Extensible light modeling and image reconstruction pipeline for reliable optical brain mapping with NeuroDOT and OXI

Accurate data-anatomy registration, pipeline standardization, and reproducibility pose significant challenges for optical brain mapping due to the inherent lack of anatomical information from functional near infrared spectroscopy (fNIRS) and diffuse optical tomography (DOT) as well as the wide variety of systems and data formats used. NeuroDOT provides customizable pipelines for array design, light modeling, and image reconstruction using any optical imaging system by providing compatibility with multiple data formats (e.g.,SNIRF, BIDS, NIRS, NIfTI, GIFTI, 4dfp, etc.) and a wide variety of commercially available systems (e.g., GowerLabs, NIRx, Artinis etc.). Additionally, NeuroDOT also provides cloud-based computing with our OXI tools (www.oxi.wustl.edu) to lessen the computational burden of processing, enhance accessibility, promote reproducibility of results, and simplify processing overall. We aim to promote modernization of the growing components of NeuroDOT by continuing to refactor the toolbox to Python, data format standardization relevant to both optical and fMRI fields, expanded documentation, tutorials, and user-targeted workshops.