NeuroTessMesh: A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement
Gaining a better understanding of the human brain continues to be one of the greatest challenges for science, largely because of the overwhelming complexity of the brain and the difficulty of analyzing the features and behavior of dense neural networks. Regarding analysis, 3D visualization has prove...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2017-06-01
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| Series: | Frontiers in Neuroinformatics |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/article/10.3389/fninf.2017.00038/full |
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| author | Juan J. Garcia-Cantero Juan J. Garcia-Cantero Juan P. Brito Juan P. Brito Susana Mata Susana Mata Sofia Bayona Sofia Bayona Luis Pastor Luis Pastor |
| author_facet | Juan J. Garcia-Cantero Juan J. Garcia-Cantero Juan P. Brito Juan P. Brito Susana Mata Susana Mata Sofia Bayona Sofia Bayona Luis Pastor Luis Pastor |
| author_sort | Juan J. Garcia-Cantero |
| collection | DOAJ |
| description | Gaining a better understanding of the human brain continues to be one of the greatest challenges for science, largely because of the overwhelming complexity of the brain and the difficulty of analyzing the features and behavior of dense neural networks. Regarding analysis, 3D visualization has proven to be a useful tool for the evaluation of complex systems. However, the large number of neurons in non-trivial circuits, together with their intricate geometry, makes the visualization of a neuronal scenario an extremely challenging computational problem. Previous work in this area dealt with the generation of 3D polygonal meshes that approximated the cells’ overall anatomy but did not attempt to deal with the extremely high storage and computational cost required to manage a complex scene. This paper presents NeuroTessMesh, a tool specifically designed to cope with many of the problems associated with the visualization of neural circuits that are comprised of large numbers of cells. In addition, this method facilitates the recovery and visualization of the 3D geometry of cells included in databases, such as NeuroMorpho, and provides the tools needed to approximate missing information such as the soma’s morphology. This method takes as its only input the available compact, yet incomplete, morphological tracings of the cells as acquired by neuroscientists. It uses a multiresolution approach that combines an initial, coarse mesh generation with subsequent on-the-fly adaptive mesh refinement stages using tessellation shaders. For the coarse mesh generation, a novel approach, based on the Finite Element Method, allows approximation of the 3D shape of the soma from its incomplete description. Subsequently, the adaptive refinement process performed in the graphic card generates meshes that provide good visual quality geometries at a reasonable computational cost, both in terms of memory and rendering time. All the described techniques have been integrated into NeuroTessMesh, available to the scientific community, to generate, visualize, and save the adaptive resolution meshes. |
| first_indexed | 2024-12-12T03:10:40Z |
| format | Article |
| id | doaj.art-2c9d6850c992471ba4ebbca69fda2901 |
| institution | Directory Open Access Journal |
| issn | 1662-5196 |
| language | English |
| last_indexed | 2024-12-12T03:10:40Z |
| publishDate | 2017-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroinformatics |
| spelling | doaj.art-2c9d6850c992471ba4ebbca69fda29012022-12-22T00:40:24ZengFrontiers Media S.A.Frontiers in Neuroinformatics1662-51962017-06-011110.3389/fninf.2017.00038255477NeuroTessMesh: A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly RefinementJuan J. Garcia-Cantero0Juan J. Garcia-Cantero1Juan P. Brito2Juan P. Brito3Susana Mata4Susana Mata5Sofia Bayona6Sofia Bayona7Luis Pastor8Luis Pastor9Department of Computer Engineering, Universidad Rey Juan Carlos, Madrid, SpainCenter for Computational Simulation, Universidad Politécnica de Madrid, Madrid, SpainCenter for Computational Simulation, Universidad Politécnica de Madrid, Madrid, SpainUniversidad Politécnica de Madrid, Madrid, SpainDepartment of Computer Engineering, Universidad Rey Juan Carlos, Madrid, SpainCenter for Computational Simulation, Universidad Politécnica de Madrid, Madrid, SpainDepartment of Computer Engineering, Universidad Rey Juan Carlos, Madrid, SpainCenter for Computational Simulation, Universidad Politécnica de Madrid, Madrid, SpainDepartment of Computer Engineering, Universidad Rey Juan Carlos, Madrid, SpainCenter for Computational Simulation, Universidad Politécnica de Madrid, Madrid, SpainGaining a better understanding of the human brain continues to be one of the greatest challenges for science, largely because of the overwhelming complexity of the brain and the difficulty of analyzing the features and behavior of dense neural networks. Regarding analysis, 3D visualization has proven to be a useful tool for the evaluation of complex systems. However, the large number of neurons in non-trivial circuits, together with their intricate geometry, makes the visualization of a neuronal scenario an extremely challenging computational problem. Previous work in this area dealt with the generation of 3D polygonal meshes that approximated the cells’ overall anatomy but did not attempt to deal with the extremely high storage and computational cost required to manage a complex scene. This paper presents NeuroTessMesh, a tool specifically designed to cope with many of the problems associated with the visualization of neural circuits that are comprised of large numbers of cells. In addition, this method facilitates the recovery and visualization of the 3D geometry of cells included in databases, such as NeuroMorpho, and provides the tools needed to approximate missing information such as the soma’s morphology. This method takes as its only input the available compact, yet incomplete, morphological tracings of the cells as acquired by neuroscientists. It uses a multiresolution approach that combines an initial, coarse mesh generation with subsequent on-the-fly adaptive mesh refinement stages using tessellation shaders. For the coarse mesh generation, a novel approach, based on the Finite Element Method, allows approximation of the 3D shape of the soma from its incomplete description. Subsequently, the adaptive refinement process performed in the graphic card generates meshes that provide good visual quality geometries at a reasonable computational cost, both in terms of memory and rendering time. All the described techniques have been integrated into NeuroTessMesh, available to the scientific community, to generate, visualize, and save the adaptive resolution meshes.http://journal.frontiersin.org/article/10.3389/fninf.2017.00038/fullgeometry-based techniquesmultiresolution techniquesGPUs and multi-core architecturescompression techniquesbioinformatics visualization |
| spellingShingle | Juan J. Garcia-Cantero Juan J. Garcia-Cantero Juan P. Brito Juan P. Brito Susana Mata Susana Mata Sofia Bayona Sofia Bayona Luis Pastor Luis Pastor NeuroTessMesh: A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement Frontiers in Neuroinformatics geometry-based techniques multiresolution techniques GPUs and multi-core architectures compression techniques bioinformatics visualization |
| title | NeuroTessMesh: A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement |
| title_full | NeuroTessMesh: A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement |
| title_fullStr | NeuroTessMesh: A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement |
| title_full_unstemmed | NeuroTessMesh: A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement |
| title_short | NeuroTessMesh: A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement |
| title_sort | neurotessmesh a tool for the generation and visualization of neuron meshes and adaptive on the fly refinement |
| topic | geometry-based techniques multiresolution techniques GPUs and multi-core architectures compression techniques bioinformatics visualization |
| url | http://journal.frontiersin.org/article/10.3389/fninf.2017.00038/full |
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