Help needed with focus stacking

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blaberus
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Help needed with focus stacking

#1 Post by blaberus » Sat Nov 21, 2020 6:07 pm

I am an entomologist who studies cockroaches (someone has to!) and although I have been using stereo dissecting microscopes for many years I have zero experience with focus stacking, or indeed taking photos through a microscope (I normally use a macro lens). Recently I purchased an old but good Leica Wild M3Z dissecting scope and would very much like to take focus stacked images of small structures. For days I have been reading articles and watching videos on the Internet and am getting very confused by all the options and sub-options of how to take photos through a microscope. I have now dismissed the idea of attaching my phone or compact camera, since I would like a more automated focus stacking system similar to Toupview. I then considered eyepiece cameras and read that the cheaper ones (i.e. the ones I can afford) have tiny sensors and that the image quality of DSLR cameras with much larger sensors is better. I am therefore now thinking of attaching my Nikon D500 to an eyepiece and have recently seen a review of a DSRL adaptor which apparently has good optics and is affordable (some cost around £1000 GBP) i.e. https://youtu.be/U9JxEPvueC0. My question now is whether there is a programme similar to Toupview which I can use with my computer and DSLR on Live View, to automatically capture a sequence of images as I move the focal plane through a specimen, in a similar way to that shown here https://youtu.be/ouVJnHBMewM. It would be so much more convenient than having to take a series of images using a remote shutter release. Any help and advice will be very gratefully received!

viktor j nilsson
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Re: Help needed with focus stacking

#2 Post by viktor j nilsson » Sat Nov 21, 2020 6:23 pm

Personally, I think you are better off keeping the M3Z for observation, and build a separate rig for photography. A stereo microscope is optimized for observation, and the increased working distance come at the expense of resolution. They are okay for pure documentation, but won't be as good as a macro rail with decent objectives. Not worth investing your money in, unless all you need is to grab some quick documentation photos.

The macro rails from stackshot, wemacro or mjkzz are great starting points for an automated stacking system. Your objective options depends on the magnification required, but you would probably need a good 1:1 macro objective for habitus photos and a few microscope objectives for details (some the generic 4x are excellent and cheap, and Nikon CF 10x finite objectives are also easy to find, cheap and produce excellent images).

The photomacrography.net forum has tons of information on macro rigs like that.

blaberus
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Re: Help needed with focus stacking

#3 Post by blaberus » Sat Nov 21, 2020 6:31 pm

Thanks very much, but I have also considered macro rails and concluded they are too much hassle and expense. I need magnifications of around 40x but I don't need competition winning photos. A friend who is a spider taxonomist uses an Amscope 10MP eyepiece camera with Toupview and the results are very good - she publishes them in her papers. However, if for a similar cost I can take even better pics with my DSLR and *IF* it can be automated with a focus stacking programme, then that would be my ideal solution. If it can't be automated (and by that I mean that the programme takes a photos at e.g. a 1 second time interval as I focuss through the specimen) then I may go for an eyepiece camera. The question would then become which one (below c. £400)?

PS. I have a very heavy stand for the microscope so am sure it won't tip over with the weight of my camera. Also I did some test shots with my phone of structures magnified 40x and was very pleased with the results.

viktor j nilsson
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Re: Help needed with focus stacking

#4 Post by viktor j nilsson » Sat Nov 21, 2020 7:08 pm

When you say 40x, do you mean the FOV that you are getting with your M3Z when set at the 40x setting? How many mm wide is that field, if you are looking at a ruler?

blaberus
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Re: Help needed with focus stacking

#5 Post by blaberus » Sat Nov 21, 2020 7:31 pm

5mm.

EYE C U
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Re: Help needed with focus stacking

#6 Post by EYE C U » Sat Nov 21, 2020 10:59 pm

YOU SHOULD CHECK OUT STACKSHOT. PERFECT FOR BUGS
1464_DSC05327_1.jpg
1464_DSC05327_1.jpg (90.38 KiB) Viewed 208 times

blaberus
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Re: Help needed with focus stacking

#7 Post by blaberus » Sun Nov 22, 2020 12:14 am

Thanks, I know about these types of systems, but this is not what I want. I want to be able to use my microscope to find a structure and then attach a DSLR or eyepiece camera to quickly and easily get a focus stacked image of it. I do not want my work table cluttered up with a system using bellows or an automatic focus stacking rail. I know that these produce the best macro images possible, but this is not what I want. I simply want the best image given the constraints of my system e.g. the M3Z microscope and Nikon D500 on an adaptor, or an eyepiece camera. I know that good images are possible, but want an easy to use focus stacking solution to make my life as simple!

