Stacking Software

Here you can discuss topics such as focus stacking, stitching and other techniques that relate to the processing of micrographs.
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Pat Thielen
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Stacking Software

#1 Post by Pat Thielen » Mon Mar 05, 2018 11:31 pm

Hey everyone!

I have a question regarding stacking software -- I'm wondering which one is the best when working with microscopic images and macro photography. Right now I use Photoshop CC, and it does work rather well but it isn't perfect. I did try Helicon Focus, but the trial period ran out before I was able to get a lot done with it. It did seem to be better than Photoshop -- It didn't get confused as easily (for lack of a better word). I know there are other products out there but I'm really not sure how they all stack up against one another. Ha! See what I did there?

Not clever.

Anyway, I would appreciate any advice, opinions, etc. on the subject. As I do more and more photography using my microscope I know I'll be doing more and more stacking. So, having something that works better than Photoshop would be quite nice to have and a good overall investment.

Thanks much!
Pat Thielen
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Re: Stacking Software

#2 Post by MichaelG. » Tue Mar 06, 2018 8:32 am

Hello Pat

I would recommend that you try Zerene Stacker

http://zerenesystems.com/cms/stacker

It's versatile, and seems very stable on my Macs.

MichaelG.
.
.
As an example; here's a tricky little subject that I tried last week:

Moss Mite : Cepheus dentratus : collected by David Copestake, and currently on the Postal Microscopical Society's circuit. [overall dimensions are stated to be 875 x 650 microns]

The whole specimen is mounted in a small cell on a standard microscope slide, and is intended for viewing by incident light on the stereo microscope.

This is the result in transmitted light, using my old Leitz Laborlux
10x objective, 3.5x projection eyepiece, and m4/3 sensor. Thirty frames at 2 micron steps.
Stack of thirty 4000x3000 pixel frames ... image reduced to 600x450 pixels for this site.
Stack of thirty 4000x3000 pixel frames ... image reduced to 600x450 pixels for this site.
IMG_1850.JPG (310.81 KiB) Viewed 14548 times
In absolute terms, it's certainly not good ... but I think the stacking software has handled it well.

MichaelG.
Last edited by MichaelG. on Tue Mar 06, 2018 10:59 am, edited 3 times in total.
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Re: Stacking Software

#3 Post by MicroBob » Tue Mar 06, 2018 8:35 am

Hi Pat,

you might have a look at PICOLAY:

http://www.picolay.de/

It is free, the users like it and the author is giving very good support.


Bob

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Re: Stacking Software

#4 Post by Hobbyst46 » Tue Mar 06, 2018 9:00 am

Picolay works fine for me. Helicon on first impression seems better than others.
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Pat Thielen
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Re: Stacking Software

#5 Post by Pat Thielen » Tue Mar 06, 2018 1:42 pm

I just tried Zerene Stacker but it doesn't work with RAW files like Helicon Focus does. So, at this point I'm looking at Helicon. Another one was mentioned that is free (I can't recall the name) so I'll give that one a try as well and see how it goes.


Thanks for the suggestions; I appreciate it!

edit: Does PICOLAY work with RAW files?
Pat Thielen
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Re: Stacking Software

#6 Post by MichaelG. » Tue Mar 06, 2018 2:27 pm

Pat Thielen wrote:edit: Does PICOLAY work with RAW files?
The answer would appear to be "some of them"
http://www.picolay.icbm.de/picolay-manual.pdf

My Panasonic RW2 files are not listed.
... but that's largely irrelevant to me, as it's 'Windows only' software.

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Re: Stacking Software

#7 Post by Pat Thielen » Tue Mar 06, 2018 2:30 pm

MichaelG. wrote:
Pat Thielen wrote:edit: Does PICOLAY work with RAW files?
The answer would appear to be "some of them"
http://www.picolay.icbm.de/picolay-manual.pdf

My Panasonic RW2 files are not listed.
... but that's largely irrelevant to me, as it's 'Windows only' software.

MichaelG.

Thanks -- I *just* figured out how to read the manual! :lol:

I'm running a test image; it is really slow and I got a memory error of some sort (I have 32 gigs of RAM). So, I dunno. I think Helicon may be better for my purposes.
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Re: Stacking Software

#8 Post by Pat Thielen » Tue Mar 06, 2018 3:21 pm

Wow... PICOLAY is still processing an 8 image stack from when I last posted on this thread. It says it's on step 3206 and it is still counting. I don't think it's going to work for me. Is this normal behavior for this program? The image files are Nikon RAW (NEF), but PICOLAY can handle those types of files.

