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A general guide for using the Forum with some rules and tips
Stack software, comparative speed, optimizations and others
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ofarcis




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PostPosted: Jul 19, 2013 22:27    Post subject: Stack software, comparative speed, optimizations and others  

Hi all,

In recent weeks I have been busy but now I've had a little time I will present a report I created from stacked processing times of the most common programs and optimizations, quirks, etc. First I is to describe the testing platform.

Hardware Computer:

- CPU: Intel I5-2500 Quad core 3.30Ghz
- MB: Asus P8 H67-M Pro
- RAM: 8 Gb DDR3 1.333Mhz Dual Chanel
- HD: SSD OCX-Vertex2 in SATA 6Gb/s
- GPU: AMD Radeon HD 6850 4Gb

Hardware take pictures

- Focus rail: MacroRail Professional
- Camera: Canon EOS 600D 18Mpx
- Microscope objective: Nikon BD Plan 5x
- Others: bellow & adaptors

Software:

- Helicon Focus v.5.3.12. Payment stack program from Helicon Soft. Can you download demo version from http://www.heliconsoft.com/software-downloads/
- CombineZP v. Free stack program. Can you download from http://www.hadleyweb.pwp.blueyonder.co.uk/CZP/Installation.htm
- Zerene Stacker v.1.04 Build T201305212130. Payment stack program from Zerene Systems. Can you download demo version from http://zerenesystems.com/cms/stacker/softwaredownloads
- Macrophotography v.1 .1 .0 . 5. Payment program to control camera, focus rail, stacks/sub-stacks, cropping, etc. Can you download demo version from:
Canon: http://MacroRail.com/software/Macrophotography_Canon_Demo_1.1.0.5.zip
Nikon: http://MacroRail.com/software/Macrophotography_Nikon_Demo_1.1.0.5.zip
User Manual: http://MacroRail.com/software/UserManual_1.1.0.5.pdf
- MS Windows 7 x64.


ENVIRONMENT:

All tests were performed on Windows without virtual memory and photographed images were executed and performed from HDD SSD to minimize the burden of the applications and / or photographs.

The times presented are solely the load time and process stack programs.

Since this forum like insects, instead of using a mineral I used the common fly killed a month ago. The images that are presented neither edited or retouched from the software mentioned above or from an editing program such as Photoshop, are presented as they were generated by stacking programs.


DESCRIPTION, RESTRICTIONS AND PROBLEMS FOUND

Before presenting data, images and displays certain characteristics that I used in the programs:

HELICON FOCUS. Good stacking program controlled processing of the lights when there are certain reflexes without editing. Apparently all loaded into memory to process images so if you do not have Windows virtual memory dynamically defined as we run out of memory. When loading images in memory the process is muy quick.

Stacks do not allow more than 255 images so if you want to stack more pictures of this amount have to use sub-stacks. For this reason, the 400 photos has had to use a sub-stack of 202/2. That is, 202 pictures per stack with 2 overlapping photographs.

COMBINEZP. Good free program but where there have been problems when stacking hairy insect photographs. The modes "Do Stack", "Do Soft Stack" and "Pyramid Do Stack Weighted" not valid. At the end of the stack is chosen by "Pyramid Weighted Average" method to get a proper result.

ZERENE STACKER. Program stack of great quality, especially in the treatment of hair, which can handle large volume of photographies without sub-stacks, but slower performance than the rest. It is advisable to make a Preview Stack of large stacks.

Macrophotography. A program to control the camera, the MacroRail, the stacking process / sub-stack, indicate the size of work or crop the image before stacking, retouch images, etc.. It supports the focus rails; MacroRail, Macrocarril, Stack Shot or any approach lane to use a motor Unipolar or Bipolar with simple or more complex electronic CNC type.


PROCESS:

I use a EOS 600D camera pictures at highest resolution JPG (18Mpx) = 5,184 W x 3,456 H = 17,915,904 pixels.

On each test 100 and 400 photographs have been stacked as follows:

- Stacking original size picture.
- Stacking cropping the size of the head of the common housefly.
- Stacking ½ the original size of the picture.
- Stacking ¼ the original size of the picture.
- Stacking 1/8 of the original size of the picture.
- Sub-stack with the original size of the picture.
- Sub-stack cropping the size of the head of the common housefly.

