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Focus stacking and post processing workflow

 
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Tarvo



Joined: 02 Oct 2017
Posts: 3
Location: Noarootsi, Estonia

PostPosted: Wed Oct 04, 2017 5:09 pm    Post subject: Focus stacking and post processing workflow Reply with quote

Hi!

I've been camera owner for years. I shoot mostly insects. Handheld and on the field. If possible I try to take shots for focus stacking. Maybe 2-10 slices with f/11 - f/16. I used PS as focus stacking software.

I have experimented with a variety of setups (reverse lenses, shorter macro lenses, tubes) but a couple of years ago I realized that my favorite is Sigma 150mm 2.8 with or without Raynox M-250 + diffused flash (diffusers are not my favorites - I built and bought these too many and still not happy).

About a month ago I bought license for ZS to experiment with focus stacking more seriously with little bit higher magnifications than 1:1.

At first I tried with living species. At night I cut some flower where some insect slept. I took it to my 'studio' and started shooting session. Because room is warm and light sooner or later insects became disquieted. Too sooner.

Then I tried to clamp insects. This was useless. If insect calmed down his antennaes or/and mandibles still moved. Besides, I think, they might get hurt sometimes.

To eliminate stacking errors I needed something static, like dead insect. Fortunately, there are many dead insects in the autumn: flies, wasps, hornets..

I built simplest focus stacking corner to my cabinet. I developed a simple diffused light set with two flashes. I made disc for my Velbon Super Mag where I can read approximated step sizes. I had dead flies, an european hornet and sawfly. I read lot of threads from here and articles form extreme-macro.co.uk. What I don't have is any satisfying photograph. All my photos look too messy. Specially when I want stack specimen from head to tail-end.
Where it comes from? Is it because of insect's condition (dead, dusty, dry)? Or there is something with my light? Step size is not perfect? Is there some post production trick what I don't know? Or this is normal, because I don't know how masters work will look straight after focus stacking software.

Here is an example. I think the subject is some blow fly, Calliphoridae.

Setup was Olympus E-600, Sigma 150mm f/2.8 with Raynox Microscopic Lens M-250, magnification was about 2:1 or littlebit more. 1'', f/4.5, ISO 200. Two speedlights with DIY diffusers (joghurt cups with 3 layers paper tissue). Fly was under the white plastic cup and on the needle. Under the insect was white plastic to illuminate fly from below. Speedlight angles around the plastic cup were about 90 and 270 degrees. Distance between flashes and plastic cup were 8cm. Flashes and insect were on the table. Camera was on the floor with tripod, ballhead and Velbon Super Mag Slider.

There is about 100 shots. At first, in Lightroom i made usual corrections like shadows/highlights, littlebit noise reduction and sharpening. Because PMax increases contrast I took contrast slider down to -20. Then I exported these 100 files as 3000px jpeg. Added to ZS. Aligned. After aligning I checked the slices. At the end of the slices, aligning algorithm was confused - it rotated some slices without any reason what I know. I changed some align options in ZS and tried again. Nothing new. Then I turned rotation off and tried one time more. Rotation turned off worked. After aligning processing I made full stack with PMax and DMap too. Then I made 3 Pmax slab batches: size 30/ overlap 15, 20/10 and 10/5 - so there would be options for retouching. I ran the batches and went to sleep.

When I woke up, I started retouching. After I finished first version and saw that mess I got an idea: I'm retouch two more versions but not so deep to eliminate this mess. One version only with head and another with selective out of focus areas. Because I was already ennuied my work wasn't very perfect (not that the first version was perfect).




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Tarvo



Joined: 02 Oct 2017
Posts: 3
Location: Noarootsi, Estonia

PostPosted: Wed Oct 04, 2017 5:26 pm    Post subject: After PS Reply with quote

After ZS I imported photos to PS and started post production. I cropped images, retouched dust particles, made contrast, explosure, noise corrections, resized, sharpened, blurred...
After these actions it looks little better, I think. But still not sufficient.


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rjlittlefield
Site Admin


Joined: 01 Aug 2006
Posts: 18252
Location: Richland, Washington State, USA

PostPosted: Wed Oct 04, 2017 9:47 pm    Post subject: Reply with quote

Tarvo, welcome aboard! Smile

The problem that you had with rotation in ZS is unusual, but not unknown. It is always best to turn off Rotation if your setup physically does not allow rotation.

I am curious why you exported the files as 3000 pixels instead of camera resolution. I wonder if you are running into a memory limitation in ZS, perhaps because the memory allocation has not been initialized. If so, then go to Options > Preferences > Memory Usage, click the Set Automatically button, restart ZS, and see if that problem goes away.

Now, about the images...

These images look odd, in a way that I cannot recall seeing before.