EYE C U
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Re: Help needed with focus stacking

#8 Post by EYE C U » Sun Nov 22, 2020 1:41 am

HAVE YOU LOOKED AT "HELICON FOCUS" SOFTWARE..

blaberus
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Re: Help needed with focus stacking

#9 Post by blaberus » Sun Nov 22, 2020 1:57 am

Does it work in Live View with a Nikon D500, in a similar way to how Toupview works with an eyepiece camera? The workflow is all important.

Scarodactyl
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Re: Help needed with focus stacking

#10 Post by Scarodactyl » Sun Nov 22, 2020 3:25 am

The M3z is a nice scope. It is modular, so it's possible to add a trinocular port/camera adapter intermediate between the head and body. These adapters are compatible throughout the entire Leica and Wild M series (aside from the M5 and M4), so almost any camera port from the past 50 years of Wild-Leica history will work. The downside to that is that they're still in high demand since these are popular scopes, so prices are a bit higher than you might expect vs accessories for other scopes of this era. You can also upgrade the main objective to plan or planapo which will improve photography a fair amount. While there are definite limitations to photography with a stereo microscope you can still get quite decent results.
You might want to look into the "micromate", which is a motorized system which grabs onto a focus knob and rotates it a set amount and triggers your camera a set number of times. I've been meaning to get one myself.
How much are you willing to spend total to get this set up?

viktor j nilsson
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Re: Help needed with focus stacking

#11 Post by viktor j nilsson » Sun Nov 22, 2020 5:09 am

blaberus wrote:
Sat Nov 21, 2020 7:31 pm
5mm.
To capture a 5mm field on your D500 sensor, you'd need a magnification of 4.7x (5mm x 4.7 = 23.5mm, which is the long edge of your sensor). I think a 4x objective would work very well for that.

I love the M3Z by the way, one of my all time favorites.

blaberus
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Re: Help needed with focus stacking

#12 Post by blaberus » Sun Nov 22, 2020 6:59 pm

Thanks viktor j nilsson. Microbe Hunter recommends the following adaptor - do you think it would be OK? See https://www.microscope.com/accessories/ ... kit-1.html

blaberus
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Re: Help needed with focus stacking

#13 Post by blaberus » Sun Nov 22, 2020 7:05 pm

Scarodactyl wrote:
Sun Nov 22, 2020 3:25 am
The M3z is a nice scope. It is modular, so it's possible to add a trinocular port/camera adapter intermediate between the head and body. These adapters are compatible throughout the entire Leica and Wild M series (aside from the M5 and M4), so almost any camera port from the past 50 years of Wild-Leica history will work. The downside to that is that they're still in high demand since these are popular scopes, so prices are a bit higher than you might expect vs accessories for other scopes of this era. You can also upgrade the main objective to plan or planapo which will improve photography a fair amount. While there are definite limitations to photography with a stereo microscope you can still get quite decent results.
You might want to look into the "micromate", which is a motorized system which grabs onto a focus knob and rotates it a set amount and triggers your camera a set number of times. I've been meaning to get one myself.
How much are you willing to spend total to get this set up?
Thanks for your suggestions. I have managed to buy the 2.0x objective so far for less than $100 US, but the one planapo I have seen for sale is exceeding expensive - over $1000 UK!! If I had an adaptor for my camera, could the camera be linked to a computer and controlled by one of the focus stacking programmes, in the same way that an eyepiece camera can be by Toupview?
Last edited by blaberus on Sun Nov 22, 2020 7:08 pm, edited 1 time in total.

blaberus
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Joined: Sat Nov 21, 2020 5:23 pm

Re: Help needed with focus stacking

#14 Post by blaberus » Sun Nov 22, 2020 7:06 pm

viktor j nilsson wrote:
Sun Nov 22, 2020 5:09 am
blaberus wrote:
Sat Nov 21, 2020 7:31 pm
5mm.
To capture a 5mm field on your D500 sensor, you'd need a magnification of 4.7x (5mm x 4.7 = 23.5mm, which is the long edge of your sensor). I think a 4x objective would work very well for that.