For the stacking test 100 photographs with a spacing of 6.6 microns to total displacement of 0.66mm. For the 400 photographs, there has been a separation of 1.6 microns with a total displacement of 0.66 mm.

Below is a table of the results I obtained. The times are in the format MM: SS. CC, where MM is minutes, SS is seconds and CC are hundredths of a second.
Looking at the table, we can see that the sub-stacks system is not recommended for small stacks of less than 100 pictures. The more pictures do more interesting is the use of sub-stacks. Especially in programs that loaded photos in memory like Helicon and Combine.

Moreover, we can see that the response speed of Helicon Focus is much faster than the other programs.

Also, sometimes piled whole picture when really only want a part of this, then the option to cut before stacking is important to save large delays.

Originally we are working with an image of 5,184x3,456 pixels, but if we tell you that we generate a stack of 1/4 of this size (1,296x864) is more than enough to see how we have our image. In fact, many times we do not use if you want this resolution to be presented at a forum as in this case. However, the stacking time being considerably reduced up to 8 times faster than the standard stack.

Sub-stacks for high number of pictures; if you use sub-stacks in Helicon Focus can gain until 30% of faster, depends of situations. In Combine ZP the difference is very little. In Zerene, the use of sub-stacks increments a little the final time.

Gradually I will publish the pictures of times achieved, working screens and insect pictures.

I feel my English is so bad, if any data is not understood please ask me.

Best regards, Oscar.



TablaBenchmark.jpg
 Description:
This is the table with the results I obtained.The times are in the format MM: SS. CC, where MM is minutes, SS is seconds and CC are hundredths of a second.
 Viewed:  22554 Time(s)

TablaBenchmark.jpg


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ofarcis




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PostPosted: Jul 19, 2013 22:53    Post subject: Re: Stack software, comparative speed, optimizations and others  

Hi to all,

This is the screen captures for 100 photographs stack test.

SETUP:
http://MacroRail.com/imagenes/Benchmark100Setup.jpg


TEST ORIGINAL SIZE:
http://MacroRail.com/imagenes/Benchmark100Test01.jpg

Stack images:
Helicon: http://MacroRail.com/imagenes/StackH001001_4.jpg
CombineZP: http://MacroRail.com/imagenes/StackC001001_4.jpg
Zerene: http://MacroRail.com/imagenes/StackZ001001_4.jpg


TEST CROP IMAGE:
http://MacroRail.com/imagenes/Benchmark100Test02.jpg

Stack images:
Helicon: http://MacroRail.com/imagenes/StackH001001_5.jpg
CombineZP: http://MacroRail.com/imagenes/StackC001001_5.jpg
Zerene: http://MacroRail.com/imagenes/StackZ001001_5.jpg


TEST OUTPUT SIZE 1/2 ORIGINAL:
http://MacroRail.com/imagenes/Benchmark100Test03.jpg

Stack images:
Helicon: http://MacroRail.com/imagenes/StackH001001_3.jpg
CombineZP: http://MacroRail.com/imagenes/StackC001001_3.jpg
Zerene: http://MacroRail.com/imagenes/StackZ001001_3.jpg


TEST OUTPUT SIZE 1/4 ORIGINAL:
http://MacroRail.com/imagenes/Benchmark100Test04.jpg

Stack images. Because this size is very small I put here this three images:
Helicon:
http://MacroRail.com/imagenes/StackH001001_1.jpg
CombineZP:
http://MacroRail.com/imagenes/StackC001001_1.jpg
Zerene:
http://MacroRail.com/imagenes/StackZ001001_1.jpg



TEST OUTPUT SIZE 1/8 ORIGINAL:
http://MacroRail.com/imagenes/Benchmark100Test05.jpg

Stack images:
Helicon: http://MacroRail.com/imagenes/StackH001001_1.jpg
CombineZP: http://MacroRail.com/imagenes/StackC001001_1.jpg
Zerene: http://MacroRail.com/imagenes/StackZ001001_1.jpg