Does anyone else have any further experience with this? Maybe I'm doing something wrong.
Pat Thielen
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Re: Stacking Software

#9 Post by MicroBob » Tue Mar 06, 2018 3:45 pm

From my limited stacking experience I would say you won't lose any resolution if you downsize the images somewhat before stacking.
One would think that from 8 images one would necessarily get a higher resolved image than from 1 image, but this is only the case if you have very finely spaced steps.
So from e.g. a 24 megapixel image you could make a 6 megapixel image and save memory and time and get the same quality of result. Use the right algorithm though, some degrade the image qualty more than others.

One 24 megapixel jpg. file is e.g. 10 MB on the disc. In the memory 8 raw images are 8 x 24000000 x 3 x 14 Bit = 8064000000 Bit = 1008000000 Byte =1008 MB = 1 GB This is quite a lot of data to work on, even for a fast computer.

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Re: Stacking Software

#10 Post by Pat Thielen » Tue Mar 06, 2018 4:11 pm

MicroBob wrote:From my limited stacking experience I would say you won't lose any resolution if you downsize the images somewhat before stacking.
One would think that from 8 images one would necessarily get a higher resolved image than from 1 image, but this is only the case if you have very finely spaced steps.
So from e.g. a 24 megapixel image you could make a 6 megapixel image and save memory and time and get the same quality of result. Use the right algorithm though, some degrade the image qualty more than others.

One 24 megapixel jpg. file is e.g. 10 MB on the disc. In the memory 8 raw images are 8 x 24000000 x 3 x 14 Bit = 8064000000 Bit = 1008000000 Byte =1008 MB = 1 GB This is quite a lot of data to work on, even for a fast computer.

Well, the thing is Photoshop handled the exact same set of images in a minute or less. At this point, it is still going well after an hour. So, either I did something wrong with how I ran the program (I just dropped in the files and let it do it's thing) or the program is simply not able to do what I need it to do. With 32 gig of RAM and a current i7 processor I would think I would have the horsepower needed to run this thing efficiently.

Hmmm...
Pat Thielen
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Re: Stacking Software

#11 Post by Hobbyst46 » Tue Mar 06, 2018 4:45 pm

Hobbyst46 wrote:Picolay works fine for me. Helicon on first impression seems better than others.
Sorry, I should have mentioned that my PICOLAY data are 10 5MP JPEG files. Took a few minutes. It is not a match for your task.
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Re: Stacking Software

#12 Post by Pat Thielen » Tue Mar 06, 2018 4:54 pm

OK -- I'm going to kill this process (it's been running nearly two hours) and bite the bullet and get Helicon. Photoshop actually does do a decent job for the most part but it does get confused by certain things and I've found when you get serious about something it is often good to buy something beyond Photoshop. While this won't improve my photography (my ever-present learning curve) it will make my stacking a bit better.

Wish me luck! I'm going to need it! :lol:
Pat Thielen
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Re: Stacking Software

#13 Post by Pat Thielen » Tue Mar 06, 2018 6:03 pm

I just did some testing in Helicon. I got some good results and some really terrible results -- Which is very strange because it worked quite well when I originally tested it back in October. So, I really don't know. I might just stick with Photoshop as at least it is consistent. I did "fix" one of the problems with it saving the output file way too light; I just restarted the program. Anyway, for the expense it may not be worth it if it isn't consistent and reliable.
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Re: Stacking Software

#14 Post by MicroBob » Tue Mar 06, 2018 6:48 pm

I would suggest to do some more tests with different settings. If this doesn't help just contact Heribert Cypionka, the developer of PICOLAY. He is very helpful and will easily spot where the problem is.
I'm sure that there is an explanation for this behaviour. These are programms with lots of adjustable parameters and extensive work processes so it is easy to get something wrong in the beginning.

Here I did a test: 20 images of a silvered paramecium, 12 MP Jpgs, 22 seconds on my 3 year old middle level notebook, cut and rezized to 1024 pixel forum width after stacking. It looks so shabby because of the inexperienced preparation and not much care about the photographing.
Attachments
Paramecium versilbert klein.jpg
Paramecium versilbert klein.jpg (296.8 KiB) Viewed 14489 times

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Re: Stacking Software

#15 Post by JimT » Tue Mar 06, 2018 7:57 pm

Pat, back in 2015 I did a simple comparison between Picolay and CombineZP (another free stacking software).

viewtopic.php?f=6&t=1494

Pretty much a toss up between the two.

