Exploring Tissue Optics Through NIRFAST-Slicer Workshop

The Optical Society (OSA) Biomedical Optics 2016 conference took place last week in Fort Lauderdale, Florida. Prior to the start of the conference, Alexis Girault from Kitware co-taught a training workshop on NIRFAST. NIRFAST is an open-source software package that researchers use to model multi-wavelength and luminescence light propagation through tissues of arbitrary shapes. At the workshop, Alexis provided instructions and support on NIRFAST-Slicer, which combines the capabilities of NIRFAST with those of another open-source solution, 3D Slicer. 3D Slicer is widely used in the medical community to segment, register, and visualize medical images.

The goal of the workshop was to help attendees become acquainted with NIRFAST and NIRFAST-Slicer through interactive case studies. The first case study outlined the basic principles of fluorescence imaging. For this case study, attendees used NIRFAST-Slicer to visualize three-dimensional (3D) images that were overlaid on a magnetic resonance imaging (MRI) Digital Imaging and Communications in Medicine (DICOM) image stack of a mouse. For the second case study, attendees generated a Jacobian matrix for a mesh created from an MRI head scan. For the third and final case study, attendees reconstructed 3D images from segmented optical data.


The workshop was well attended with more than 30 participants from all over the world. With the expanding NIRFAST user-base, NIRFAST-Slicer will help to accelerate the use of powerful image analysis and visualization tools in near-infrared imaging research. NIRFAST-Slicer is just one example of how 3D Slicer can be leveraged to create custom optical imaging applications. To learn how Kitware can tailor NIRFAST-Slicer and 3D Slicer, among other open-source solutions, to meet clinical and research needs, please contact kitware@kitware.com.


Research reported in this publication was supported by NIH/NCI under Award Number R01CA184354. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

2 Responses to Exploring Tissue Optics Through NIRFAST-Slicer Workshop

  1. af61 says:

    Very nice! I am trying to understand what NIRFAST actually is – is it a customized Slicer application? Or Slicer extension? Or something else? The link to the source code points to a repository that seems to mainly consist of Matlab files …

  2. Nirfast is a Matlab package, whereas Nirfast-Slicer is a combination of customized Slicer with the addition of Nirfast Matlab package. There are a few links in the article.

Questions or comments are always welcome!