TEST SUB-STACK ORIGINAL 36/4:
http://MacroRail.com/imagenes/Benchmark100Test06.jpg

Stack images:
Helicon: http://MacroRail.com/imagenes/StackH001001_6.jpg
CombineZP: http://MacroRail.com/imagenes/StackC001001_6.jpg
Zerene: http://MacroRail.com/imagenes/StackZ001001_6.jpg


TEST SUB-STACK CROP 36/4:
http://MacroRail.com/imagenes/Benchmark100Test07.jpg

Stack images:
Helicon: http://MacroRail.com/imagenes/StackH001001_7.jpg
CombineZP: http://MacroRail.com/imagenes/StackC001001_7.jpg
Zerene: http://MacroRail.com/imagenes/StackZ001001_7.jpg

Regards, Oscar.
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PostPosted: Jul 19, 2013 22:58    Post subject: Re: Stack software, comparative speed, optimizations and others  

Hi to all,

This is some screen captures for 400 photographs stack test. .

Regards, Oscar.



Benchmark400SetupAndCrop.jpg
 Description:
SETUP & cropping head of mousefly
 Viewed:  22608 Time(s)

Benchmark400SetupAndCrop.jpg



Benchmark400SampleSubStack.jpg
 Description:
Sub-stack sample (CombineZP)
 Viewed:  22614 Time(s)

Benchmark400SampleSubStack.jpg


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ofarcis




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PostPosted: Jul 19, 2013 23:30    Post subject: Re: Stack software, comparative speed, optimizations and others  

Hi to all,

This is the screen captures for 400 photographs stack test.

TEST ORIGINAL SIZE:
http://MacroRail.com/imagenes/Benchmark400Test01.jpg

Stack images:
Helicon: http://MacroRail.com/imagenes/StackH000476_4.jpg
CombineZP: http://MacroRail.com/imagenes/StackC000476_4.jpg
Zerene: http://MacroRail.com/imagenes/StackZ000476_4.jpg


TEST CROP IMAGE:
http://MacroRail.com/imagenes/Benchmark400Test02.jpg

Stack images:
Helicon: http://MacroRail.com/imagenes/StackH000476_5.jpg
CombineZP: http://MacroRail.com/imagenes/StackC000476_5.jpg
Zerene: http://MacroRail.com/imagenes/StackZ000476_5.jpg


TEST OUTPUT SIZE 1/2 ORIGINAL:
http://MacroRail.com/imagenes/Benchmark400Test03.jpg

Stack images:
Helicon: http://MacroRail.com/imagenes/StackH000476_3.jpg
CombineZP: http://MacroRail.com/imagenes/StackC000476_3.jpg
Zerene: http://MacroRail.com/imagenes/StackZ000476_3.jpg


TEST OUTPUT SIZE 1/4 ORIGINAL:
http://MacroRail.com/imagenes/Benchmark400Test04.jpg

Stack images. Because this size is very small I put here this three images:
Helicon:
http://MacroRail.com/imagenes/StackH000476_1.jpg
CombineZP:
http://MacroRail.com/imagenes/StackC000476_1.jpg
Zerene:
http://MacroRail.com/imagenes/StackZ000476_1.jpg



TEST OUTPUT SIZE 1/8 ORIGINAL:
http://MacroRail.com/imagenes/Benchmark400Test05.jpg

Stack images:
Helicon: http://MacroRail.com/imagenes/StackH000476_1.jpg
CombineZP: http://MacroRail.com/imagenes/StackC000476_1.jpg
Zerene: http://MacroRail.com/imagenes/StackZ000476_1.jpg


TEST SUB-STACK ORIGINAL 36/4:
http://MacroRail.com/imagenes/Benchmark400Test06.jpg

Stack images:
Helicon: http://MacroRail.com/imagenes/StackH000476_6.jpg
CombineZP: http://MacroRail.com/imagenes/StackC000476_6.jpg
Zerene: http://MacroRail.com/imagenes/StackZ000476_6.jpg


TEST SUB-STACK CROP 36/4:
http://MacroRail.com/imagenes/Benchmark400Test07.jpg

Stack images:
Helicon: http://MacroRail.com/imagenes/StackH000476_7.jpg
CombineZP: http://MacroRail.com/imagenes/StackC000476_7.jpg
Zerene: http://MacroRail.com/imagenes/StackZ000476_7.jpg
(all links normalized by FMF)

Regards, Oscar.
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ofarcis




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PostPosted: Jul 19, 2013 23:32    Post subject: Re: Stack software, comparative speed, optimizations and others  

Hi to all,

I've posted all the information and images relating to the tests I have done. If you have any comments or want to expand any of the information, will be welcome.

