Nikon RAW), bringing it into Lightroom as a DNG and then doing all post production in LR/PS6. My monitors are color-calibrated. You're probably gagging at this point.

No, not gagging at all. If Nikon behaved sensibly, we would produce DNG files straight out of the camera--there really is no need for camera companies to have proprietary formats. I'm not a Lightroom fan, but plenty of people are. Like you, I calibrate my monitors.

I'm very new to this forum and it seems a little out of my league but fascinating. Very arcane stuff. Can you recommend others?

I can understand your feeling--this forum is a bit like the Manhattan Project of macro/micro photography, and some of our posts are like academic papers (and serve a fairly similar purpose). But this community tends to be very nice to people who want to learn.

I don't know much about other macro fora. When I've glanced at a few (generally because I've followed a link from somewhere else), I've often been chagrined at the level of misinformation to be found there. Misinformation isn't prevalent here, and when it occurs, it's corrected as soon as possible.

So I'd suggest you stick around, make yourself at home, and ask whatever questions you like.

Cheers,

--Chris

[lavery]

Chris, What a great piece of engineering! It has evolved a lot since the days of the Nikon bellows (I used to have a PB-4). I hope Don Wilson has gotten some business off of your posts. He's a great resource.

I'm inspired by this forum and think I may dip my toe into the sub-1:1 macrophotograhy world again and pick up another bellows and/or extension tubes etc. I think there are some issues fitting a PB-6 to a D800 due to the camera body size. I also have a D200 but would prefer to use the D800 if I can find a bellows that will work. Any ideas?

Also, I'm curious; there can't be a lot of light hitting the camera sensor with this rig so what are your exposure and ISO settings like? Obviously high ISO's bring lots of noise. How do you manage this?

Lastly, what started off this conversation was a discussion about focusing rails and I concluded that in the low magnification realm I've been in, using the focusing ring is just fine. I may be revisiting that whole issue and looking at the Cognisys products again.

Also I downloaded Zerene Stacker and Helicon Focus and ran some side-by-side comparisons with Photoshop CS6 using just 20, 36Mp images (D800) while using each of their algorithms. Regardless of the scenario, they crush PS it terms of processing time. I have not critically reviewed image quality but will do so. With Zerene Stacker do you happen to know the difference between the Prosumer and Professional Editions? The differences seem a bit vague.

Your thoughts would be appreciated. Thanks especially for the links into the Bratcam and it's evolution.

[rjlittlefield]

With Zerene Stacker do you happen to know the difference between the Prosumer and Professional Editions? The differences seem a bit vague.

The information you want may be in the Zerene Stacker FAQs. The very first one is What are the differences between Personal, Prosumer, and Professional?

That writeup is too long to copy here in its entirety, but probably the key snippet is

Prosumer Edition is our flagship product for non-professional users. It includes all the technical features from Professional Edition, but at a reduced price for advanced consumers.

If you need further information, please let me know. I'm the fellow who wrote and supports Zerene Stacker, so I'm always interested in how to improve the product and documentation.

--Rik

[lavery]

Rik - Thank you for weighing in on my Zerene question to Chris. It was very helpful.

On a stacking question a little off-topic from particular stacking software I would like your input. At magnifications of 1:1 or lower (i.e. 1:2, 1:3 etc.) is a macro focusing rail superior to rotating the focusing ring? Are the stacking algorithms having to "work less" with alignment and other image issues when stacked from a rail. Will the resulting un-retouched images be qualitatively better all else being equal? If I go higher than 1:1 I will get a rail (probably Stackshot) but is a rail [u]always[/u] ideal?

Your expert commentary would be greatly appreciated and thanks.

[Chris S.]

Chris, What a great piece of engineering! It has evolved a lot since the days of the Nikon bellows (I used to have a PB-4). I hope Don Wilson has gotten some business off of your posts. He's a great resource.

Thanks, Lavery. The Bratcam has continued to evolve since my last documentary post--one of these days, I'll get around to sharing the updates.

I do still use the bellows, though--it's just that I now have the choice of bellows or tube lens. (Since you're new to high-magnification macro, be aware that with some (generally newer) microscope objectives, you must place an additional lens between the objective and the camera; with older objectives, you need empty air between the objective and camera. The "need empty air" objectives are called "finites," and the "need a lens" objectives are called "infinites." This second lens can be called a "converging lens" or "tube lens.") I now use my tube lens more often than my bellows, but the bellows definitely has its place, as some remarkable lenses require a bellows or tubes.

