Massively parallel data processing for quantitative total flow imaging with optical coherence microscopy and tomography

Abstract

We present an application of massively parallel processing of quantitative flow measurements data acquired using spectral optical coherence microscopy (SOCM). The need for massive signal processing of these particular datasets has been a major hurdle for many applications based on SOCM. In view of this difficulty, we implemented and adapted quantitative total flow estimation algorithms on graphics processing units (GPU) and achieved a 150 fold reduction in processing time when compared to a former CPU implementation. As SOCM constitutes the microscopy counterpart to spectral optical coherence tomography (SOCT), the developed processing procedure can be applied to both imaging modalities. We present the developed DLL library integrated in MATLAB (with an example) and have included the source code for adaptations and future improvements. Program summaryProgram title: CudaOCMprocCatalogue identifier: AFBT_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFBT_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU GPLv3No. of lines in distributed program, including test data, etc.: 913552No. of bytes in distributed program, including test data, etc.: 270876249Distribution format: tar.gzProgramming language: CUDA/C, MATLAB.Computer: Intel x64 CPU, GPU supporting CUDA technology.Operating system: 64-bit Windows 7 Professional.Has the code been vectorized or parallelized?: Yes, CPU code has been vectorized in MATLAB, CUDA code has been parallelized.RAM: Dependent on users parameters, typically between several gigabytes and several tens of gigabytesClassification: 6.5, 18.Nature of problem: Speed up of data processing in optical coherence microscopySolution method: Utilization of GPU for massively parallel data processingAdditional comments: Compiled DLL library with source code and documentation, example of utilization (MATLAB script with raw data)Running time: 1,8 s for one B-scan (150 × faster in comparison to the CPU data processing time)