Give CombineZP a try. I prefer CombineZP because I have been using it for so long.

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Re: Stacking Software

#16 Post by amanda1 » Tue Mar 06, 2018 8:07 pm

try Altami Studio program, it's free, maybe it'll help you, I use it myself http://alelso.com/projects/altami-studio/

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Re: Stacking Software

#17 Post by MicroBob » Wed Mar 07, 2018 1:13 pm

Hi amanda1,

Altami studio sais its free as a DEMO-version.
What are the retrictions of this DEMO-version?

Bob

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Re: Stacking Software

#18 Post by McConkey » Thu Mar 08, 2018 5:08 am

While I don't have the comparison data anymore to show you, I did some decent testing between Photoshop, Zerene and Helicon and opted for Zerene Stacker. Helicon does have a really nice look to it and ended up being the fastest stacking program but i found the final image output to be less sharp and not as "deep". I don't know all the technical details on how stacking programs work but I understand how to play with settings and spent hours trying every combination of all settings in all programs using the same data and picked Zerene Stacker's results every time. I had multiple data sets, some with only 4 images, some with 30 images and some with lots of different colours going on. Granted, sometimes it was a very close call but overall Zerene Stacker, for me, came up the winner. I also like to process my RAW files myself and the guy who made Zerene Stackers has a really good understanding of how RAW files work and explains himself very well for the reasons not to include RAW file support. He's also part of this hobbies community which for me is a big plus and while i've never needed any customer support, i know he would be extremely helpful in helping out. As for me, I've been using photoshop since the early 2000's...very early 2000's....longer than i'd like to admit actually because it just confirms how damn old i'm getting but even still, i opted for Zerene over photoshop's automated stacking. Having the individual layers and all of photoshop's tools to work with was really nice and incredibly familiar but again the quality of the final image wasn't the same. I save all my stacks as 16 bit TIFF's and then export to photoshop for any touch ups that Zerene didn't get and then a final image re-size for forum posts but everything else is handled by Zerene. I found the touching up tools in Zerene and Helicon to be almost identical so no real points there. Zerene is really user friendly and the settings are really easy to work with, especially with the tutorials but keep in mind this is just my experience and in no way am i an expert when it comes to stacking! If you havn't already, it's well worth checking out the Zerene website and reading over the FAQ and tutorials! Plus there is always a free trail Feel free to ask any questions you may have about it!!

Hope this helped a little!
Karl
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Re: Stacking Software

#19 Post by Hobbyst46 » Thu Mar 08, 2018 10:29 am

Hi Karl
Do you shoot RAW files, transfer to the computer with the Canon utility, convert to tiff with a Canon software, then manipulate and stack the tiffs in Zerene?
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Re: Stacking Software

#20 Post by MichaelG. » Thu Mar 08, 2018 11:06 am

For easy reference: I have copied the text from Zerene's FAQ, concerning RAW files

MichaelG.
.
.

Does Zerene Stacker handle raw files?

To process raw files takes two separate steps. First you convert the raw files to some RGB format, typically TIFF, and then you stack the TIFF files.

For highest quality, we recommend converting raw files to 16-bit TIFF using your favorite raw converter and whatever settings make it work the best. After stacking the 16-bit TIFFs, tell Zerene Stacker to save its output also as 16-bit TIFF.

Because 16-bit TIFF files are lossless and have more bits per pixel than are captured by current cameras, this process retains all of the image quality intrinsic to the raw formats.

Zerene Systems does not provide raw converters. You can download those separately, or use software provided by your camera manufacturer.

If you use Lightroom, then be aware that there's a Lightroom plugin for Zerene Stacker that handles raw conversion automatically. When using Lightroom with the plugin, processing raw files is just a matter of selecting them and doing an Export to Zerene Stacker. See Working with Lightroom for more details about this "Pro-only" feature.

A longer explanation is that no stacking software really works directly with raw files.

The structure of data in a typical raw image file, one value per photosite with color implied by a mosaic Bayer filter pattern, is fundamentally incompatible with the image alignment process that is required for stacking.

Some stacking software from other companies deals with this aspect by accepting raw files at the level of the user interface, then converting them to some RGB format, typically TIFF, in a background process that is easy to overlook and may be difficult to optimize.