Don Wilson is a fabulous resource. Having a working relationship with a really good fabricator is very freeing. And yes, he has done work for some other forum members.

I'm inspired by this forum and think I may dip my toe into the sub-1:1 macrophotograhy world again and pick up another bellows and/or extension tubes etc. I think there are some issues fitting a PB-6 to a D800 due to the camera body size. I also have a D200 but would prefer to use the D800 if I can find a bellows that will work. Any ideas?

Hurray, we've done it again!

I'm sure you can use a PB-6 bellows on your D800. If it doesn't fit directly, just put a short extension tube between the two. FYI, better tubes with electrical connectivity often vignette in this use, on full frame. The cheap, manual tubes have larger inner diameter, and often work better.

I quite like the PB-6, and recommend it. The Novoflex seems nice, but overpriced. There are some older, built-like-tank bellows that have been discussed from time to time and may offer greater clearance for bigger camera bodies. Since I'm happy with my own bellows, I haven't paid enough attention to know what these would be. Asahi?

Also, I'm curious; there can't be a lot of light hitting the camera sensor with this rig so what are your exposure and ISO settings like? Obviously high ISO's bring lots of noise. How do you manage this?

Actually, a lot of light gets through to the sensor. Remember that when the subject is very small, you can put the light close, and light intensity is squared as distance is halved.

In some particular circumstances, I do need all the light I can get. Very high magnifications (such as 100x) are light hungry, as the effective f/stop is small. And I often use cross polarization, which can waste 7/8 of the light. Before running the light source through the polarizing sheet, I may diffuse it, which cuts the light by maybe 3/4. All this can make the light pretty dim.

I always shoot studio macro at base ISO, and now mostly shoot with continuous light (which is more repeatable and WYSIWYG than flash). But the Bratcam is very stable, so I can use long exposure durations. In the light-hungry scenario described above, 16 or 20-second shots can be necessary. At lower magnifications and without cross-pol, some fraction of a second would be fine.

BUT another issue raises its head with our Nikon bodies: Even if we use mirror-up or exposure delay, the vibration from opening the shutter can cause very significant image softening. Canon offers an electronic shutter mode that, in some models, eliminates the problem (it's called "EFSC"--electronic first shutter curtain). Nikon has introduced this only recently, in the D810. There are at least four ways to get around this: Trade up to a D810, shoot with flash, use a long-enough exposure that the roughly 1/4-second shutter vibration period contributes insignificantly to the exposure, or turn your continuous light off and on so that during the time that shutter-curtain vibration is dissipating, the sensor doesn't see any light. Currently, I'm doing the third method of these most of the time, and will soon move to the fourth method. So right now, I use an 8-second shutter speed, which renders shutter vibration invisible, but often requires that I attenuate the light sources by closing their irises almost completely. They are quartz-halogen illuminators, so I don't want to cycle the bulb with every shot. I have electric shutters on the illuminators, and will (as soon as I get around to it) finish a controller that will blink open and shut with every shot. So my eight-second shutter speeds will go way down, saving me time with deep stacks. LED lights can be electronically gated, eliminating the need for shuttered lights--but I have reasons for preferring halogen illuminators.

I may be revisiting that whole issue and looking at the Cognisys products again.

Cognisys makes great stuff at a reasonable price--essentially impossible to beat if it matches well with your needs. And their customer support is wonderful.

Also I downloaded Zerene Stacker and Helicon Focus and ran some side-by-side comparisons with Photoshop CS6 using just 20, 36Mp images (D800) while using each of their algorithms. Regardless of the scenario, they crush PS it terms of processing time. I have not critically reviewed image quality but will do so.

You might also want to check out the two stacking programs capabilities to retouching stacked outputs from individual input frames, or stacked outputs made using different approaches. Last I checked (some time ago), this was a huge distinguishing difference between Zerene Stacker and Helicon Focus.

Regarding your question to Rik about whether it's better to turn the focus ring or use a rail, you probably didn't get a chance to notice that the reference I pointed you toward, in my first post in your thread, was actually written by Rik. So you already have his considered opinion, written out with care--though no doubt he'll be happy to fill in any blanks you still have.

Cheers,

--Chris

--edited typo