Towards real-time whisker tracking in rodents for studying sensorimotor disorders

The rodent whisker system is a prominent experimental subject for the study of sensorimotor integration and active sensing. As a result of improved video-recording technology and progressively better neurophysiological methods, there is now the prospect of precisely analyzing the intact vibrissal sensori-motor system. The vibrissae and snout analyzer (ViSA), a widely used algorithm based on computer vision and image processing, has been proven successful for tracking and quantifying rodent sensorimotor behavior, but at a great cost in processing time. In order to accelerate this offline algorithm and eventually employ it for online whisker tracking (less than 1 ms/frame latency), we have explored various optimizations and acceleration platforms, including OpenMP multithreading, NVidia GPUs and Maxeler Dataflow Engines. Our experimental results indicate that the optimal solution for an offline implementation of ViSA is currently the OpenMP-based CPU execution. By using 16 CPU threads, we achieve more than 4,500x speedup compared to the original Matlab serial version, resulting in an average processing latency of 1.2 ms/frame, which is a solid step towards real-time (and online) tracking. Analysis shows that running the algorithm on a 32-thread-enabled machine can reduce this number to 0.72 ms/frame, thereby enabling real-time performance. This will allow direct interaction with the whisker system during behavioral experiments. In conclusion, our approach shows that a combination of software optimizations and the careful selection of hardware platform yields the best performance increase

Overview of recent physics results from the national spherical torus experiment (NSTX)

The National Spherical Torus Experiment (NSTX) has made considerable progress in advancing the scientific understanding of high performance long-pulse plasmas needed for future spherical torus (ST) devices and ITER. Plasma durations up to 1.6 s (five current redistribution times) have been achieved at plasma currents of 0.7 MA with non-inductive current fractions above 65% while simultaneously achieving beta(T) and beta(N) values of 17% and 5.7 (%m T MA(-1)), respectively. A newly available motional Stark effect diagnostic has enabled validation of current-drive sources and improved the understanding of NSTX 'hybrid'-like scenarios. In MHD research, ex-vessel radial field coils have been utilized to infer and correct intrinsic EFs, provide rotation control and actively stabilize the n = 1 resistive wall mode at ITER-relevant low plasma rotation values. In transport and turbulence research, the low aspect ratio and a wide range of achievable in the NSTX provide unique data for confinement scaling studies, and a new microwave scattering diagnostic is being used to investigate turbulent density fluctuations with wavenumbers extending from ion to electron gyro-scales. In energetic particle research, cyclic neutron rate drops have been associated with the destabilization of multiple large toroidal Alfven eigenmodes (TAEs) analogous to the 'sea-of-TAE' modes predicted for ITER, and three-wave coupling processes have been observed for the first time. In boundary physics research, advanced shape control has enabled studies of the role of magnetic balance in H-mode access and edge localized mode stability. Peak divertor heat flux has been reduced by a factor of 5 using an H-mode-compatible radiative divertor, and lithium conditioning has demonstrated particle pumping and results in improved thermal confinement. Finally, non-solenoidal plasma start-up experiments have achieved plasma currents of 160 kA on closed magnetic flux surfaces utilizing coaxial helicity injection.X1132Nsciescopu

The value of open-source clinical science in pandemic response: lessons from ISARIC

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