Open source software for multi-modal optical molecular imaging
Tutorials & Help



Tutorial/Exercise: MRI-coupled NIR spectral imaging of human breast (Updated 5/4/16): This exercise uses a sample MRI to segment the tissue and create a 3D mesh. It also includes an exercise for completing multi-spectral reconstructions on a 2-D breast mesh.


Introduction to NIRFAST (Updated 4/24/16) These are the slides used at the OSA 2016 workshop that introduces the historical development of NIRFAST, plus some of the basic information including the utilised file formats for NIRFAST.


Tutorial: MRI-coupled fluorescence tomography of small animals (Updated 4/19/16). Use this sample data to generate MRI-FMT images of a tumor xenograft from start-to-finish: Load MRI DICOMS, place sources and detectors, segment the tissue into regions, create a 3-D mesh, calibrate and reconstruct data, and visualize optical images overlaid on MR images.


Using NIRFASTSlicer: Image processing and visualization in NIRFAST (Updated 4/19/16). NIRFASTSlicer, built on the 3DSlicer platform, is the name of the new image processing and visualization front-end for NIRFAST. This tutorial covers the basic structure, functions and use of NIRFASTSlicer and includes contextual background on the 3DSlicer project and extensions.


Tutorial for using head models to generate spectroscopic data and simple parameter recovery. This tutorial allows you to create FEM meshes based on a pre-segmented head model: Use this sample segmented head. Alternatively, NIRFAST mesh files have been created together with a single source and three detectors on the forehead: Use this sample zip file and uncompress. Two different matlab script files demonstrate how we can use basic scripts to generate data, calculate the Jacobian and recover parameters: Use this for a simple homogeneous head OR Use this for a layered head.


Basic tutorial for tomographic imaging and simulations. The script file standard_example.m outlines the simulation of data for a simple 2D circle at a single wavelength and tomographic reconstruction.The script file spectral_example.m outlines the simulation of data for a simple 2D circle at at multiple wavelengths simultaneously and tomographic reconstruction.