Image stacking question

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gekko
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Image stacking question

#1 Post by gekko » Sun Jun 12, 2016 2:18 pm

In another thread 75RR showed several images of Spirogyra focus stack, one of the whole focus stack, one of a partial stack from the top surface to the plane of the nucleus, and also a single image showing only the plane of the nucleus. I posed the following question:

Thank you! That is very helpful. So with the partial stack, you can see the chloroplasts on the surface as well as the nucleus, but then when you use the whole stack, the image of the chloroplasts on the other side of the filament get superimposed on the nucleus and obscure it somewhat. That is what I thought, but this confirms it.

Expanding on that: so the focus stack basically forms an image of a glass object. I wonder if there is a way (i.e. a setting of the stacking program) to make the stack more "opaque" so what is above hides what is below, or would that be nonsensical or at least not useful? Any ideas?

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Re: Image stacking question

#2 Post by 75RR » Sun Jun 12, 2016 6:48 pm

I tried changing the order - placed # 26, 27 and 28 at the end but no luck, result was identical.
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Re: Image stacking question

#3 Post by Johann » Mon Jun 13, 2016 5:37 am

It may not be the ideal solution, but maybe using the blur tool in Photoshop could work? Blur the areas on the bottom layers that you don't want to show?
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Re: Image stacking question

#4 Post by mrsonchus » Tue Jun 14, 2016 3:45 am

Hmm, this is a problem we always face with the transparent specimens that have 'overlapping' focused planes - i.e. stacked locations that are in the same spot on the image?
Perhaps masking would be of use in building a multi-layered mage with Photoshop for example?
It's a tantalising problem in that if performed well it seems to promise much?
I'm going to have a play around with it tomorrow as see what happens - I think this has been suggested quite a few times, but I can't remember by whom - sorry.
:)
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Re: Image stacking question

#5 Post by gekko » Tue Jun 14, 2016 5:52 pm

75RR, Johann, and John, many thanks for your replies. I'm still not sure if my question actually makes sense. I was thinking, for example, of a sphere with detail both on the surface and inside its volume, that, after stacking would show the detail of the upper hemisphere all in focus, but without the stuff inside obscuring the image. Again, my question may be nonsensical, and if so, please say so :) .

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Re: Image stacking question

#6 Post by mrsonchus » Tue Jun 14, 2016 6:37 pm

gekko wrote:75RR, Johann, and John, many thanks for your replies. I'm still not sure if my question actually makes sense. I was thinking, for example, of a sphere with detail both on the surface and inside its volume, that, after stacking would show the detail of the upper hemisphere all in focus, but without the stuff inside obscuring the image. Again, my question may be nonsensical, and if so, please say so :) .
Makes perfect sense gekko - you effectively need to stack only the surface detail in the same manner as I stack pollen grain images but of course they have had their surface (of the spheroid) rendered more opaque, with stain, making it far easier.

I suppose you would be stacking concentric rings, each at a separate depth from the top or bottom of the object assuming it's spheroid. Each ring in the set would be masked from the following stack-layer (ring), moving on to a larger a larger (assuming moving 'downwards') ring etc etc as focus progresses downwards (or vice-versa of course) - the limit of course will be the equatorial plane....

Not easy, an interesting problem.. :)
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Re: Image stacking question

#7 Post by billben74 » Tue Jun 14, 2016 8:41 pm

Nice topic gekko.
Sometimes this, the superposition of objects going up/down focus stack, can produce some nice "artistic" effects. A big spider pic I showed on a post had a bit of that going on. But sometimes its a pain.
In zerine stacker you can sort of do what you are talking about, but not automatically.
Zerine stacker (as I mention in that great thread about about stacking, that sadly I just gave up looking for) has a retouching mode.
In this you can air brush anything in you stack over a stacked image. So you can put the top of the stack image in after the automatic stacking.
I don't know if you can do this in other stacking software. I did this kind of thing with hairs on the spider.

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Re: Image stacking question

#8 Post by gekko » Tue Jun 14, 2016 10:31 pm

mrsonchus wrote:
gekko wrote:75RR, Johann, and John, many thanks for your replies. I'm still not sure if my question actually makes sense. I was thinking, for example, of a sphere with detail both on the surface and inside its volume, that, after stacking would show the detail of the upper hemisphere all in focus, but without the stuff inside obscuring the image. Again, my question may be nonsensical, and if so, please say so :) .
Makes perfect sense gekko - you effectively need to stack only the surface detail in the same manner as I stack pollen grain images but of course they have had their surface (of the spheroid) rendered more opaque, with stain, making it far easier.

I suppose you would be stacking concentric rings, each at a separate depth from the top or bottom of the object assuming it's spheroid. Each ring in the set would be masked from the following stack-layer (ring), moving on to a larger a larger (assuming moving 'downwards') ring etc etc as focus progresses downwards (or vice-versa of course) - the limit of course will be the equatorial plane....

Not easy, an interesting problem.. :)
Many thanks, John. As you know, I am too lazy to undertake difficult projects, hence my avoidance of plant sections :) I was hoping there would be a setting in the stacking program to do this, but apparently it is not that simple.

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Re: Image stacking question

#9 Post by gekko » Tue Jun 14, 2016 10:40 pm

billben74 wrote:Nice topic gekko.
Sometimes this, the superposition of objects going up/down focus stack, can produce some nice "artistic" effects. A big spider pic I showed on a post had a bit of that going on. But sometimes its a pain.
In zerine stacker you can sort of do what you are talking about, but not automatically.
Zerine stacker (as I mention in that great thread about about stacking, that sadly I just gave up looking for) has a retouching mode.
In this you can air brush anything in you stack over a stacked image. So you can put the top of the stack image in after the automatic stacking.
I don't know if you can do this in other stacking software. I did this kind of thing with hairs on the spider.
Thank you billben for your interesting comments. I have eyed Zerine Stacker for a long time, but could not justify buying it because I rarely use focus stacks. What you say seems makes a lot of sense (but lazy people like me try to avoid spending the time necessary to learn complex programs :oops:). Thanks again for your input.

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Re: Image stacking question

#10 Post by ChrisR » Tue Jun 14, 2016 11:22 pm

Hi
I'm come over from photomacrography.net. Not wedded to Zerene stacker, in case anyone thinks...

What you can do, if you have a more foreground structure, is a Partial Stack of just those frames.
It's important that the WHOLE er, pile of pictures is Aligned , though.
When you do the Partial stack, turn any (further) alignments OFF, so it doesn't distort what you're working on.

Then you Retouch from that Partial stack output. The Stacking software is a bit cleverer than Photoshop in Zerene's case and I expect Helicon's as well, in that the retouching tool has something clever going on, which helps things blend.

If you've got a real hairball to stack then there's nothing to help, much. You have to retouch all over the frame.

Helicon has more bells & whistles than Zerene so I expect it can also switch between source frames to quickly see what's what.
Helicon has a thing where you can click on the first stacked image, and it takes you to the source frame it picked from.

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Re: Image stacking question

#11 Post by mrsonchus » Tue Jun 14, 2016 11:41 pm

[quote="ChrisR"]Hi
I'm come over from photomacrography.net. Not wedded to Zerene stacker, in case anyone thinks...

...thinks what?
Are you an 'Administrator' over at 'the other place'?
:|
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Re: Image stacking question

#12 Post by 75RR » Wed Jun 15, 2016 12:19 pm

Note: These are the original images that gekko referred to in his first post

viewtopic.php?f=6&t=3231

Have combined 3 crops in one image in order to make the comparison easier.
From left to right:
images from 21 to 31 (original image),
images from 21 to 28, left out 29, 30 and 31 in order to uncover nucleus.
images from 21 to 31 with the areas of images 29, 30 and 31 that are over the nucleus removed with clone stamp.

As can be seen, it does work - it just needs a little more care in the execution.

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Re: Image stacking question

#13 Post by mrsonchus » Wed Jun 15, 2016 2:36 pm

Nicely done - that's a good job to my eyes 75. :)
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Re: Image stacking question

#14 Post by ChrisR » Thu Jun 16, 2016 12:01 pm

ChrisR wrote:Hi
I'm come over from photomacrography.net. Not wedded to Zerene stacker, in case anyone thinks...

...thinks what?
Are you an 'Administrator' over at 'the other place'?
Yes, we mostly have "registering" duties in different time zones. (It was seeing your posts come, and go, that brought me here). I see several familiar usernames :) .
What I meant was, that although the site owner wrote Zerene Stacker (& I do have it) nobody else in the site has any "interest" in ZS.
We get a lot of stacking queries.
I think one can do partial stacking in most programs, but the important thing is that the stacker, doing its aligning thing, doesn't align the partial stack differently from the rest of the stack.
You can obviously submit different sets to the programs, but it needs to have aligned the lot first.

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Re: Image stacking question

#15 Post by mrsonchus » Thu Jun 16, 2016 1:36 pm

Hi, I've (obviously) removed the tirade that I regrettably posted here earlier - it was ill-judged of me and I apologize to any and all members that have been offended by it or just plain disliked it.
It was posted as a response to prior troubles within the other forum that I joined recently, although I have since left - definitely for the best.

