We don’t live or work in a vacuum

We don’t live or work in a vacuum

Interdisciplinary work and collaborations are the norm for my area of research. So it only makes sense to collaborate with my science friends on G+. Thanks Rajini Rao for giving me the chance to collaborate on a ScienceSunday post. I’m looking forward to everyone’s collaborative posts next Sunday. Unless you have a thick skull (hint) don’t miss my collaborative post with Erin Kane next #ScienceSunday

Originally shared by Rajini Rao

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

http://www.youtube.com/watch?v=zlw-50RHoec