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rocking diatoms
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nanometer



Joined: 30 Apr 2016
Posts: 165
Location: Tucson, AZ

PostPosted: Mon Dec 25, 2017 11:17 pm    Post subject: rocking diatoms Reply with quote

Thanks to Mike Tuell, I have finally tried Zerene. Amazing program. I went after a few diatoms with the Leitz 90x apo Pv and Heine condenser, and created a few rocking gifs. The Pv objectives have the phase ring at higher NA than the 160mm Floutar objectives which was helpful. Now I'm hoping to get new life out of my 40x Apo Pv 0.95 Smile






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Lou Jost



Joined: 04 Sep 2015
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Location: Ecuador

PostPosted: Tue Dec 26, 2017 6:06 am    Post subject: Reply with quote

Wow, these are stunning, though I can't quite figure out the middle one. Very inspiring.
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carlos.uruguay



Joined: 23 Feb 2012
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PostPosted: Tue Dec 26, 2017 6:11 am    Post subject: Reply with quote

Super!!!
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JH



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

PostPosted: Tue Dec 26, 2017 10:35 am    Post subject: Reply with quote

Easy to see the shape, nicely done!
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Jörgen Hellberg
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rjlittlefield
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Joined: 01 Aug 2006
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Location: Richland, Washington State, USA

PostPosted: Tue Dec 26, 2017 11:19 am    Post subject: Reply with quote

Very nice!

Lou, I take the middle one to be every other wedge is forward/backward, so 3 wedges in front, 3 behind. The floating purple blobs in the middle could be some sort of imaging artifact, or they could really be physical blobs inside the specimen, perhaps being distorted by a rippled surface in front of them.

nanometer, what does direct observation tell you about the floating purple blobs?

--Rik
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nanometer



Joined: 30 Apr 2016
Posts: 165
Location: Tucson, AZ

PostPosted: Tue Dec 26, 2017 11:28 am    Post subject: Reply with quote

Thanks for looking guys. Rik, I would say that central region is more like your latter description rather than some imaging artifact. That's a funny one to look at while rocking for me. Sometimes, I see every other 3 high and then the next time, I see the highs and lows reversed. Sometimes I see two adjacent ones both high, and then it goes away.

I'm interested enough to do some more of this! It's amazing to see how well rocking gives you information compared to just a simple one-view stack. The latter can look like a bit of a mess, but then it all makes sense in rocking. Can't say enough great stuff about Zerene. When my trial period ends, I'll be buying the license.
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Lou Jost



Joined: 04 Sep 2015
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PostPosted: Tue Dec 26, 2017 11:34 am    Post subject: Reply with quote

Rik and nanometer, I see it now, but it grates against my expectation that a diatom shell is encasing a 3-dimensional body....
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rjlittlefield
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PostPosted: Tue Dec 26, 2017 12:04 pm    Post subject: Reply with quote

Lou, the actual surface relief is not as much as these images make it appear to be. But yes, those diatoms have a definite up/down/up/down structure to their shell. See http://www.nhm.ac.uk/content/dam/nhmwww/our-science/our-work/biodiversity/actinoptychus-diatom-sem-two-column.jpg (at http://www.nhm.ac.uk/our-science/our-work/biodiversity/diatom-research.html) for an SEM image of a similar (not identical!) structure.

nanometer, have you tried these in stereo? I did a little trial with images 4 apart in your sequence, and for me it worked well.

--Rik
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nanometer



Joined: 30 Apr 2016
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PostPosted: Tue Dec 26, 2017 1:24 pm    Post subject: Reply with quote

Rik, I did try some stereo images and they turned out well, but I prefer rocking to crossing my eyes Smile
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Lou Jost



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PostPosted: Tue Dec 26, 2017 1:36 pm    Post subject: Reply with quote

Me too, these rocking images are easy to look at compared to cross-eyed things.
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nanometer



Joined: 30 Apr 2016
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PostPosted: Tue Dec 26, 2017 3:07 pm    Post subject: Reply with quote

Rik,

I looked at the diatom again today, and I can tell you that that central structure is definitely a phase contrast artifact that changes with focus.

Steve
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Smokedaddy



Joined: 07 Oct 2006
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PostPosted: Tue Dec 26, 2017 3:16 pm    Post subject: Reply with quote

Very nice.
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rjlittlefield
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PostPosted: Tue Dec 26, 2017 6:23 pm    Post subject: Reply with quote

nanometer wrote:
... central structure is definitely a phase contrast artifact that changes with focus.

Great, thanks for the info.

--Rik
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rjlittlefield
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PostPosted: Tue Dec 26, 2017 6:36 pm    Post subject: Reply with quote

nanometer wrote:
Sometimes, I see every other 3 high and then the next time, I see the highs and lows reversed. Sometimes I see two adjacent ones both high, and then it goes away.

There are lots of interesting ways for shape-from-motion to go weird.

With some effort, I can consciously shift between sharp patterns in front versus fuzzy patterns in front. That's OK, but then sometimes I get it one way on the left and the other way on the right, and then the apparent motion becomes a flexing/folding across the almost vertical line. First time it happened, I wondered "Say what?!"

None of those things happen to me with stereo. And of course stereo has the advantage that it does not require an electronic display.

But I agree that under a lot of circumstances, rocking works better. When I present to an audience, I always show the rocking form, usually implemented by forward/backward keystrokes in PowerPoint. Rolling Eyes

--Rik
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nanometer



Joined: 30 Apr 2016
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Location: Tucson, AZ

PostPosted: Tue Dec 26, 2017 7:00 pm    Post subject: Reply with quote

Rik,

Just for you, here's a stereo of a diatom very similar to the one in the article you linked above. This is DF with the 40x .95 APO. Not the cleanest, but the stereo image turned out nice--even the little glass tubes sticking out. I tried 40x phase, but the tubes didn't show up very well. I do see what you mean. The stereo image is just cleaner and there is no ambiguity as to what is high and what is low.

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