scholarly journals TeraVR Empowers Precise Reconstruction of Complete 3-D Neuronal Morphology in the Whole Brain

2019 ◽  
Author(s):  
Yimin Wang ◽  
Qi Li ◽  
Lijuan Liu ◽  
Zhi Zhou ◽  
Yun Wang ◽  
...  
Keyword(s):  
Virtual Reality ◽  
Open Source ◽  
Three Dimensional ◽  
Neuronal Morphology ◽  
Imaging Data ◽  
Cell Type ◽  
Neuron Morphology ◽  
Whole Brain ◽  
Annotation System ◽  
Quantitative Profiling

AbstractNeuron morphology is recognized as a key determinant of cell type, yet the quantitative profiling of a mammalian neuron’s complete three-dimensional (3-D) morphology remains arduous when the neuron has complex arborization and long projection. Whole-brain reconstruction of neuron morphology is even more challenging as it involves processing tens of teravoxels of imaging data. Validating such reconstructions is extremely laborious. We developed TeraVR, an open-source virtual reality annotation system, to address these challenges. TeraVR integrates immersive and collaborative 3-D visualization, interaction, and hierarchical streaming of teravoxel-scale images. Using TeraVR, we produced precise 3-D full morphology of long-projecting neurons in whole mouse brains and developed a collaborative workflow for highly accurate neuronal reconstruction.

scholarly journals SlicerDMRI: Diffusion MRI and Tractography Research Software for Brain Cancer Surgery Planning and Visualization

2020 ◽  
pp. 299-309 ◽  
Author(s):  
Fan Zhang ◽  
Thomas Noh ◽  
Parikshit Juvekar ◽  
Sarah F. Frisken ◽  
Laura Rigolo ◽  
...  
Keyword(s):  
Open Source ◽  
Diffusion Tensor ◽  
Intraoperative Imaging ◽  
Time Integration ◽  
Three Dimensional ◽  
High Grade Glioma ◽  
Patient Specific ◽  
Imaging Data ◽  
3D Slicer ◽  
Research Software

PURPOSE We present SlicerDMRI, an open-source software suite that enables research using diffusion magnetic resonance imaging (dMRI), the only modality that can map the white matter connections of the living human brain. SlicerDMRI enables analysis and visualization of dMRI data and is aimed at the needs of clinical research users. SlicerDMRI is built upon and deeply integrated with 3D Slicer, a National Institutes of Health–supported open-source platform for medical image informatics, image processing, and three-dimensional visualization. Integration with 3D Slicer provides many features of interest to cancer researchers, such as real-time integration with neuronavigation equipment, intraoperative imaging modalities, and multimodal data fusion. One key application of SlicerDMRI is in neurosurgery research, where brain mapping using dMRI can provide patient-specific maps of critical brain connections as well as insight into the tissue microstructure that surrounds brain tumors. PATIENTS AND METHODS In this article, we focus on a demonstration of SlicerDMRI as an informatics tool to enable end-to-end dMRI analyses in two retrospective imaging data sets from patients with high-grade glioma. Analyses demonstrated here include conventional diffusion tensor analysis, advanced multifiber tractography, automated identification of critical fiber tracts, and integration of multimodal imagery with dMRI. RESULTS We illustrate the ability of SlicerDMRI to perform both conventional and advanced dMRI analyses as well as to enable multimodal image analysis and visualization. We provide an overview of the clinical rationale for each analysis along with pointers to the SlicerDMRI tools used in each. CONCLUSION SlicerDMRI provides open-source and clinician-accessible research software tools for dMRI analysis. SlicerDMRI is available for easy automated installation through the 3D Slicer Extension Manager.

Nested U-Net Architecture Based Image Segmentation for 3D Neuron Reconstruction

2021 ◽  
Vol 11 (5) ◽  
pp. 1348-1356
Author(s):  
Jian Yang ◽  
Yong Zhang ◽  
Yuanlin Yu ◽  
Ning Zhong
Keyword(s):  
Image Segmentation ◽  
Signal To Noise Ratio ◽  
Scale Space ◽  
Neuronal Morphology ◽  
Reconstruction Algorithms ◽  
Working Mechanism ◽  
Neuron Morphology ◽  
Whole Brain ◽  
Neuron Reconstruction ◽  
Digital Reconstruction