I love the M3Z by the way, one of my all time favorites.
Thanks! Microbe Hunter recommends the following adaptor - do you think it would be OK? See https://www.microscope.com/accessories/ ... kit-1.html

viktor j nilsson
Posts: 269
Joined: Thu Aug 23, 2018 10:12 pm
Location: Lund, Sweden

Re: Help needed with focus stacking

#15 Post by viktor j nilsson » Sun Nov 22, 2020 7:43 pm

blaberus wrote:
Sun Nov 22, 2020 7:06 pm
viktor j nilsson wrote:
Sun Nov 22, 2020 5:09 am
blaberus wrote:
Sat Nov 21, 2020 7:31 pm
5mm.
To capture a 5mm field on your D500 sensor, you'd need a magnification of 4.7x (5mm x 4.7 = 23.5mm, which is the long edge of your sensor). I think a 4x objective would work very well for that.

I love the M3Z by the way, one of my all time favorites.
Thanks! Microbe Hunter recommends the following adaptor - do you think it would be OK? See https://www.microscope.com/accessories/ ... kit-1.html
Sorry, don't know if it'll work okay on your M3Z. I have never tried any of the no name adapters so I can't say. It's not entirely clear to me how the Omano adapter works and what type of optics it contains. It looks to me as if it is based on the principle of using a regular viewing eyepiece as a projection eyepiece by lifting it up a bit. Without knowing how it works I think it's impossible to say if you are able to achieve good field coverage, parfocality and decent image quality at the same time. But based on Oliver's video, it does look like it works okay (but hard to make a definitive judgement since Oliver appear to be using non-plan achromats). Still, I'm not sure if this would be more convenient than a dedicated stacking rig (sorry for being repetetive).

Are you planning on using your regular binocular eyepiece tube for this? Or are you waiting until you find a trinocular attachment? I wouldn't put the weight of a dslr on your binocular head.

blaberus
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Re: Help needed with focus stacking

#16 Post by blaberus » Sun Nov 22, 2020 8:47 pm

viktor j nilsson wrote:
Sun Nov 22, 2020 7:43 pm
blaberus wrote:
Sun Nov 22, 2020 7:06 pm
viktor j nilsson wrote:
Sun Nov 22, 2020 5:09 am


To capture a 5mm field on your D500 sensor, you'd need a magnification of 4.7x (5mm x 4.7 = 23.5mm, which is the long edge of your sensor). I think a 4x objective would work very well for that.

I love the M3Z by the way, one of my all time favorites.
Thanks! Microbe Hunter recommends the following adaptor - do you think it would be OK? See https://www.microscope.com/accessories/ ... kit-1.html
Sorry, don't know if it'll work okay on your M3Z. I have never tried any of the no name adapters so I can't say. It's not entirely clear to me how the Omano adapter works and what type of optics it contains. It looks to me as if it is based on the principle of using a regular viewing eyepiece as a projection eyepiece by lifting it up a bit. Without knowing how it works I think it's impossible to say if you are able to achieve good field coverage, parfocality and decent image quality at the same time. But based on Oliver's video, it does look like it works okay (but hard to make a definitive judgement since Oliver appear to be using non-plan achromats). Still, I'm not sure if this would be more convenient than a dedicated stacking rig (sorry for being repetetive).

Are you planning on using your regular binocular eyepiece tube for this? Or are you waiting until you find a trinocular attachment? I wouldn't put the weight of a dslr on your binocular head.
Very many thanks for all your suggestions! My budget for an 'imaging solution' is < £500 and I doubt I could get a trinocular attachment for less than this. Also having to manually take pics with my DSLR, then download them onto my computer, and then import them into a Photo stacking programme, is more hassle than I really want. I would like a quick and easy system, where if I want a photo, I can quickly attach a camera and get reasonable quality results fast. I will only be needing photos very occasionally e.g. when I am writing a paper describing a new species of cockroach and I need to illustrate small structures. I think the best solution for me is probably an eyepiece camera controlled by Toupview. This leads to a series of additional questions e.g. what brand of camera to get and how many megapixels do I need. The friend I mentioned earlier has a 10MP Amscope camera and she gets very good images which she publishes in her papers. I have read that one should calculate the resolution of one's microscope to work out how many megapixels the camera needs to be, but the calculation is beyond me! Do you have experience with eyepiece cameras and if so, can you recommend one?