I repeated the tests four times and times of each other vary little.

Best regards, Oscar.
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ofarcis




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PostPosted: Jul 20, 2013 19:38    Post subject: Re: Stack software, comparative speed, optimizations and others  

Hi to all,

In the first post i talk about the CombineZP problems with high number of phtographs to process:

Quote:
COMBINEZP. Good free program but where there have been problems when stacking hairy insect photographs. The modes "Do Stack", "Do Soft Stack" and "Pyramid Do Stack Weighted" not valid. At the end of the stack is chosen by "Pyramid Weighted Average" method to get a proper result.


I solve this problem with two ways; one of the is to use Sub-stack another is to change to Pyramid Weighted Average" method.

You can see an example of the problems that present when i use these modes that present problems:

Regards, Oscar.



StackCError000476_4.jpg
 Description:
Nomal stack 400 photographs. Bad stack result
 Viewed:  22563 Time(s)

StackCError000476_4.jpg



StackCError000476_5.jpg
 Description:
Nomal stack 400 photographs. Bad stack result
 Viewed:  22593 Time(s)

StackCError000476_5.jpg



StackCError000476_6.jpg
 Description:
Sub-stack 400 photographs. Good stack result
 Viewed:  22584 Time(s)

StackCError000476_6.jpg



StackCError000476_7.jpg
 Description:
Sub-stack 400 photographs. Good stack result
 Viewed:  22589 Time(s)

StackCError000476_7.jpg


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Mike Wood




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PostPosted: Jul 21, 2013 11:55    Post subject: Re: Stack software, comparative speed, optimizations and others  

Oscar, you deserve a medal for showing us all this detailed information. I can't imagine how much time you have spent doing all this, besides finding the time to share it on this forum. It is extremely useful and important, not least because it saves us mortals time and effort to improve our photography.
Don't worry about your english, amigo; it is better than many English speakers would type !

Best regards,
Mike
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PostPosted: Jul 21, 2013 12:36    Post subject: Re: Stack software, comparative speed, optimizations and others  

Hi Mike,

Thanks for you comment. I really needed a complete week to run the test four times, capture screen 14x3x4=168, preparing results, repeat some test for problems with Helicon & CombineZP, summarize, etc. But if you see this study and the results we can save time in future stacks.

Regards, Oscar.
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PostPosted: Jul 25, 2013 03:18    Post subject: Re: Stack software, comparative speed, optimizations and others  

Hi all,

I performed a test using Adobe Photoshop to stack 100 photos of the first stack.

Specifically I used Adobe Photoshop CS3 and the result is very bad. In fact, I would say that this version is not able to stack.

On the process, is as follows for the stack to original size:

1. - Photomerge load in layers: 3:42
2. - Align layers: 8:20
3. - Blend layers: 4:47

Total time: 16:49. Approximately the double of Zerene Stacker

Regards, Oscar.
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PostPosted: Jul 25, 2013 11:04    Post subject: Re: Stack software, comparative speed, optimizations and others  

Hi to all,

I run some times the test now with Adobe Photoshop CS4 and works some times but not ever, some times block the Photoshop.

In some times too need a long time (i think block but not).

I only can run the 100 photographs, the test of 400 it's impossible in my computer with CS4 version.

See the table attach to this post. You can compare the total time with my first table in the first post. The time to process is very high compared with specific stack programs. Now see the stacked images.

