Tuesday, August 04, 2015

Hacking Zebrafish thoughts

The last lab from Scalable Machine Learning with Spark features a guest lecture by Jeremy Freeman, a professor of neuroscience at Janelia Farm Research Campus.

His group produced this gorgeous video of a living zebrafish brain. Little fish thoughts sparkle away, made visible by a technique called light-sheet flourescent microscopy in which engineered proteins that light up when the neurons fire are engineered into the fish.

The lab covers principal component analysis in a lively way. Principal components are extracted from time-series data and mapped onto an HSV color wheel and used to color an image of the zebrafish brain. In the process, we use some fun matrix manipulation to aggregate the time series data in two different ways - by time relative to the start of a visual stimulus and by the directionality of the stimulus (shown below).

The whole series of labs from the Spark classes was nicely done, but this was an especially fun way to finish it out.

Check out the Freeman Lab's papers: