Seeing More by Showing Less: Orientation-Dependent Transparency Rendering for Fiber Tractography Visualization.
Ontology highlight
ABSTRACT:
SUBMITTER: Tax CM
PROVIDER: S-EPMC4596805 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:In diffusion MRI, the advent of high angular resolution diffusion imaging (HARDI) and HARDI with compressed sensing (HARDI+CS) has led to clinically practical signal acquisition techniques which allow for the assessment of white matter architecture in routine patient studies. However, the reconstruction and visualization of fiber pathways by tractography has not yet been established as a standard methodology which can easily be applied. This is due to various algorithmic problems, such as a lack of robustness, error propagation and the necessity of fine-tuning parameters depending on the clinical question. In the framework of a clinical study of glioma patients, we compare two different whole-brain tracking methods to a local connectivity mapping approach which has recently shown promising results in an adaptation to diffusion MRI. The ability of the three methods to correctly depict fiber affection is analyzed by comparing visualization results to representations of local diffusion profiles provided by orientation distribution functions (ODFs). Our results suggest that methods beyond fiber tractography, which visualize local connectedness rather than global connectivity, should be evaluated further for pre-surgical assessment of fiber affection.
| S-EPMC6907809 | biostudies-literature
Project description:Diffusion MRI allows us to make inferences on the structural organisation of the brain by mapping water diffusion to white matter microstructure. However, such a mapping is generally ill-defined; for instance, diffusion measurements are antipodally symmetric (diffusion along x and -x are equal), whereas the distribution of fibre orientations within a voxel is generally not symmetric. Therefore, different sub-voxel patterns such as crossing, fanning, or sharp bending, cannot be distinguished by fitting a voxel-wise model to the signal. However, asymmetric fibre patterns can potentially be distinguished once spatial information from neighbouring voxels is taken into account. We propose a neighbourhood-constrained spherical deconvolution approach that is capable of inferring asymmetric fibre orientation distributions (A-fods). Importantly, we further design and implement a tractography algorithm that utilises the estimated A-fods, since the commonly used streamline tractography paradigm cannot directly take advantage of the new information. We assess performance using ultra-high resolution histology data where we can compare true orientation distributions against sub-voxel fibre patterns estimated from down-sampled data. Finally, we explore the benefits of A-fods-based tractography using in vivo data by evaluating agreement of tractography predictions with connectivity estimates made using different in-vivo modalities. The proposed approach can reliably estimate complex fibre patterns such as sharp bending and fanning, which voxel-wise approaches cannot estimate. Moreover, histology-based and in-vivo results show that the new framework allows more accurate tractography and reconstruction of maps quantifying (symmetric and asymmetric) fibre complexity.
| S-EPMC6318223 | biostudies-literature
Project description:Gradient-echo MRI has revealed anisotropic magnetic susceptibility in the brain white matter. This magnetic susceptibility anisotropy can be measured and characterized with susceptibility tensor imaging (STI). In this study, a method of fiber tractography based on STI is proposed and demonstrated in the mouse brain. STI experiments of perfusion-fixed mouse brains were conducted at 7.0T. The magnetic susceptibility tensor was calculated for each voxel with regularization and decomposed into its eigensystem. The major eigenvector is found to be aligned with the underlying fiber orientation. Following the orientation of the major eigenvector, we are able to map distinctive fiber pathways in 3D. As a comparison, diffusion tensor imaging (DTI) and DTI fiber tractography were also conducted on the same specimens. The relationship between STI and DTI fiber tracts was explored with similarities and differences identified. It is anticipated that the proposed method of STI tractography may provide a new way to study white matter fiber architecture. As STI tractography is based on physical principles that are fundamentally different from DTI, it may also be valuable for the ongoing validation of DTI tractography.
| S-EPMC3235503 | biostudies-literature
Project description:Sustained visual attention is a well-studied cognitive capacity that is relevant to many developmental outcomes. The development of visual attention is often construed as an increased capacity to exert top-down internal control. We demonstrate that sustained visual attention, measured in terms of momentary eye gaze, emerges from and is tightly tied to sensory-motor coordination. Specifically, we examined whether and how changes in manual behavior alter toddlers' eye gaze during toy play. We manipulated manual behavior by giving one group of children heavy toys that were hard to pick up and giving another group of children perceptually identical toys that were lighter and easy to pick up and hold. We found a tight temporal coupling of visual attention with the duration of manual activities on the objects, a relation that cannot be explained by interest alone. Toddlers in the heavy-object condition looked at objects as much as toddlers in the light-object condition but did so through many brief glances, whereas looks to the same objects were longer and sustained in the light-object condition. We explain the results based on the mechanism of hand-eye coordination and discuss its implications for the development of visual attention.
| S-EPMC7670876 | biostudies-literature
Project description:BACKGROUND: In comparison to more modern imaging methods, conventional light microscopy still offers a range of substantial advantages with regard to contrast options, accessible specimen size, and resolution. Currently, tomographic image data in particular is most commonly visualized in three dimensions using volume rendering. To date, this method has only very rarely been applied to image stacks taken from serial sections, whereas surface rendering is still the most prevalent method for presenting such data sets three-dimensionally. The aim of this study was to develop standard protocols for volume rendering of image stacks of serial sections, while retaining the benefits of light microscopy such as resolution and color information. RESULTS: Here we provide a set of protocols for acquiring high-resolution 3D images of diverse microscopic samples through volume rendering based on serial light microscopical sections using the 3D reconstruction software Amira (Visage Imaging Inc.). We overcome several technical obstacles and show that these renderings are comparable in quality and resolution to 3D visualizations using other methods. This practical approach for visualizing 3D micro-morphology in full color takes advantage of both the sub-micron resolution of light microscopy and the specificity of histological stains, by combining conventional histological sectioning techniques, digital image acquisition, three-dimensional image filtering, and 3D image manipulation and visualization technologies. CONCLUSIONS: We show that this method can yield "true"-colored high-resolution 3D views of tissues as well as cellular and sub-cellular structures and thus represents a powerful tool for morphological, developmental, and comparative investigations. We conclude that the presented approach fills an important gap in the field of micro-anatomical 3D imaging and visualization methods by combining histological resolution and differentiation of details with 3D rendering of whole tissue samples. We demonstrate the method on selected invertebrate and vertebrate specimens, and propose that reinvestigation of historical serial section material may be regarded as a special benefit.
