Multiple challenges exist in standardization of data format and processing pipelines for optical functional neuroimaging. We present here a fully self-contained and end-user-friendly tool that provides the flexibility for multiple array-based imaging modalities, and offers format compatibility, spatial registration, and analytical breadth and sophistication for postprocessing. NeuroDOT, available on GitHub, is written in MATLAB in the style of a conventional MATLAB toolbox with functionality distributed across 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. 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 NeuroDOT toolbox currently supports a wide variety of standard data file formats (e.g., NIFTI, GIFTI, and others). Help sections exist for each function and are searchable from the MATLAB command line, with a Help Viewer version as well. Both are 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. Several tutorials are also included, each of which runs a data sample through a given pipeline to help the user harness the power and flexibility of NeuroDOT.