scatterBrains: an open database of human head models and companion optode locations for realistic Monte Carlo photon simulations
Abstract
SIGNIFICANCE: Monte Carlo (MC) simulations are currently the gold standard in the near-infrared and diffuse correlation spectroscopy (NIRS/DCS) communities for generating light transport paths through tissue. However, realistic and diverse models that capture complex tissue layers are not easily available to all; moreover, manually placing optodes on such models can be tedious and time consuming. Such limitations may hinder the adoption of representative models for basic simulations and the use of these models for large-scale simulations, e.g., for training machine learning algorithms.
AIM: We aim to provide the NIRS/DCS communities with an open-source, user-friendly database of morphologically and optically realistic head models, as well as a succinct software pipeline to prepare these models for mesh-based Monte Carlo simulations of light transport.
APPROACH: Sixteen anatomical models were created from segmented T1-weighted magnetic resonance imaging (MRI) head scans and converted to tetrahedral mesh volumes. Approximately 800 companion scalp surface locations were distributed on each model, comprising full head coverage. A pipeline was created to place custom source and optical detectors at each location, and guidance is provided on how to use these parameters to set up MC simulations.
RESULTS: The models, head surface locations, and all associated code are freely available under the scatterBrains project on Github.
CONCLUSIONS: The NIRS/DCS community benefits from having…
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