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Desmids - now in 3D
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blepharopsis



Joined: 28 Nov 2014
Posts: 143
Location: Virginia, USA

PostPosted: Sat Nov 29, 2014 2:26 pm    Post subject: Desmids - now in 3D Reply with quote

Greetings! We all love desmids - or at least have some appreciation for their beauty/weirdness of their forms. I had a little romantic affair with those algae last year, since then I moved on - but I'm left with a bunch of confocal data that, knowing my total lack of diligence when it comes to backing up files, may never see the light of day. I don't recall seeing many three-dimensional renderings of desmids out there, so perhaps I have something somewhat unique in my hands. Posting red-cyan anaglyphs is best I can do here since the site doesn't host movies or GIFs, but maybe you can point me to a place where I could upload 3D rotational views of desmids, pediastrum algae, rotifers and such? Do you have any interest in that at all?
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blepharopsis



Joined: 28 Nov 2014
Posts: 143
Location: Virginia, USA

PostPosted: Sat Nov 29, 2014 2:33 pm    Post subject: Reply with quote





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JH



Joined: 09 Mar 2013
Posts: 1264
Location: Vallentuna, Stockholm, Sweden

PostPosted: Sat Nov 29, 2014 3:33 pm    Post subject: Reply with quote

Amazing pictures!
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rjlittlefield
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Joined: 01 Aug 2006
Posts: 20353
Location: Richland, Washington State, USA

PostPosted: Sat Nov 29, 2014 3:48 pm    Post subject: Reply with quote

Igor, these are excellent and most appreciated (by me, anyway)!

This site photomacrography.net does support uploading gif's, up to the maximum file size of 300 KB. That's about 470x313 x 2 frames, if you had in mind a rocking animation.

For movies, YouTube is the most heavily used host.

While I have you here, let me ask a question: what's the difference between the top half and the bottom half of each desmid? I get the feeling that I'm looking at a montage of two different imaging techniques, one that captures mostly the surface and a second that looks deeper inside. Is that what's going on, or something else?

--Rik
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blepharopsis



Joined: 28 Nov 2014
Posts: 143
Location: Virginia, USA

PostPosted: Sat Nov 29, 2014 5:33 pm    Post subject: Reply with quote

Hi Rik, I collected the fluorescence of cell wall (stained with Calcofluor White) and autofluorescence of chlorophyll in separate channels, made R-C anaglyphs from both of them and then merged those in Photoshop simply rubbing out the top layer (cuticle in this case) to expose the chloroplast. Do you actually own a pair of those old school 3D glasses? Mine came with with a comic book "Freddy's dead - The final nightmare", from the 80's, I believe Very Happy
Cheers!



rjlittlefield wrote:
what's the difference between the top half and the bottom half of each desmid? I get the feeling that I'm looking at a montage of two different imaging techniques, one that captures mostly the surface and a second that looks deeper inside. Is that what's going on, or something else?

--Rik
Very Happy
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blepharopsis



Joined: 28 Nov 2014
Posts: 143
Location: Virginia, USA

PostPosted: Sat Nov 29, 2014 5:45 pm    Post subject: Reply with quote

OK, let's see if that works... I had to trim off 80% of frames and down-sample the image. Here it goes...


rjlittlefield wrote:
This site photomacrography.net does support uploading gif's, up to the maximum file size of 300 KB. That's about 470x313 x 2 frames, if you had in mind a rocking animation.


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rjlittlefield
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Joined: 01 Aug 2006
Posts: 20353
Location: Richland, Washington State, USA

PostPosted: Sat Nov 29, 2014 6:00 pm    Post subject: Reply with quote

The rotating image works fine, although the rotation is too fast for my tastes. (Also, I admin-edited your post to add a required [/quote] tag so the message would format properly.)

Thanks for the information about top versus bottom halves.

Yes, I have several pairs of anaglyph glasses. Some of them use the old cardboard frames. I also have a newer pair with plastic frames and slightly close-up lenses. Mine are all red in the left eye. I went to check just now and discovered at http://www.berezin.com/3d/3dglasses.htm#Anaglyph that some newer formats require a different convention.