Anyway, my sincere apologies to everyone. :)

p.s. hopefully I'm still welcome in this forum, if not please let me know and I'll act accordingly.
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Re: Image stacking question

#16 Post by gekko » Thu Jun 16, 2016 5:35 pm

ChrisR wrote:Hi
I'm come over from photomacrography.net. Not wedded to Zerene stacker, in case anyone thinks...

What you can do, if you have a more foreground structure, is a Partial Stack of just those frames.
It's important that the WHOLE er, pile of pictures is Aligned , though.
When you do the Partial stack, turn any (further) alignments OFF, so it doesn't distort what you're working on.

Then you Retouch from that Partial stack output. The Stacking software is a bit cleverer than Photoshop in Zerene's case and I expect Helicon's as well, in that the retouching tool has something clever going on, which helps things blend.

If you've got a real hairball to stack then there's nothing to help, much. You have to retouch all over the frame.

Helicon has more bells & whistles than Zerene so I expect it can also switch between source frames to quickly see what's what.
Helicon has a thing where you can click on the first stacked image, and it takes you to the source frame it picked from.
Many thanks, Chris, for your very helpful input. I will save your suggestions so I can refer to them in the future.
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Re: Image stacking question

#17 Post by gekko » Thu Jun 16, 2016 6:00 pm

75RR wrote:Note: These are the original images that gekko referred to in his first post

viewtopic.php?f=6&t=3231

Have combined 3 crops in one image in order to make the comparison easier.
From left to right:
images from 21 to 31 (original image),
images from 21 to 28, left out 29, 30 and 31 in order to uncover nucleus.
images from 21 to 31 with the areas of images 29, 30 and 31 that are over the nucleus removed with clone stamp.

As can be seen, it does work - it just needs a little more care in the execution.
Many thanks, 75RR. Yes, very nice work. And I didn't mean to make you do all that work to actually demonstrate!

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Re: Image stacking question

#18 Post by mrsonchus » Thu Jun 16, 2016 8:24 pm

gekko wrote: Please ignore John B's unhelpful comments.
Apologies gekko.
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Re: Image stacking question

#19 Post by ChrisR » Thu Jun 16, 2016 9:35 pm

Please ignore John B's unhelpful comments.
Didn't see 'em! I saw the history at the other place, am somewhat perplexed. Looks like a case of some unfortunate choice of words creating an unintended impression. I was enjoying John's posts.
(I'm too new here to be allowed to send pms, it seems)

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Re: Image stacking question

#20 Post by gekko » Thu Jun 16, 2016 9:36 pm

Many thanks, John. I do appreciate it.
And thanks again, Chris.

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Re: Image stacking question

#21 Post by mrsonchus » Thu Jun 16, 2016 9:42 pm

gekko wrote:Many thanks, John. I do appreciate it.
And thanks again, Chris.
You're a good fellow gekko, I regret offending you very much. :)
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Re: Image stacking question

#22 Post by gekko » Thu Jun 16, 2016 9:50 pm

mrsonchus wrote:
gekko wrote:Many thanks, John. I do appreciate it.
And thanks again, Chris.
You're a good fellow gekko, I regret offending you very much. :)
Not a problem now-- we all make mistakes. The civility in this forum is exceptional, and it would be nice to keep it that way. Thank you again, John.

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Re: Image stacking question

#23 Post by billben74 » Thu Jun 16, 2016 9:54 pm

Thanks again gekko for starting this interesting thread and your kind comments towards my post.
Thanks ChrisR. I had heard something on partial stacking from vesselle, who posts here and over at "your" place, but your comments have brought that to my mind and will almost certainly improve my technique (and no doubt other forum members)in the future.

John, you are certainly welcome over "here" and sounds like you might be more welcome than you think over at the over place (I'm starting to enjoy this parlimentary lingo).
I think it sounds like you (John) stayed up too late again (and got tired?) due to your admirable microscopy zeal at some point?
Anyway apologies if this is far from the truth but you (John) are great guy who has given a great deal to this forum.

It sounds like ChrisR holds no bad feelings (quite the reverse I think) so no harms been done.

ChrisR -->please keep posting. I do occationally visit (and post to the other place) but I'm time poor and find it hard to look at one forum and no doubt other forum users would benefit from your knowledge here.

John keep posting as you are a friend and source of interest, knowledge and warmth to many of us.

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Re: Image stacking question

#24 Post by gekko » Thu Jun 16, 2016 9:56 pm

billben, thank you: you said it very well.

