Open source software for multi-modal optical molecular imaging

A brief history of NIRFAST:
NIRFAST was originally developed in 2001 as a MATLAB-based package used to model near-infrared light propagation through tissue and reconstruct images of optical biomarkers. As research in optical imaging advanced, many of the major innovations introduced in the field, such as coupling optical imaging system with conventional medical imaging modalities to enable multi-modal "spatial priors") imaging, were included in the NIRFAST software.

In the early 2010’s, NIRFAST developers introduced a major update to the software by releasing a vtk-based user interface to import medical images (DICOMS) from conventional imaging systems (MRI, CT, etc.), segment those images into tissue regions, create NIRFAST-compatible finite element meshes, and use those meshes to reconstruct images of optical biomarkers. While closely linked, users still had to download the image processing front-end (called “NIRView”) and MATLAB-based optical computation packages (called “NIRFAST”) separately.

March, 2016: Introducing NIRFASTSlicer
NIRFASTSlicer is the latest version of NIRFAST now available for download, and marks another major milestone for the NIRFAST project. NIRFASTSlicer integrates the traditional NIRFAST optical computation engine (MATLAB code) into a customized version of 3DSlicer, which now handles all of the medical image processing/analysis tasks (replacing NIRView). 3DSlicer is an open-source medical image processing software package well-known in the medical imaging research community. It is maintained by a large community of developers, is highly extensible, and facilitates creation of custom versions for specific applications. In addition to offering a stable, well-maintained platform with cutting edge imaging processing tools for the NIRFAST workflow, this update also provides a single installer.

March, 2018: Major update released as NIRFASTSlicer 2.0 and NIRFASTMatlab 9.1
This released introduced:
  • A much more sophisticated and user-friendly set of segmentation tools.
  • Support for unstructured mesh visualization through the "Models" module. This enabled drag-and-drop loading to view NIRFAST Finite Element meshes. Consequently, the custom 3-D visualization package in NIRFASTMatlab used previously to view volumetric meshes was deprecated.
  • NIRFAST-Matlab was unbundled from NIRFAST-Slicer (now requiring separate downloads) to make project management more efficient.

Ongoing development and archives:
NIRFAST-MATLAB and NIRFAST-Slicer are developed and maintained on GitHub, and can be accessed by anyone at the links below. We welcome community input/development!:

NIRFAST-MATLAB component on Github

NIRFAST-Slicer component on Github