Also, to view your original images I used StereoPhoto Maker to convert your anaglyphs to side-by-side grayscale. I'm not very fond of anaglyphs because always some amount of the wrong image bleeds through each filter and contaminates the stereo.

--Rik
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Jacek



Joined: 02 Oct 2011
Posts: 5351
Location: Poland

PostPosted: Sun Nov 30, 2014 6:19 am    Post subject: Reply with quote

Shocked Shocked Shocked
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https://photos.app.goo.gl/MV9IynUtBdaKkVj53
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Pau
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Joined: 20 Jan 2010
Posts: 4911
Location: Valencia, Spain

PostPosted: Sun Nov 30, 2014 7:43 am    Post subject: Reply with quote

Wow!
Great work!
May be you could post stereo pairs, that would render better quality than anaglyphs
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Pau
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blepharopsis



Joined: 28 Nov 2014
Posts: 143
Location: Virginia, USA

PostPosted: Sun Nov 30, 2014 12:52 pm    Post subject: Reply with quote

Hi Rik, thanks for the feedback! I feel I should upgrade my gear; plastic stereo glasses with magnifying lenses sound way cooler than the cardboard ones I own. I will start preparing stereo pairs from my stacks then - I am noticing a general bias towards their favor.
The rotation appears way too fast, I agree - will try to fix it (see below). Sorry for messing up with the formatting. One day I will get all the elements right...

Cheers!







rjlittlefield wrote:
The rotating image works fine, although the rotation is too fast for my tastes. (Also, I admin-edited your post to add a required tag so the message would format properly.)(...)
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blepharopsis



Joined: 28 Nov 2014
Posts: 143
Location: Virginia, USA

PostPosted: Sun Nov 30, 2014 12:59 pm    Post subject: Reply with quote

one more movie... This time the cell wall (of M. americanum) only...

Notice how chubby those desmids are!

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hkv



Joined: 02 Jan 2013
Posts: 443
Location: Sweden

PostPosted: Sun Nov 30, 2014 2:05 pm    Post subject: Reply with quote

These are so great!

Would you share the basic workflow and what type of equipment you have been using for capturing these images?
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blepharopsis



Joined: 28 Nov 2014
Posts: 143
Location: Virginia, USA

PostPosted: Sun Nov 30, 2014 2:14 pm    Post subject: Reply with quote

Thanks! Sure, here it is:
Fixed in 2% PFA, cell walls stained with Calcofluor White, mounted in 0.5% low melting agarose using #1 coverslip "sandwich" (I make a petroleum jelly barrier around the drop of agarose to prevent it from drying out too fast). Imaged with Zeiss confocal laser scanning microscope LSM 710 using 405 and 562 laser lines, objective 40x NA 1.3. Rotational movies made with Icy.



hkv wrote:
These are so great!

Would you share the basic workflow and what type of equipment you have been using for capturing these images?
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hkv



Joined: 02 Jan 2013
Posts: 443
Location: Sweden

PostPosted: Sun Nov 30, 2014 2:47 pm    Post subject: Reply with quote

blepharopsis wrote:
Thanks! Imaged with Zeiss confocal laser scanning microscope LSM 710 using 405 and 562 laser lines, objective 40x NA 1.3.


Thanks! Too bad these Zeiss LSM 710 scopes start at $535,000... Crying or Very sad
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blepharopsis



Joined: 28 Nov 2014
Posts: 143
Location: Virginia, USA

PostPosted: Sun Nov 30, 2014 3:18 pm    Post subject: Reply with quote

hkv wrote:
Thanks! Too bad these Zeiss LSM 710 scopes start at $535,000... Crying or Very sad


I don't personally know many private owners of a confocal microscope Smile
I've changed my professional occupation (protein biochemistry ---> neurobiology) to get an access to the machine!

Off topic - is this website acting up on your end too? It takes ages to open posts etc. I hope my joining the group yesterday wasn't the straw that broke the camel's back... Smile
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