Original size:
http://MacroRail.com/imagenes/StackP001001_1.jpg

Cropping size:
http://MacroRail.com/imagenes/StackP001001_2.jpg

1/2 original size:
http://MacroRail.com/imagenes/StackP001001_3.jpg

1/4 original size:
http://MacroRail.com/imagenes/StackP001001_4.jpg

1/8 original size.
http://MacroRail.com/imagenes/StackP001001_5.jpg
(links normalized by FMF)

Curiously the time to align the images cropping is very high (See red text in table). I repeat three times; the first and second need a lot of time respect to the rest of test. The third block the Photoshop.

The quality of result is very poor in Photoshop CS4. See the image attach to this post and click to see more better.

Some object missing, the texture is poor near to the hairs, etc.

I think that Photoshop not is a solution for good stacks, the time is very high, some times block the Photoshop and to process a big number of pictures, need a very high memory capacity.

Regards, Oscar.



BenchMarkPhotoshopCS4.jpg
 Description:
Times to stack 100 images with Adobe Photoshop CS4
 Viewed:  22338 Time(s)

BenchMarkPhotoshopCS4.jpg



CompareZerenePhotoshopCS4.jpg
 Description:
Compare results. Left Zerene 1/2 original size, Right Photoshop CS4 1/2 Original size. Click to see better
 Viewed:  22336 Time(s)

CompareZerenePhotoshopCS4.jpg


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Don Lum




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PostPosted: Oct 15, 2013 11:32    Post subject: Re: Stack software, comparative speed, optimizations and others  

Mike Wood wrote:
Oscar, you deserve a medal for showing us all this detailed information. I can't imagine how much time you have spent doing all this, besides finding the time to share it on this forum. It is extremely useful and important, not least because it saves us mortals time and effort to improve our photography.
Don't worry about your english, amigo; it is better than many English speakers would type !

Best regards,
Mike

Hi Oscar, I agree with Mike. You do remarkable work.

With best wishes,

Don

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Adrian Pripoae




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PostPosted: Sep 10, 2014 13:37    Post subject: Re: Stack software, comparative speed, optimizations and others  

Hi Oscar

First things first... You are doing an amazing work... 400 stacks..... I've just done 12 with my combineZP software. You can see the result in my post "First attempt".

I would need some advice from a professional. I am using a Zeiss Stemi 2000 binocular microscope with a Canon Rebel 3Ti camera with a EF 55 mm 1:1.4 lens. I am somehow restricted by the mount of my camera to the microscope (direct vertical - when focusing the camera is moving vertically - the lens is connected to the mount and to the microscope - any suggestions?)... For the moment is working. My maximum optical magnification is 80x (after ocular (1.6 objective X 5 multiplication prism x 10 ocular lens). Also I am trying to use a Canon G16 but I don't have a remote shooting software compatible with this camera - Any suggestions?

And now to the photo techniques:

Is there a way to estimate how many steps you have to take in order to have a proper set of photos for a good stack? My microscope does not have a fine tuning button for adjusting focus. Currently I am trying to focus on different zones of the subject and after that stack the set.

The software: I don't know how but my software is crushing to many times to my liking. I was thinking that the image size was to big (5184x3456 pxls) but I see that you use a full frame size and is still working. Is there a proper way to do things like align first and stack (which is the best method in your opinion)

Thanks
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ofarcis




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PostPosted: Sep 10, 2014 14:16    Post subject: Re: Stack software, comparative speed, optimizations and others  

Hi Adrian,

You don't work to 80x, really works to 8x because the ocular not is used by the camera. Normally you mount the camera in adaptor, this to multiply len and next the len. In this case use 1.6 * 5x = 8x.

I recomended you to read this article; http://www.mineral-forum.com/message-board/viewtopic.php?t=3316

To know exactly your magnification range can use a calibration microscope crystal like this:
http://www.ebay.com/itm/New-0-01mm-Microscope-Stage-Micrometer-Calibration-Slide-/260898793383?pt=LH_DefaultDomain_0&hash=item3cbec7a7a7
(link normalized by FMF)

Take a picture and calculate the real magnification.

Some people need until 1.600 stack photos, normally to take insects pictures of 60x-120x, real magnification not supossed magnification when use a binocular.

My experience except very expensive microscope is that the best results is obtained when use a camera with a bellow and a microscope objective. Reduce the intermediated lens and win in quality results.

Sorry but the Canon G16 havent SDK from Canon and can't development software to show/capture, etc.