For your first image, the histogram is a very sharp peak at around level 77. 75% of the pixels have luminosity between 62 and 96, with no pixels at all above 167 and not many below 32. The result is that the image looks dark and washed out.

Adding a levels adjustment layer to stretch the histogram gives me a result that looks more like your second set of images.

These have more "pop", but they still look odd. The colors now look too saturated. Further, even the unobstructed foreground areas do not look sharp.

I am puzzled by the lack of sharpness. Normally when images do not look sharp I suspect either 1) diffraction from stopping down too far, or 2) movement due to mirror or shutter movement. But with your lens combination and setting, you will be around effective f/9, which should be OK for diffraction. With flash, vibration should not be a problem. Consistent with that, I see only symmetric softening, not any streaking like with motion blur. Using PMax, there should be no problem with softening during the stacking.

It might help if we could see a 100% crop of the center of the face, showing some of the big and small bristles. Same crop from the stacked result and one of the original images might be best.

--Rik
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Tarvo



Joined: 02 Oct 2017
Posts: 3
Location: Noarootsi, Estonia

PostPosted: Thu Oct 05, 2017 10:22 am    Post subject: Reply with quote

Thank you for help, Rik!

Quote:
I am curious why you exported the files as 3000 pixels instead of camera resolution. I wonder if you are running into a memory limitation in ZS, perhaps because the memory allocation has not been initialized. If so, then go to Options > Preferences > Memory Usage, click the Set Automatically button, restart ZS, and see if that problem goes away.


'Set Automatically' was first thing when I configured ZS first time. I'm in the country house all summer and autumn and I have here 10 years old Macbook pro: 2,4 GHz Intel Core 2 Duo; upgraded to 6GB memory; NVIDIA GeForce 8600M GT 256 MB. At the beginning of use Zerene I experimented with full resolution jpegs and tiffs. With stacking algorithms computation time I have no problem - I'm take it into account and software can do its job when I dont use the computer. (Still, here some occasions where Zerene crashes). Problems begin when I start retouching process. For me there is too long delay when I change slice or substack. Retouching process with default brush is slow too. Cursor sticks and after releasing it takes too long until it renders results. I found if I want smooth workflow , 2000px is fine to me. 3000px is compromise between 2000px and full resolution. With 3000px resolution there is some space to experiment with composition through crop. So far, when there is no satisfactory results, I dont wanna waste my time for waiting.

Quote:
For your first image, the histogram is a very sharp peak at around level 77. 75% of the pixels have luminosity between 62 and 96, with no pixels at all above 167 and not many below 32. The result is that the image looks dark and washed out.


Yes, I'm aware of this. I cheked histogram from camera before shooting process. I tried to take some actions against this thin histogram. I moved flashes and changed exposure time. What I achieved, is little changes in histrogram and (too) bright areas on fly. I think, I need more work to do with my illumination. I opened Lightroom with my settings before I exported last stack and I see here boosted explosure +.50 and reduced contrast -20.
I'll try it with new settings.

Quote:
The colors now look too saturated.

Yes, I raised vibrance in Lightroom. I will set it to zero.

When I get time I'll shoot completely new stack after working with illumination. On this image is an possibility that flashlights go against the sensor because flashes are perpendicular to the lens.
Right now I'll try Zerene with new settings. Something like these:



Quote:
Normally when images do not look sharp I suspect either 1) diffraction from stopping down too far, or 2) movement due to mirror or shutter movement.


Had 1 second exposure time. Room was not completely dark, but dim. One second gives time to illuminate background too. I use remote cable and mirror lock that is set to 2 seconds.
I put the phone on the lens and measured vibrations with SensorKinetics app. The graph shows enviromental noise, after that here is little vibration during the mirror rise, then again some enviromental noise and after 3 seconds there again little amount more vibrations because the exposure ends.

There is sometimes XY 'nano' movements between shots.

Quote:
But with your lens combination and setting, you will be around effective f/9, which should be OK for diffraction.


Thank you for information! Do you know what is max effective aperture with Sigma 150mm + Raynox MSN-202 in terms of diffraction?
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Harald



Joined: 13 May 2011
Posts: 395
Location: Steinberg, Norway

PostPosted: Wed Nov 15, 2017 7:41 am    Post subject: Reply with quote

Hi there Tarvo,
I took the liberty to do some minor adjustments in PS on your first image.
Adjusted RGB separately and then made a slight "S" curve on the RGB channel to add contrast. All made in curves. Then I redused the "blues" in hue/saturation.
It looks your image is slightly underexposed. More light or slower shutter speed.


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Harald

Lier Fotoklubb / NSFF
AFIAP / CPS
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http://www.500px.com/blender11
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