Digital reconstruction of neurons is a critical step in studying neuronal morphology and exploring the working mechanism of the brain. In recent years, the focus of neuronal morphology reconstruction has gradually shifted from single neurons to multiple neurons in a whole brain. Microscopic images of a whole brain often have low signal-to-noise-ratio, discontinuous neuron fragments or weak neuron signals. It is very difficult to segment neuronal signals from the background of these images, which is the first step of most automatic reconstruction algorithms. In this study, we propose a Nested U-Net based Ultra-Tracer model (NUNU-Tracer) for better multiple neurons image segmentation and morphology reconstruction. The NUNU-Tracer utilizes nested U-Net (UNet++) deep network to segment 3D neuron images, reconstructs neuron morphologies under the framework of the Ultra-Tracer and prunes branches of noncurrent tracing neurons. The 3D UNet++ takes a 3D microscopic image as its input, and uses scale-space distance transform and linear fusion strategy to generate the segmentation maps for voxels in the image. It is capable of removing noise, repairing broken neurite patterns and enhancing neuronal signals. We evaluate the performance of the 3D UNet++ for image segmentation and NUNU-Tracer for neuron morphology reconstruction on image blocks and neurons, respectively. Experimental results show that they significantly improve the accuracy and length of neuron reconstructions.

Live Neuron Morphology Automatically Reconstructed From Multiphoton and Confocal Imaging Data

2008 ◽  
Vol 100 (4) ◽  
pp. 2422-2429 ◽  
Author(s):  
Bradley E. Losavio ◽  
Yong Liang ◽  
Alberto Santamaría-Pang ◽  
Ioannis A. Kakadiaris ◽  
Costa M. Colbert ◽  
...  
Keyword(s):  
Background Noise ◽  
Laser Scanning ◽  
Three Dimensional ◽  
Dendritic Morphology ◽  
Confocal Imaging ◽  
Laser Scanning Microscopy ◽  
Imaging Data ◽  
Neuron Morphology ◽  
Software Suite ◽  
Experimental Conditions

We have developed a fully automated procedure for extracting dendritic morphology from multiple three-dimensional image stacks produced by laser scanning microscopy. By eliminating human intervention, we ensure that the results are objective, quickly generated, and accurate. The software suite accounts for typical experimental conditions by reducing background noise, removing pipette artifacts, and aligning multiple overlapping image stacks. The output morphology is appropriate for simulation in compartmental simulation environments. In this report, we validate the utility of this procedure by comparing its performance on live neurons and test specimens with other fully and semiautomated reconstruction tools.

scholarly journals Immersive 3D virtual reality imaging in planning minimally invasive and complex adult cardiac surgery

2020 ◽  
Vol 1 (1) ◽  
pp. 62-70
Author(s):  
Amir H Sadeghi ◽  
Wouter Bakhuis ◽  
Frank Van Schaagen ◽  
Frans B S Oei ◽  
Jos A Bekkers ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Virtual Reality ◽  
Cardiac Surgery ◽  
Heart Surgery ◽  
Preoperative Planning ◽  
Operating Time ◽  
Three Dimensional ◽  
Cardiothoracic Surgery ◽  
Planning Tool ◽  
Computed Tomography Images

Abstract Aims Increased complexity in cardiac surgery over the last decades necessitates more precise preoperative planning to minimize operating time, to limit the risk of complications during surgery and to aim for the best possible patient outcome. Novel, more realistic, and more immersive techniques, such as three-dimensional (3D) virtual reality (VR) could potentially contribute to the preoperative planning phase. This study shows our initial experience on the implementation of immersive VR technology as a complementary research-based imaging tool for preoperative planning in cardiothoracic surgery. In addition, essentials to set up and implement a VR platform are described. Methods Six patients who underwent cardiac surgery at the Erasmus Medical Center, Rotterdam, The Netherlands, between March 2020 and August 2020, were included, based on request by the surgeon and availability of computed tomography images. After 3D VR rendering and 3D segmentation of specific structures, the reconstruction was analysed via a head mount display. All participating surgeons (n = 5) filled out a questionnaire to evaluate the use of VR as preoperative planning tool for surgery. Conclusion Our study demonstrates that immersive 3D VR visualization of anatomy might be beneficial as a supplementary preoperative planning tool for cardiothoracic surgery, and further research on this topic may be considered to implement this innovative tool in daily clinical practice. Lay summary Over the past decades, surgery on the heart and vessels is becoming more and more complex, necessitating more precise and accurate preoperative planning. Nowadays, operative planning is feasible on flat, two-dimensional computer screens, however, requiring a lot of spatial and three-dimensional (3D) thinking of the surgeon. Since immersive 3D virtual reality (VR) is an upcoming imaging technique with promising results in other fields of surgery, we aimed in this study to explore the additional value of this technique in heart surgery. Our surgeons planned six different heart operations by visualizing computed tomography scans with a dedicated VR headset, enabling them to visualize the patient’s anatomy in an immersive and 3D environment. The outcomes of this preliminary study are positive, with a much more reality-like simulation for the surgeon. In such, VR could potentially be beneficial as a preoperative planning tool for complex heart surgery.

