Monday, November 14, 2011

Undergrads are like a supercomputer

Yesterday I saw the talk from Winfried Denk. Why is Winfried Denk awesome? He practically invented the two photon microscope. He now invented a technique to image large brain volumes and trace all neurites in it. How he does it is as interesting as the results. Computer tracing did not provide the results he wanted. There were a lot of misses, partially traced neurites, wrong combinations, etc. Manual tracing performs much better, but is very time consuming since all tracing at the ultrastructural level is done by outlining the neurites in every slice. This is slow, as Winfried showed us by playing a movie of someone outlining neurites section by section. Or as Winfried put it: "This is so slow, I can't look at it!". His new tracing methods only involves clicking every few slices in the neurite you're tracing. This results in a 'skeleton' trace of the neurons. By having a small army of undergrads every neuron is traced multiple times after which the computer can evaluate the differences in tracing and by a 'democratic' process selects the correct 'skeleton'. The really cool part is where the automatic segmentation is overlaid on each skeleton. Now each neuron has a volumetric model. For a small piece of retina it cost ~30.000 hours to trace 1m of neurite from a few hundred of cells.

So, by combining a sloppy computer segmentation with the awesomeness of the paid undergrad brain you can reconstruct sections or a whole brain at the ultrastructure level. He is some sort of scientific Chuck Norris!

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