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Re: Image stacking question

#25 Post by ChrisR » Fri Jun 17, 2016 10:50 am

ChrisR -->please keep posting. I do occationally visit (and post to the other place) but I'm time poor and find it hard to look at one forum and no doubt other forum users would benefit from your knowledge here.
Thanks. Yes there's just too much to read!. Like this one, PM.net is a forum where posts are mostly fairly grown-up, not dominated by comments such as "awesome capture" or why my black and glass thing is better than yours. It can be a bit techy/geeky, but also has some great photographers.
Rik started the site years ago, found that the current stacking programs were a bit lacking for micro/macro applications, and being keen on several relevant areas, and clever, wrote his own. Hence a lot of traffic about stackers there. Helicon appeared to wake up, and incorporated similar actions (key was the "pyramidal" method) into their software, plus extra bells & whistles as well, some of which are very nice. CombineZP (free) also improved, so the differences are less than they were. I believe the Contrast method Helicon has, though a relatively simple one, works well for a lot of microscope images - I'm not sure why. ZS doesn't have that one.

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Re: Image stacking question

#26 Post by gekko » Fri Jun 17, 2016 2:50 pm

ChrisR wrote: My wife would like to repeat that accumulating stuff, is ,is not a substutute for personal development... The message isn't sinking in.
    :D
I'm sure many here will empathize.

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Re: Image stacking question

#27 Post by c-krebs » Sat Jun 18, 2016 8:24 pm

gekko:
wonder if there is a way (i.e. a setting of the stacking program) to make the stack more "opaque" so what is above hides what is below, or would that be nonsensical or at least not useful? Any ideas?
Some years ago I tried a stacking program named AllFocus from a company called Saphicon. What intrigued me about this program was that it stated an ability to "prioritize beginning or end of stack". At this time I was comparing as many stacking programs as I could and this seemed a unique and desirable feature. Ultimately I preferred the overall results from other software so I didn't pursue it in depth. Your post piqued my curiosity once again, and I have contacted them to see if the software has received any further development, or if it has stayed the same. While there might be other programs that allow such a feature I am not aware of them.

The question is a good one and it can be an issue in stacking. Ultimately as things are now, if there is good detail at several levels through a subject it requires some "manual" intervention and decision making by the photographer. This can be accomplished to a degree in the current popular programs like Helicon Focus and Zerene Stacker, but it would certainly be nice to be able to do at least some of it "automatically".


To clarify something stated earlier in regards to PMN
ChrisR:
Rik started the site years ago,
A correction. The site was started in April 2004. The principals involved were Tom Webster, Michael Keniston, Danny Young, and Sue Aldren. (Certainly not to take anything away from Rik... he's been an excellent driving force for some time). At that time Tom was heavily into photomicrography and it was about the only English "speaking" forum that had sections geared primarily to photography through the microscope. I know Tom worked hard to get the microscope aspect established, so I want to be sure his contributions are acknowledged.

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Re: Image stacking question

#28 Post by zzffnn » Sat Jun 18, 2016 10:03 pm

Wow, that is Charles Krebs! Welcome to this forum! What a honor to be the first one to welcome you here!

Where are the "like" or "follow" buttons for this forum.........
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Re: Image stacking question

#29 Post by billben74 » Sat Jun 18, 2016 11:30 pm

I'll second that welcome. Great to have you onboard.

Its almost like there is some kind of marriage (between PM.net and this place).

This can only be good.

I agree with you Charles that stacking software designers could consider automation of partial stack/top/bottom priority.

Perhaps even photoshop/gimp like selection tools to allow defining a part of the image top/ middle / bottom / background?

While we are on this vibe can anything automate stacking and stitching? (Mmm. perhaps I just thought of a possible answer in image J... will look into this...)
In fact I'll start a new thread for this one as I'm going off topic...

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Re: Image stacking question

#30 Post by gekko » Mon Jun 20, 2016 1:34 am

c-krebs wrote:gekko:
wonder if there is a way (i.e. a setting of the stacking program) to make the stack more "opaque" so what is above hides what is below, or would that be nonsensical or at least not useful? Any ideas?
Some years ago I tried a stacking program named AllFocus from a company called Saphicon. What intrigued me about this program was that it stated an ability to "prioritize beginning or end of stack". At this time I was comparing as many stacking programs as I could and this seemed a unique and desirable feature. Ultimately I preferred the overall results from other software so I didn't pursue it in depth. Your post piqued my curiosity once again, and I have contacted them to see if the software has received any further development, or if it has stayed the same. While there might be other programs that allow such a feature I am not aware of them.

The question is a good one and it can be an issue in stacking. Ultimately as things are now, if there is good detail at several levels through a subject it requires some "manual" intervention and decision making by the photographer. This can be accomplished to a degree in the current popular programs like Helicon Focus and Zerene Stacker, but it would certainly be nice to be able to do at least some of it "automatically".
Thank you very much for your comprehensive reply. I just googled Saphicon, and they seem to make also hardware for motorized focusing and related hardware. Thank you again.

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