Zerene Stacker goes the other route, exposing the conversion process and encouraging users to deal with it as what we think it really is: a key part of the overall workflow that deserves some attention in order to get best results.
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Re: Stacking Software

#21 Post by Hobbyst46 » Thu Mar 08, 2018 11:53 am

MichaelG. wrote:For easy reference: I have copied the text from Zerene's FAQ, concerning RAW files
Very helpful. Thanks.
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Re: Stacking Software

#22 Post by McConkey » Thu Mar 08, 2018 11:21 pm

Hobbyst46 wrote:Hi Karl
Do you shoot RAW files, transfer to the computer with the Canon utility, convert to tiff with a Canon software, then manipulate and stack the tiffs in Zerene?

I shoot raw but i just take out my memory card and throw it into my desktop to grab the files. I then open them in camera RAW within photoshop and batch process them all at once...a very light sharpen, noise reduction, etc the batch processing saves them as 16bit TIFF's which i then stack in Zerene....save as another 16bit TIFF and bring back into photoshop to make any touch ups! It might seem like alot of back and forth but 90% of the process is automated, i usually go boil the kettle while it does it's thing!

MichaelG - Thank you for posting the FAQ for the RAW! Hopfully others find it useful!
Karl
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Re: Stacking Software

#23 Post by Pat Thielen » Fri Mar 09, 2018 4:02 am

I think I'll give Zerene another try once I'm off work next week. While I was put off by it not handling RAW files directly I could of course alter my workflow and convert the ones I want to stack beforehand. I don't think it would be nearly as big a deal as my brain wants me think it is. Right now I'm having a bit of trouble with Helicon but I'm getting them sorted out -- I needed to update the DNG converter from Adobe.

Thanks for all the help and suggestions on this.
Pat Thielen
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Re: Stacking Software

#24 Post by amanda1 » Wed Mar 21, 2018 9:31 am

MicroBob wrote:Hi amanda1,

Altami studio sais its free as a DEMO-version.
What are the retrictions of this DEMO-version?

Bob
Hi, Bob

The demo version differs only in that it reboots every 15 minutes, but all settings are saved. I saw that these days you can get a free license, check this page out: https://www.facebook.com/AltamiElectronicSolutions/

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Re: Stacking Software

#25 Post by hermitdog » Thu Apr 12, 2018 1:51 pm

I've used Helicon Focus for just two weeks and love it.
This link is an image of a wasp's foot - rendered from a stack of 45 "captures": http://hermitdog.com/microscope/wasp_fo ... _large.png

This is the foot of a stinkbug - also 45 captures: http://hermitdog.com/microscope/Stinkbu ... _large.png

Here's a joint on the antenna of the same stinkbug: http://hermitdog.com/microscope/Stinkbu ... elicon.png

In all three of these images, I found the farthest away point that was in focus (in the depth of field), made note of that; then I found the closest in-focus point in the depth of field and made note of that. I started with the former and worked toward the latter in tiny increments: making a "capture" of each layer, then rendered those layers using Helicon's Method C (pyramid.)

I have much to learn about Helicon software, but so far I'm thinking it is well worth the investment.

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Re: Stacking Software

#26 Post by MikeA » Thu Apr 12, 2018 4:00 pm

Just like to add another vote for CombineZP from Alan Hadley - I have used Zerene and HF over the years and agree they do a fine job, but have not found fault with CombineZP and it is free! No idea how/if it works with RAW but can say it has handled many (up to 25) multi-megabyte images quite well, and that is on Win10, 64 bit, with only 12 Gb RAM and a duocore processor at 2.90GHz.

Just my $.02... :D
All the best,
Mike
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Re: Stacking Software

#27 Post by billbillt » Thu Apr 12, 2018 6:10 pm

Hi,

I have to say Picolay works well for me.. Also free...

BillT

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Re: Stacking Software Tested

#28 Post by RobBerdan » Sun Dec 23, 2018 2:36 am

I tested Zerene, Helicon Focus and Photoshop for photomicrography. Helicon performed best and I could use it with RAW files.
I still use Photoshop for quick tests with my RAW files and it also works well most of the time.

See my test pictures and article here if interested :
https://www.canadiannaturephotographer. ... cking.html

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Re: Stacking Software

#29 Post by janvangastel » Sun Dec 23, 2018 7:36 am

A stacking program much used by astrophotographists is autostakkert. It's free and works very well. Maybe worth trying. https://www.autostakkert.com/

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Re: Stacking Software Tested

#30 Post by MichaelG. » Sun Dec 23, 2018 8:54 am

RobBerdan wrote:See my test pictures and article here if interested :
https://www.canadiannaturephotographer. ... cking.html
Excellent article, Rob ... Many thanks for the link.

MichaelG.
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