scholarly journals Minimally Invasive Mini-orbitozygomatic Approach for Clipping an Anterior Communicating Artery Aneurysm: Virtual Reality Surgical Planning

2020 ◽  
Author(s):  
Nicolás González Romo ◽  
Franco Ravera Zunino
Keyword(s):  
Virtual Reality ◽  
Minimally Invasive ◽  
Surgical Planning ◽  
Artery Aneurysm ◽  
Patient Specific ◽  
Anterior Communicating Artery ◽  
Imaging Data ◽  
Advantages And Disadvantages ◽  
Orbitozygomatic Approach ◽  
Skull Base Anatomy

AbstractVirtual reality (VR) has increasingly been implemented in neurosurgical practice. A patient with an unruptured anterior communicating artery (AcoA) aneurysm was referred to our institution. Imaging data from computed tomography angiography (CTA) was used to create a patient specific 3D model of vascular and skull base anatomy, and then processed to a VR compatible environment. Minimally invasive approaches (mini-pterional, supraorbital and mini-orbitozygomatic) were simulated and assessed for adequate vascular exposure in VR. Using an eyebrow approach, a mini-orbitozygomatic approach was performed, with clip exclusion of the aneurysm from the circulation. The step-by-step process of VR planning is outlined, and the advantages and disadvantages for the neurosurgeon of this technology are reviewed.

The functional vascular anatomy of the swine for research

Vascular ◽  
2021 ◽  
pp. 170853812199650
Author(s):  
Joseph Edwards ◽  
Hossam Abdou ◽  
Neerav Patel ◽  
Marta J Madurska ◽  
Kelly Poe ◽  
...  
Keyword(s):  
Translational Research ◽  
Functional Anatomy ◽  
Three Dimensional ◽  
Vascular Anatomy ◽  
Review Article ◽  
Imaging Data ◽  
Preclinical Research ◽  
Iodinated Contrast ◽  
Translational Research Program ◽  
And Function

Objectives Swine ( Sus Scrofa) are utilized broadly in research settings, given similarities to human vessel size and function; however, there are some important differences for clinicians to understand in order to interpret and perform translational research. This review article uses angiograms acquired in the course of a translational research program to present a description of the functional anatomy of the swine. Methods Digital subtraction angiography and computed tomography angiography were obtained throughout the course of multiple studies utilizing power injection with iodinated contrast. Subtracted two-dimensional images and three-dimensional multiplanar reformations were utilized post image acquisition to create maximal intensity projections and three-dimensional renderings of using open-source software (OsiriX). These imaging data are presented along with vessel measurements for reference. Results An atlas highlighting swine vascular anatomy, with an emphasis on inter-species differences that may influence how studies are conducted and interpreted, was compiled. Conclusions Swine are utilized in broad-reaching fields for preclinical research. While many similarities between human and swine vasculature exist, there are important differences to consider when conducting and interpreting research. This review article highlights these differences and presents accompanying images to inform clinicians gaining experience in swine research.

scholarly journals How Can I Grab That?

i-com ◽  
2020 ◽  
Vol 19 (2) ◽  
pp. 67-85
Author(s):  
Matthias Weise ◽  
Raphael Zender ◽  
Ulrike Lucke
Keyword(s):  
Virtual Reality ◽  
User Experience ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Advantages And Disadvantages ◽  
Multiple Dimensions ◽  
Application Developers ◽  
Three Dimensional Space

AbstractThe selection and manipulation of objects in Virtual Reality face application developers with a substantial challenge as they need to ensure a seamless interaction in three-dimensional space. Assessing the advantages and disadvantages of selection and manipulation techniques in specific scenarios and regarding usability and user experience is a mandatory task to find suitable forms of interaction. In this article, we take a look at the most common issues arising in the interaction with objects in VR. We present a taxonomy allowing the classification of techniques regarding multiple dimensions. The issues are then associated with these dimensions. Furthermore, we analyze the results of a study comparing multiple selection techniques and present a tool allowing developers of VR applications to search for appropriate selection and manipulation techniques and to get scenario dependent suggestions based on the data of the executed study.

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