Nirfast is an open source software package that allows users to easily model Near-Infrared light transport in tissue. The software is cross-platform, and can be downloaded for free on the Nirfast website. The program allows for the integration of Near-Infrared Spectroscopy (NIRS) into other modalities such as Magnetic Resonance Imaging (MRI), and initially was developed by the Optics in Medicine Laboratory at Dartmouth as a tool for imaging breast cancer. Nirfast’s integration of NIRS into MRI provides radiologists more molecular-specific information about the lesions they are assessing in the image.
The Finite element method (FEM) based software package allows users to easily model 1.) standard single wavelength absorption and reduced scatter, 2.) multi-wavelength spectrally constrained models, and 3.) fluorescence models. Nirfast addresses the entire workflow of light modeling: starting with actual medical images—which are stored in the Digital Imagining and Communications in Medicine (DICOM) format—Nirfast segments each DICOM, creates a FEM-based mesh, models the data, and then visualizes the results for the user. For its mesh creation, Nirfast uses meshing tools developed in its sibling project, Nirfast-meshing, which was also created by the Optics in Medicine Laboratory.
While Nirfast and Nirfast-meshing work seamlessly with one another, the programs were built separately for two reasons. First, decoupling the meshing software and the Finite Element code enables users to integrate either Nirfast element into the meshing or FEM-based software that is already installed on their laboratories’ equipment. Secondly, building the two aspects of Nirfast separately makes it easier for members of the Optics in Medicine Laboratory to develop a software package that is able to perform two different computational functions either independently or in tandem.
Nirfast is a collaborative project that is kept under content revision control. The program’s source code is housed on Google code, a free code-hosting site that allows programmers to remotely log in, review Nirfast’s source code, and submit their revisions to the members of the Optics in Medicine Laboratory. One of the responsibilities of Michael Jermyn, a second-year graduate student in the Optics in Medicine Laboratory, is to review these revisions and compile the usable submissions into patches. These patches are then published on the program’s website where they can be downloaded for free.
While Professor Keith Paulsen developed the first code leading to Nirfast almost 20 years ago, a number of Dartmouth graduate students and researchers have advanced the software package since the late 90s: Professor Hamid Dehghani improved upon Paulsen’s code and transferred it to MATLAB, Scott Davis created a fluorescence tool box that allows the software to image tissues in the presence of a fluorophore, Subhadra Srinivasan built the spectral toolbox which allowed the program to analyze multiple wavelengths of light in tandem, Hamid Ghadyani added an automatic meshing toolbox which allows for the integration of clinical images into Nirfast, and now Michael Jermyn has both transferred the program to an open source format and developing a number of new user interfaces. For the work that he is doing on Nirfast, Michael was selected as a Graduate Fellow by Dartmouth’s Neukom Institute during the 2011-12 academic year.
Since 2009, the National Institute of Health (NIH) and its National Cancer Institute (NCI) has funded the development of Nirfast. This funding has enabled members of the Optics In Medicine Laboratory to customize Nirfast into a truly open source shareware, and work with researchers worldwide to train them in its use.
Each year, the Optics In Medicine Laboratory runs a number of workshops that strengthen the Nirfast community. Held not only at Dartmouth College, but also the Optics Society of America’s (OSA) Miami conference and the international society for optics and photonics’s (SPIE) San Francisco conference, these workshops provide comprehensive Nirfast training to academics and industry professionals. At these workshops, members of the Optics in Medicine Lab also provide custom software modification for Nirfast users so that the program is able to function properly on the equipment used in their laboratories.
Since NIH and NCI began funding the project in 2009, Nirfast has received over 700 unique downloads annually. While small patches are submitted to the Nirfast repository on a weekly basis, the Optics in Medicine Laboratory usually receives three major submissions each year. Michael carefully reviews each of these revisions, and publishes a full software release about once a month.