PS. Another friend takes exceedingly good focus stacked images of seashells using his DSLR on a copy stand. I may buy a stand and try the same with insects. This would be far cheaper and simpler than a macro rail, and if I got really 'into' it I could upgrade to a more sophisticated setup. I suspect that I will only occasionally want to do such imaging. I prefer photographing live insects with my macro lens in the tropics!!

viktor j nilsson
Posts: 269
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Location: Lund, Sweden

Re: Help needed with focus stacking

#17 Post by viktor j nilsson » Sun Nov 22, 2020 9:09 pm

blaberus wrote: I would like a quick and easy system, where if I want a photo, I can quickly attach a camera and get reasonable quality results fast. I will only be needing photos very occasionally e.g. when I am writing a paper describing a new species of cockroach and I need to illustrate small structures. I think the best solution for me is probably an eyepiece camera controlled by Toupview.
Based on your needs, I think that this sounds like a wise choice. It'll be convenient, fast and it sounds like it will suit your work flow. Image quality should probably be comparable to any other solution you could build around your M3Z. And, perhaps most importantly, it would still be a quite useful thing to have for quick & easy documentation, even if you were to build a dedicated macro rig later.

I know mrsonchus has used toupview's live stacking function and reviewed it favorably.

blaberus
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Re: Help needed with focus stacking

#18 Post by blaberus » Sun Nov 22, 2020 9:13 pm

viktor j nilsson wrote:
Sun Nov 22, 2020 9:09 pm
blaberus wrote: I would like a quick and easy system, where if I want a photo, I can quickly attach a camera and get reasonable quality results fast. I will only be needing photos very occasionally e.g. when I am writing a paper describing a new species of cockroach and I need to illustrate small structures. I think the best solution for me is probably an eyepiece camera controlled by Toupview.
Based on your needs, I think that this sounds like a wise choice. It'll be convenient, fast and it sounds like it will suit your work flow. Image quality should probably be comparable to any other solution you could build around your M3Z. And, perhaps most importantly, it would still be a quite useful thing to have for quick & easy documentation, even if you were to build a dedicated macro rig later.

I know mrsonchus has used toupview's live stacking function and reviewed it favorably.
Thanks very much for all your help!

viktor j nilsson
Posts: 269
Joined: Thu Aug 23, 2018 10:12 pm
Location: Lund, Sweden

Re: Help needed with focus stacking

#19 Post by viktor j nilsson » Sun Nov 22, 2020 9:21 pm

blaberus wrote: PS. Another friend takes exceedingly good focus stacked images of seashells using his DSLR on a copy stand. I may buy a stand and try the same with insects. This would be far cheaper and simpler than a macro rail, and if I got really 'into' it I could upgrade to a more sophisticated setup. I suspect that I will only occasionally want to do such imaging. I prefer photographing live insects with my macro lens in the tropics!!
Yeah, there's many ways to build a good studio macro rig. I started out doing stacks manually with a newport micrometer-driven linear stage. But having grown tired of that, I built a horizontal one on an optical breadboard, with an THK KR15 industrial rail controlled with the MJKZZ IR controller. I have spent way more than I want to think about building a positioning stage with xyz, rotation, pitch and yaw movement. It's nice to have, but absolutely not necessary. My horizontal rig works fine for the small flies I specialize in. For genitalia photos I use my microscope. At some point I'll probably automate focus stacking on the microscope using a stepper motor (similar to Wemacro's Micromate), I should be able to use the same MJKZZ controller.

Sometimes i wish I had a vertical rig, such as your friend's copy stand. The Wemacro 2.0 stand can be used both horizontally and vertically. That to me seems like a pretty good option.

Scarodactyl
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Re: Help needed with focus stacking

#20 Post by Scarodactyl » Sun Nov 22, 2020 10:04 pm

One other option is to get a motic trinocular port. They have made clones of the m3 and m7 for a while and rhey are quite good. I think Martin Microscope might sell them?

Scarodactyl
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Re: Help needed with focus stacking

#21 Post by Scarodactyl » Sun Nov 22, 2020 10:57 pm

And one other other option might be this: https://www.ebay.com/itm/303582730298
I have seen heada from thr vision engineering Beta mounted on wild m3s before so the mount shoukd be compatible.

blaberus
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Re: Help needed with focus stacking

#22 Post by blaberus » Mon Nov 23, 2020 11:20 pm

Many thanks everyone! I have decided to buy an 18MB eyepiece USB3 camera as I am pretty sure it will give results good enough for publication in taxonomic journals and, most importantly, I want a system which is quick and easy to use. I have also purchased a very nice used Kaiser RS1 copy stand so I can begin to experiment with focus stacking using my macro lens. I'll see how I get on and may decide in the future to get systems which produce really professional results.

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