title: Large-scale neural circuit mapping data analysis accelerated with the graphical processing unit (GPU).
abstract: BACKGROUND
  Modern neuroscience research demands computing power. Neural circuit mapping studies such as those using laser scanning photostimulation (LSPS) produce large amounts of data and require intensive computation for post hoc processing and analysis.
  
  
  METHODS
  Here we report on the design and implementation of a cost-effective desktop computer system for accelerated experimental data processing with recent GPU computing technology. A new version of Matlab software with GPU enabled functions is used to develop programs that run on Nvidia GPUs to harness their parallel computing power.
  
  
  RESULTS
  We evaluated both the central processing unit (CPU) and GPU-enabled computational performance of our system in benchmark testing and practical applications. The experimental results show that the GPU-CPU co-processing of simulated data and actual LSPS experimental data clearly outperformed the multi-core CPU with up to a 22× speedup, depending on computational tasks. Further, we present a comparison of numerical accuracy between GPU and CPU computation to verify the precision of GPU computation. In addition, we show how GPUs can be effectively adapted to improve the performance of commercial image processing software such as Adobe Photoshop.
  
  
  CONCLUSIONS
  To our best knowledge, this is the first demonstration of GPU application in neural circuit mapping and electrophysiology-based data processing.
  
  
  CONCLUSIONS
  Together, GPU enabled computation enhances our ability to process large-scale data sets derived from neural circuit mapping studies, allowing for increased processing speeds while retaining data precision.
authors.affiliation: Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697-1275, United States.
authors.forename: Yulin
authors.initials: Y
authors.lastname: Shi
authors.affiliation: Department of Computer Science, University of California, Irvine, CA 92697-3435, United States.
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Veidenbaum
authors.affiliation: Department of Computer Science, University of California, Irvine, CA 92697-3435, United States.
authors.forename: Alex
authors.initials: A
authors.lastname: Nicolau
authors.affiliation: Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697-1275, United States; Department of Biomedical Engineering, University of California, Irvine, CA 92697-2715, United States; Department of Electrical Engineering and Computer Science, University of California, Irvine, CA 92697-2625, United States. Electronic address: xiangmin.xu@uci.edu.
authors.forename: Xiangmin
authors.initials: X
authors.lastname: Xu
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation; D006801:Humans; D011381:Programming Languages; D012984:Software; D013223:Statistics as Topic
keywords: CPU; Data analysis; GPU; Neural circuit mapping; Parallel processing