NeuroDOT: an extensible Matlab toolbox for streamlined optical brain mapping (Conference Presentation)

Adam T. Eggebrecht; David Muccigrosso; Joseph P. Culver

doi:10.1117/12.2510526

4 March 2019 NeuroDOT: an extensible Matlab toolbox for streamlined optical brain mapping (Conference Presentation)

Adam T. Eggebrecht, David Muccigrosso, Joseph P. Culver

Proceedings Volume 10874, Optical Tomography and Spectroscopy of Tissue XIII; 108741F (2019) https://doi.org/10.1117/12.2510526
Event: SPIE BiOS, 2019, San Francisco, California, United States

Abstract

As with the functional magnetic imaging community, multiple challenges exist in standardization of data format and processing pipelines. NeuroDOT is a MATLAB-based toolbox in the style of a conventional MATLAB toolbox. Its functionality is distributed among several pipelines, with extensive functions for data quality analysis and visualization. To aid in end-user support at multiple levels of familiarity and expertise, beyond the basic functionality, NeuroDOT contains data samples, support files, help sections, appendices, and tutorials. Specifically, a set of anonymized and published data samples have been chosen to reflect common experimental paradigms in neuroimaging (e.g., retinotopy and language based tasks), and are provided in both raw and pre-processed versions to aid in troubleshooting and training for the new user. The extensive support files contain geometric information for some of our diffuse optical tomography caps, sensitivity matrices, spectroscopy matrices, and standard atlases. Together with the documentation, these files provide a blueprint for users to create counterparts for their own systems. The toolbox currently supports a wide variety of standard data file formats. Help sections for each function are searchable from the MATLAB command line, with a Help Viewer version as well, each written and formatted in the style of their native MATLAB counterparts for familiarity and ease of use. Several appendices detail data structures, pipelines and their construction, and select visualizations of our pipelines’ results for multiple data samples. Multiple tutorials provide guidance to process data through a given pipeline to help the user harness the power and flexibility of NeuroDOT.

Conference Presentation

Citation Download Citation

Adam T. Eggebrecht, David Muccigrosso, and Joseph P. Culver "NeuroDOT: an extensible Matlab toolbox for streamlined optical brain mapping (Conference Presentation)", Proc. SPIE 10874, Optical Tomography and Spectroscopy of Tissue XIII, 108741F (4 March 2019); https://doi.org/10.1117/12.2510526

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