Double your Science Sunday Pleasure: As a theme for next week’s ScienceSunday , Chad Haney proposes Google+…

Double your Science Sunday Pleasure: As a theme for next week’s ScienceSunday , Chad Haney proposes Google+ Collaborations. Combine your expertise to create synergy and more awesome #sciencesunday posts. As an example, this beautiful sectioning of a flower, set to the haunting lilts of a waltz, has the hallmark of a post from Rajini Rao . Chad Haney provides expert insight on the imaging. So, what are you waiting for science enthusiasts?

The Beauty Within: Beauty, as they say, lies in the eye of the beholder. Arabidopsis is an insignificant flowering plant of the mustard family (Brassicaceae) that holds special beauty to plant geneticists and molecular biologists. It has only 5 chromosomes, completely sequenced, and a short life span of 6 weeks from germination to seed maturation. A large collection of mutant lines are freely available as a scientific resource, and genes can be readily introduced by infecting with Agrobacterium tumifaciens. A model organism worthy of modeling in this imaging video.

Deconstructing a Flower: 248 sections of an Arabidopsis flower that was paraffin-embedded and sectioned at 20 microns. Sections were stained with Safranin and Fast Green and photographed with a consumer-grade camera mounted on a Nikon Eclipse 50i at 20X.

Chemical clearing vs. digital clearing. The method for plants requires a controlled substance and many samples are too thick for it to work. So they used Adobe After Effects to digitally remove the background making it easier to visualize the sample. They imported JPEGs of each histological slide into AE to create a 3D “stack”. It took 1 hour to align 60 slides after they gained some practice. Images that were lost due to processing issues were excluded. Because they did not use software designed for this, I doubt they were able to get the spacing correct, i.e., have blank slices. There are tons of segmentation algorithms in medial imaging that could have been used. Unfortunately, it would like require some code writing or very expensive medical imaging software. So hats off to them for a cost effective, brute force method. However, as we posted a while ago, the Visible Human Project was funded to develop software that can be used for this project (http://goo.gl/cv2xU).

Video: GRAND PRIZE WINNER in the 3rd ChloroFilms Contest: http://www.ChloroFilms.org

There is a 3D version! Arabidopsis Flower in True 3D

#sciencesunday ScienceSunday Robby Bowles Allison Sekuler

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10 Responses to Double your Science Sunday Pleasure: As a theme for next week’s ScienceSunday , Chad Haney proposes Google+…


  1. My mind is still blown from your “Do viruses have colour” post, Rajini Rao. It will be weeks before I recover, I expect.

  2. Brian Clint says:


    man you aint seen her cooking yet!

  3. Rajini Rao says:


    Haha, actually, I was planning to share my chili hot sauce recipe today..I guess I’d better wait for a cooling off period. Wouldn’t want a Google + burn out. 🙂

  4. Brian Clint says:


    Iil chill awhile.


  5. made me think of this one too:


    http://www.seas.harvard.edu/softmat/downloads/2011-03.pdf


    (edit: correct link now!)

  6. hina ali says:


    I discussed this post with 3 people in a hangout.


  7. Just wanted to mention that, while I find Google+ to be an uninspired interface (to put it mildly) I really enjoy following your posts. Thanks !

  8. Rajini Rao says:


    Felix Woitzel , thanks for pointing me to a very interesting study! Although the details of the math are beyond my expertise, I loved the paper. In some ways, it perfectly illustrates how I view the scientific method: (1) scientist thinks opening of a flower is cool (2) observes it in some detail (films/time lapse) and reads up on the mechanism (3) comes up with a theory that better explains it (4) does a limited test, combining theory with simulation. Cool, the results make sense! (5) publishes in a top rated journal by adding one sentence in abstract justifying the work (biomimetics, engineering “deployable structures”…peer reviewers don’t care because the work is cool). (5) Makes reference to 1790 work by Goethe for the WIN.


    I do so love science 😛


  9. I have another exciting one, that is even more practical. check out the two links from this tweet! https://twitter.com/#!/kcimc/status/189086456319442944

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