Dynamic Brain workshop 2016

Last two weeks I have spend in an amazing place in Friday Harbor Labs around Seattle. I participated at the course co-organized by Allen Institute and University of Washington. It was an amazing place, where together with many PhD students and post-docs from all over the world learned how to analyze the complex datasets recorded the mouse brain to better understand vision and connectivity. We learned how to use Python and got access to the terabytes of fresh neuroscience data! All students made wonderful one-week projects, with the topics ranging from network modeling and data-analysis to brain-connectivity visualization.

Short review of our activity is present here:


In our project we looked into coding properties of V1 neurons during presentation of the visual stimuli in vivo. We tried to decode the stimulus characteristics such as the direction of the drifting gratings, based on neural activity in the visual cortex. We found that application of the novel spike-sorting algorithm to the noisy Ca-imaging data from Allen Brain Observatory could significantly improve the decoding performance . The preliminary results already sound promising, reliable performance with 70% accuracy based on inferred spikes, it is 10% better than decoding based on Ca signals themselves. If spike extraction would work properly, it would allow to apply all the repertoire of technics to analyze firing-patterns to get better idea into features computed in the visual cortex. I am looking forward to check our findings with larger data-sets to make the firm conclusion.

P. S. By the wonderful coincidence the Green Fluorescent Protein (GFP) has been discovered there in Friday Haror Labs, partially by Osamu Shimomura (https://en.wikipedia.org/wiki/Osamu_Shimomura). It was absolutely fascinating to see the bioluminescent jelly-fishes and sparking plankton at night. Sparse bursts of fluorescent jellies and plankton we saw during the night were essentially similar to the neuron discharges we analyzed in mouse cortex during vision! All neurons of the transgenic mouse we studied have the same protein genetically encoded by GCamp-f vector. It was absolutely fascinating to see this wonderful coincidence, which I guess was prepared by the organizers :)

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