Paid Internship on Acceleration of HPC/BigData Algorithms for Behavioral Experiments

Tracking of mouth whiskers in many mammals is characteristic of their brain activity, similar to what finger movement is in humans. Neuroscientists can deduce a plethora of information on behavior by mounting whisker-tracking experiments, i.e. experiments where animals (typically, mice, rats) are being tracked for their whisker movements subject to various stimuli such as air puff in their eyes, auditory stimuli, and so on. In the Erasmus MC we have developed an experimental setup which records whisker movements on head-fixed mice. Recording is done through a high-speed camera that generates large amounts of image stacks which are then sent to a computer for post-processing through a powerful yet slow Matlab program (http://bwtt.sourceforge.net/docs/). Current experiment runs generate 15 seconds of whisker-tracking video which occupies 2-4 GB of disk space to store and takes about 2 weeks of post-processing in Matlab. At the moment, dozens of videos are generated per week, which puts high pressure not only on the storage equipment needed but is also detrimental to the fast and efficient analysis of the behavioral experiments.

The goal is to study the open-source Matlab code and port the compute- and data-intensive parts of it to a high-performance, FPGA-based computing platform (Maxeler). This not only will accommodate experiments in the lab but will also be the first, crucial step for supporting closed-loop behavioral experiments, where specific whisker movements will evoke (in real time) a suitable response by the analysis machine, leveraging a crucial class of neuroscientifically relevant experiments.

Internship details

A student internship is offered on the topic (salary depending on candidate expertise) for a minimum duration of 6 months and a maximum of 12 months. Productivity bonuses are possible.

Job Category: Interships
Job Type: Full Time

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