Photoshop CS6 v Helicon v Zerene,and the rest

Here you can discuss topics such as focus stacking, stitching and other techniques that relate to the processing of micrographs.
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Dave S
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Photoshop CS6 v Helicon v Zerene,and the rest

#1 Post by Dave S » Fri Sep 06, 2019 6:27 pm

I note that this subject was discussed here back in 2018, resulting in some mixed opinions.

As there will have been much water passed under the bridge since then, I am very interested in the current thinking among you guys, when it comes to stacking software.

I have Photoshop CS6, and Lightroom 5. I also have Maxim DL, Astroart, and Pixinsight from my astro-imaging days, which all made an excellent job of aligning, and stacking multiple astro images.

Although a seasoned photographer, and astro-imager, I am relatively new to microscopy. My question is, should I use what I have for stacking my micro images, or should I be looking at the likes of Helicon, and Zerene?
.
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MicroBob
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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#2 Post by MicroBob » Fri Sep 06, 2019 7:02 pm

Hi Dave,
I can't comment on these alternatives as I use PICOLAY, which is free.
In my limited experience it has always worked fine and the developer even helps when there is a problem.

Bob

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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#3 Post by Dave S » Fri Sep 06, 2019 7:06 pm

Thanks Bob, well it costs nothing to try it then :)

I note from previous discussions that some people like Helicon, while others like Zerene, but none of them are as cheap as the Picolay that you suggest. :D
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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#4 Post by Dave S » Fri Sep 06, 2019 7:31 pm

Well, I gave it a try Bob, and it made a brave effort but there was a lot of misaligned detail in the final stacked image.

Maybe I was expecting too much of it, as the variation in focus points across image, was quite significant.

I found a dead Wasp. pulled off a wing, and put it on a slide, under a cover slip. Because at 100x it was quite undulating (far from flat), there was a significant difference between the in focus sections. I took 13 images at different focus points.

I could be wrong, but I think if the specimen was flatter, the software would have coped better.

I might download a trial version of Helicon, and compare how it copes with the same images.
Brunel SP100 (with 4x, 10x, 40x,60x, and 100x (oil) plan objectives), and Canon EOS 4000d Camera (microscopy use only)

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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#5 Post by Dave S » Fri Sep 06, 2019 7:50 pm

Hmm!!, better alignment with Helicon, but not impressed with the final stacked image. I'll look to find a different specimen, and have another 'play' tomorrow.
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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#6 Post by MichaelG. » Fri Sep 06, 2019 9:00 pm

If you want to try Zerene, Dave ... here's the page:
http://zerenesystems.com/cms/stacker/softwaredownloads

I use it ... but I haven't tried the competitors

MichaelG.
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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#7 Post by Dave S » Fri Sep 06, 2019 9:15 pm

It has to be worth a try Michael, albeit from what I read from various reviews, there seems to be little to choose between Helicon and Zerene.

Having CS6 I really don't need all the processing bits that Zerene and Helicon offer, more a simple alignment and stacking program. Maybe given that Helicon couldn't effectively handle the task I gave it, then given a less demanding task, perhaps picolay, or combineZP, might do the job for free. I'll play more tomorrow.
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Scarodactyl
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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#8 Post by Scarodactyl » Sat Sep 07, 2019 3:20 am

Helicon has worked well for me in almost all cases, though it occasionally needs some cleanup. Could you post example images of what is going wrong?

MicroBob
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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#9 Post by MicroBob » Sat Sep 07, 2019 4:59 am

Hi together,
In Picolay there is a menu point " Set stacking parameters" from where I start the stacking process. There is a tick box "Align immages" - obviously it has to be selected to let Picolay do any alignment.

#when I first stacked images I was quite disappointed. My idea was that more images can only lead to more information in the combined image. But to acheive this one really needs a lot of images. 13 images for a threedimensional object sounds like far too little to me.

Bob

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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#10 Post by Dave S » Sat Sep 07, 2019 10:39 am

It was a quick 'rough & ready' assessment, with what I could lay may hands on at the time, and a dead wasp just happened be on the window ledge (lol).

I have 30 days to try Helicon, will likely get the same with Zerene, and of course, I have the free Picolay. I might even try CombineZP, another 'freebie'

Its all good fun experimenting, and I will post some examples in due course.

In the mean time, I also need to explore the capabilities of the new microscope. I did get the Kohler illumination aligned yesterday.

If I get some acceptable results, I might create a 'MIcro' section on my photography website, and post them there.

Watch this space :)
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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#11 Post by viktor j nilsson » Sat Sep 07, 2019 12:17 pm

Stacking very often improves things dramatically, even if you're only using three or four images. That said, you do need to be a bit careful when taking the pictures. If you haven't stacked microscopic subjects before (or any subjects, for that matter) I wouldn't rule out the possibility that your pictures might be the limiting factor, not the software.

Becausee many microscopic subjects are semi-transparent, the stacking algorithm can get confused if you try to stack images with overlaying details. It's usually best to capture images from the midpoint and up, so to speak. And make sure you use appropriately small steps. A 10x 0.25 objective needs about a 0.0088mm step size.

See e.g. http://zerenesystems.com/cms/stacker/do ... romicrodof

I use Zerene, developed by Rik Littlefield, who is extremely knowledgeable and always helpful over at photomacrography.net. But Helicon seems great as well.

Regarding the editing capabilities of these programs that you said you may not need, on very good function is the capability of manually retouching details from one layer onto the final stack. This can really help in some cases where there's complex, overlapping morphology.

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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#12 Post by Dave S » Sat Sep 07, 2019 3:32 pm

Thanks for that info Viktor, much appreciated.
Brunel SP100 (with 4x, 10x, 40x,60x, and 100x (oil) plan objectives), and Canon EOS 4000d Camera (microscopy use only)

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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#13 Post by Dave S » Sat Sep 07, 2019 8:10 pm

Some success with Picolay.

14 images taken at different focus points, and stacked

Two images shown, one of the individual images from the un-stacked bunch, and one with the 14 images stacked in Picolay.

I have shrunk them down to small GIFs for direct posting here.

There is some false colour aberration, but this is not present in the eyepiece view, only in the image.

BTW, its one of the smaller wings off a dead wasp.

So, an encouraging step forward I think.

non stacked__small.gif
non stacked__small.gif (191.5 KiB) Viewed 1839 times
picolay stack_ps_small.gif
picolay stack_ps_small.gif (221.01 KiB) Viewed 1839 times
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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#14 Post by MichaelG. » Sat Sep 07, 2019 8:57 pm

Keep it coming, Dave
... Looks like you're on a roll.

MichaelG.
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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#15 Post by Dave S » Sat Sep 07, 2019 9:02 pm

Thanks Michael, certainly a step forward, room for improvement, but encouraging. :)
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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#16 Post by viktor j nilsson » Sat Sep 07, 2019 9:31 pm

Looks promising for sure. But it seems like you lost much of the dynamic range when you converted them to .gif - as seen in the stepped, not smooth, color gradient in the background. Probably better to save them as jpegs.

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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#17 Post by Dave S » Sat Sep 07, 2019 9:56 pm

That is true Viktor, but we only get 512k here for images. I resized the jpegs down three times and they were still too big, so I got fed up with it, and GIF'd them :lol:
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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#18 Post by MichaelG. » Sun Sep 08, 2019 6:28 am

Dave S wrote:
Sat Sep 07, 2019 9:56 pm
That is true Viktor, but we only get 512k here for images. I resized the jpegs down three times and they were still too big, so I got fed up with it, and GIF'd them :lol:
For what you are investigating/demonstrating, Dave ... I think it might be preferable to crop the images [to show only a specific region of interest] instead of reducing the overall quality.

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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#19 Post by david_b » Sun Sep 08, 2019 6:38 am

MichaelG. wrote:
Sun Sep 08, 2019 6:28 am
Dave S wrote:
Sat Sep 07, 2019 9:56 pm
That is true Viktor, but we only get 512k here for images. I resized the jpegs down three times and they were still too big, so I got fed up with it, and GIF'd them :lol:
For what you are investigating/demonstrating, Dave ... I think it might be preferable to crop the images [to show only a specific region of interest] instead of reducing the overall quality.

MichaelG.
Or better still, use a free remote hosting service like imgur.com

Just upload your photo there, copy the BBCode link and paste it here. Couldn't be easier!

Image

MicroBob
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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#20 Post by MicroBob » Sun Sep 08, 2019 6:53 am

Hi Dave,
this really looks good! I think your photography and astronomy background gives you a very good start in micro photography.
The 512kB limit is a bit tight, but enough for forum sized images - here is how I make the best use of it:
I use Irfan view, an image viewer with basic editing capabilities. This allows to set the option output size (make sure to set it back though!)
Irfanview does all that is needed for normal non-micro-images of good quality for micro images I often use GIMP first as it offers better control over colour and contrast. It can be set to english of cause.
JPG makes beter use of the 512 kB limit than GIF.

Bob
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Irfanviev file size.jpg (132.28 KiB) Viewed 1782 times

Dave S
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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#21 Post by Dave S » Sun Sep 08, 2019 12:48 pm

Thanks Bob, Michael, 'scaro', David, and Viktor, for your input. Much appreciated.

I do have a server based photo storage facility at Google Photos, but only use this for my micro images, and these experimental ones weren't worth saving. I won't use the GIF format anymore for direct uploads, but 'Save for Web' jpeg's, as although compressed, are not as destructive as GIFs.
Brunel SP100 (with 4x, 10x, 40x,60x, and 100x (oil) plan objectives), and Canon EOS 4000d Camera (microscopy use only)

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Re: Photoshop CS6 v Helicon v Zerene,and the rest

#22 Post by Dave S » Thu Sep 12, 2019 10:57 am

From the limited amount of testing I've done so far, I can't really see any difference in the stacked result, between Picolay, and Helicon.

I should add that I only aligned, and stacked in both, applying none of the enhancement tools, as Photoshop can deal with this.

This has so far been limited to macro images, not micro.

A 17 macro image stack using PIcolay, created today.

ImageHover Fly - 17 image Stack by Dave, on Flickr
Brunel SP100 (with 4x, 10x, 40x,60x, and 100x (oil) plan objectives), and Canon EOS 4000d Camera (microscopy use only)

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