Fast segmentation and high-quality three-dimensional volume mesh creation from medical images for diffuse optical tomography

Abstract

Abstract. Multimodal approaches that combine near-infrared (NIR) and conventional imaging modalities have been shown to improve optical parameter estimation dramatically and thus represent a prevailing trend in NIR imaging. These approaches typically involve applying anatomical templates from magnetic resonance imaging/ computed tomography/ultrasound images to guide the recovery of optical parameters. However, merging these data sets using current technology requires multiple software packages, substantial expertise, significant time-commitment, and often results in unacceptably poor mesh quality for optical image reconstruction, a reality that represents a significant roadblock for translational research of multimodal NIR imaging. This work addresses these challenges directly by introducing automated digital imaging and communications in medicine image stack segmentation and a new one-click three-dimensional mesh generator optimized for multimodal NIR imaging, and combining these capabilities into a single software package (available for free download) with a streamlined workflow. Image processing time and mesh quality benchmarks were examined for four common multimodal NIR usecases (breast, brain, pancreas, and small animal) and were compared to a commercial image processing package. Applying these tools resulted in a fivefold decrease in image processing time and 62% improvement in minimum mesh quality, in the absence of extra mesh postprocessing. These capabilities represent a significant step toward enabling translational multimodal NIR research for both expert and nonexpert users in an open-source platform. © The Authors. Published by SPIE under a Creative Commons Attribution 3.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.

Time resolved diffuse optical spectroscopy with geometrically accurate models for bulk parameter recovery

“…Due to the widespread availability of 3D scanning systems, coupled with the availability of open source meshing software (e.g. NIRVIEW [23]), this is now readily achievable and the approach can find immediate application. One possible application is the characterization of tissue-like phantoms as demonstrated in this work, this approach may be more accurate and timeefficient than making measurements on large slabs of excess material as is otherwise required [17].…”

“…The proposed method incorporates subject-specific temporal point spread functions (TPSFs) using geometrically accurate finite element models as opposed to the simple but geometrically inaccurate semi-infinite slab models typically employed. This was achieved using open source light modelling software [12,23] which uses the diffusion approximation to make fast calculations in a practical time-frame: In the work presented here, for the mouse phantom, the total time for creating the model specific TPSF libraries was approximately 10 minutes using a laptop with a 2.9 GHz Intel Core i7 and 8 GB of RAM.…”

Quantitative evaluation of atlas-based high-density diffuse optical tomography for imaging of the human visual cortex

“…Data calibration is a critical aspect of image reconstruction regardless of the modeling method utilized and is covered in detail elsewhere [5]. Regardless of whether using subject specific or atlas-based models, the domain of interest needs to be segmented and meshed, which is achieved using NIRVIEW [33]. For model based image reconstruction, different models of light propagation in tissue can be utilized; in this work we use a finite element model (FEM) of the head using the open source package NIRFAST [34].…”

Diffuse optical mammotomography: state-of-the-art and prospects

“…The most well-known are the package TOAST (Temporal Optical Absorption and Scattering Tomography, University College London, Great Britain) [29,45,224,274] and NIRFAST (Near Infrared Fluorescence and Spectral Tomography, Thayer School of Engineering at Dartmouth College, USA) [275,276]. Note, that the field of application of these packages is not restricted to DOT as such, but also includes the DFMT and the diffuse optical correlation tomography.…”