The combine ZP is a very poor software to stack minerals, the best results can obtain with Helicon Focus method B and in some especific cases method C. And yes, i working with full frame of the camera. I used a software that i develop.

Regards, Oscar.
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PostPosted: Sep 10, 2014 15:05    Post subject: Re: Stack software, comparative speed, optimizations and others  

Thank you very much

I just got a quote for a fine tuning focus adjusting mount (Stemi Mount coarse/fine for 32 mm) of 2200 CAD so aprox.1600 euros. Is it excessive? For the magnification factor I use a graphic scale - with the same parameters intermediately after I am taking a shot at a 1 cm plastic ruler and I am adding it to the final picture. So I understand that you have your own remote shooting software! Is it better than what Canon is having for DSLR cameras? I downloaded the demo but I am stuck when validating my copy - I get error code 316.

Once again Thanks and I will keep you in the loop with my results.

Adrian Pripoae
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PostPosted: Sep 10, 2014 21:54    Post subject: Re: Stack software, comparative speed, optimizations and others  

Hi Adrian,

For this price you have a complete solution in MacroRail.com used a bellow/lens or use microscope or both.

Sorry but for commercial questions contact by private message.

Regards, Oscar.
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PostPosted: Sep 10, 2014 22:07    Post subject: Re: Stack software, comparative speed, optimizations and others  

Yes you are right. Sorry!!
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newryqs




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PostPosted: Sep 11, 2014 08:08    Post subject: Re: Stack software, comparative speed, optimizations and others  

If the columns in your table represent hours of processing time you should upgrade your computer. I just ran a 200 photo stack for both dmap and pmax in Zerene and the stacks took 10 minutes or a little more. Try a gamer's computer with 8 quads of processing and 16gb of RAM. In the 1980's. I had a16khz Apple computer and I tried to draw a crystal of cuprite in reduced point group symmetry and it took overnight to process. That computer died and the next generation up, which was only a Mac Plus would perform the same calculation in 2 minutes.
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ofarcis




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PostPosted: Sep 11, 2014 09:11    Post subject: Re: Stack software, comparative speed, optimizations and others  

Seeing his response clearly has not read the article. Simply that you had read the first post you had seen both the characteristics of the computer used as the measured times are in minutes, seconds and hundredths of seconds.

Please, next time before you say something, read the article, thanks.

Regards, Oscar.
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Don Lum




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PostPosted: Jun 15, 2015 14:21    Post subject: Re: Stack software, comparative speed, optimizations and others  

Olympus has a new camera that has built-in focus stacking capabilities. It doesn't stack 100 or 400 photographs unfortunately. I thought this might be of interest to some of the FMF members.

Olympus’ TG-3 Tough Cam Sports Serious Macro Capabilities Like Focus Stacking

Published on March 30, 2014 by DL Cade





The PEN-like Stylus SH-1 wasn’t the only camera to get its debut tonight. Olympus also introduced a new Tough camera, the Stylus Tough TG-3, whose claim to fame is impressive macro photography capabilities including an automatic focus stacking feature that’ll help expand your depth of field when you’re shooting really tiny subjects.

Basic specs are the same as the SH-1: a 16-megapixel 1/2.3-inch BSI CMOS sensor is joined by a TruePic VII processor, a 3-inch 460k-dot LCD (this one’s not touch) and built-in WiFi. On top of that, the TG-3 also boasts a fastest-in-class 4x 25-100mm equivalent f/2.0-4.9 lens, GPS, water depth and elevation sensors, and an e-compass.

Additionally, as you might expect from a Tough camera, this little shooter can withstand a great deal of abuse. The TG-3 is freezeproof to 14-degrees F, waterproof down to 50ft, shockproof from 7 feet up, crushproof to 220 pounds and dustproof.

Here are a few more pictures of the red model (it also comes in black):

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sarahah




Joined: 06 Sep 2017
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PostPosted: Sep 06, 2017 06:48    Post subject: Re: Stack software, comparative speed, optimizations and others  

I was looking for the same Helicon Focus v.5.3.12. Payment stack program from Helicon Soft. Thanks for the shared link.
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