| S-EPMC2876090 | biostudies-other
Project description:Diffusion tensor imaging (DTI) infers the trajectory and location of large white matter tracts by measuring the anisotropic diffusion of water. DTI data may then be analyzed and presented as tractography for visualization of the tracts in 3 dimensions. Despite the important information contained in tractography images, usefulness for neurosurgical planning has been limited by the inability to define which are critical structures within the mass of demonstrated fibers and to clarify their relationship to the tumor.To develop a method to allow the interactive querying of tractography data sets for surgical planning and to provide a working software package for the research community.The tool was implemented within an open source software project. Echo-planar DTI at 3 T was performed on 5 patients, followed by tensor calculation. Software was developed that allowed the placement of a dynamic seed point for local selection of fibers and for fiber display around a segmented structure, both with tunable parameters. A neurosurgeon was trained in the use of software in < 1 hour and used it to review cases.Tracts near tumor and critical structures were interactively visualized in 3 dimensions to determine spatial relationships to lesion. Tracts were selected using 3 methods: anatomical and functional magnetic resonance imaging-defined regions of interest, distance from the segmented tumor volume, and dynamic seed-point spheres.Interactive tractography successfully enabled inspection of white matter structures that were in proximity to lesions, critical structures, and functional cortical areas, allowing the surgeon to explore the relationships between them.
| S-EPMC3112275 | biostudies-literature
Project description:Fiber tracking produces large tractography datasets that are tens of gigabytes in size consisting of millions of streamlines. Such vast amounts of data require formats that allow for efficient storage, transfer, and visualization. We present TRAKO, a new data format based on the Graphics Layer Transmission Format (glTF) that enables immediate graphical and hardware-accelerated processing. We integrate a state-of-the-art compression technique for vertices, streamlines, and attached scalar and property data. We then compare TRAKO to existing tractography storage methods and provide a detailed evaluation on eight datasets. TRAKO can achieve data reductions of over 28x without loss of statistical significance when used to replicate analysis from previously published studies.
| S-EPMC7597368 | biostudies-literature
Project description:In recent years, several new diffusion MRI approaches have been proposed to explore microstructural properties of the white matter, such as Q-ball imaging and spherical deconvolution-based techniques to estimate the orientation distribution function. These methods can describe the estimated diffusion profile with a higher accuracy than the more conventional second-rank diffusion tensor imaging technique. Despite many important advances, there are still inconsistent findings between different models that investigate the "crossing fibers" issue. Due to the high information content and the complex nature of the data, it becomes virtually impossible to interpret and compare results in a consistent manner. In this work, we present novel fiber tractography visualization approaches that provide a more complete picture of the microstructural architecture of fiber pathways: multi-fiber hyperstreamlines and streamribbons. By visualizing, for instance, the estimated fiber orientation distribution along the reconstructed tract in a continuous way, information of the local fiber architecture is combined with the global anatomical information derived from tractography. Facilitating the interpretation of diffusion MRI data, this approach can be useful for comparing different diffusion reconstruction techniques and may improve our understanding of the intricate white matter network.
| S-EPMC3839966 | biostudies-literature
Project description:Recent MRI studies at high field have observed that, in certain white matter fiber bundles, the signal in T(2)*-weighted MRI (i.e. MRI sensitized to apparent transverse relaxivity) is dependent on fiber orientation ? relative to B(0). In this study, the characteristics of this dependency are quantitatively investigated at 7 T using ex-vivo brain specimens, which allowed a large range of rotation angles to be measured. The data confirm the previously suggested variation of R(2)* (=1/T(2)*) with ? and also indicate that this dependency takes the shape of a combination of sin2? and sin4? functions, with modulation amplitudes (=?R(2)*) reaching 6.44±0.15 Hz (or ?T(2)*=2.91±0.33 ms) in the major fiber bundles of the corpus callosum. This particular dependency can be explained by a model of local, sub-voxel scale magnetic field changes resulting from magnetic susceptibility sources that are anisotropic. As an illustration of a potential use of the orientation dependence of R(2)*, the feasibility of generating fiber orientation maps from R(2)* data is investigated.
| S-EPMC3119254 | biostudies-literature
Project description:MotivationLive cell imaging plays a pivotal role in understanding cell growth. Yet, there is a lack of visualization alternatives for quick qualitative characterization of colonies.ResultsSeeVis is a Python workflow for automated and qualitative visualization of time-lapse microscopy data. It automatically pre-processes the movie frames, finds particles, traces their trajectories and visualizes them in a space-time cube offering three different color mappings to highlight different features. It supports the user in developing a mental model for the data. SeeVis completes these steps in 1.15 s/frame and creates a visualization with a selected color mapping.Availability and implementationhttps://github.com/ghattab/seevis/.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC6513157 | biostudies-literature