NeuroDOT, a MATLAB-based self-contained toolbox, addresses common challenges in processing of functional near infrared spectroscopy (fNIRS) and diffuse optical tomography (DOT) data and supports multiple common pre-processing and analytical pipelines, including: simulation, data-anatomy alignment and modeling, pre-processing, data quality control, reconstruction, spectroscopy, post-processing, and extensive data visualizations at all stages of processing. The toolbox contains a set of pre-assembled (anonymized) and published data samples from our lab, chosen to reflect common experimental paradigms in neuroimaging including visual and language tasks for human brain mapping. The data are provided in both raw and pre-processed versions to aid in troubleshooting and training. Visualization and analysis tools provide powerful and intuitive explorations of data and data quality at every stage of processing and analysis. Data from common optical systems (CW, FD, TR, etc.) are supported or will soon be added.