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Seeing More Is Knowing More: V3D Enables Real-Time 3D Visualization and Quantitative Analysis of Large-Scale Biological Image Data Sets [chapter]

Hanchuan Peng, Fuhui Long
2011 Lecture Notes in Computer Science  
Everyone understands seeing more is knowing more.  ...  However, for large-scale 3D microscopic image analysis, it has not been an easy task to efficiently visualize, manipulate and understand high-dimensional data in 3D, 4D or 5D spaces.  ...  Everyone understands seeing more is knowing more.  ... 
doi:10.1007/978-3-642-20036-6_30 fatcat:a5uuhq7ktragjop4jtrw5t6nki

Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model

H. Peng, Z. Ruan, D. Atasoy, S. Sternson
2010 Bioinformatics  
However, despite a number of existing studies, this task is still challenging, especially when a 3D microscopic image has low single-to-noise ratio and discontinued segments of neurite patterns.  ...  Then we optimized a discrete deformable curve model to achieve visually more satisfactory reconstructions.  ...  ACKNOWLEDGEMENTS We thank Tzumin Lee laboratory, Gerry Rubin laboratory and Julie Simpson laboratory for some of the test data, Lei Qu and Benny Lam for help in neurite reconstruction, Fuhui Long, Gene  ... 
doi:10.1093/bioinformatics/btq212 pmid:20529931 pmcid:PMC2881396 fatcat:tdlalsywnraprmq4d3i2g3iuni

Bioimage Informatics in the context of Drosophila research

Florian Jug, Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak
2014 Methods  
Bioimage Informatics is an emerging research field that covers all aspects of biological image analysis from data handling, through processing, to quantitative measurements, analysis and data presentation  ...  As the imaging approaches become more complex and ambitious, there is an increasing need for quantitative, computer-mediated image processing and analysis to make sense of the imagery.  ...  Vaa3D excels in 3D image visualization and enables biologist to interact with very large 3D imagery in an interactive manner [140] .  ... 
doi:10.1016/j.ymeth.2014.04.004 pmid:24732429 fatcat:trrhw3bzyjaoljxp7ockcnkdeu

New Approach to Accelerated Image Annotation by Leveraging Virtual Reality and Cloud Computing

Corentin Guérinot, Valentin Marcon, Charlotte Godard, Thomas Blanc, Hippolyte Verdier, Guillaume Planchon, Francesca Raimondi, Nathalie Boddaert, Mariana Alonso, Kurt Sailor, Pierre-Marie Lledo, Bassam Hajj (+2 others)
2022 Frontiers in Bioinformatics  
Three-dimensional imaging is at the core of medical imaging and is becoming a standard in biological research.  ...  Moreover, simultaneous data analysis and visualization in VR is computationally demanding.  ...  H., and Myers, E. W. (2010). V3d Enables Real-Time 3d Visualization and Quantitative Analysis of Large-Scale Biological Image Data Sets. Nat.  ... 
doi:10.3389/fbinf.2021.777101 fatcat:g3mpyxplpjdzzl4lqynyatxy3y

Enabling user-guided segmentation and tracking of surface-labeled cells in time-lapse image sets of living tissues

David N. Mashburn, Holley E. Lynch, Xiaoyan Ma, M. Shane Hutson
2012 Cytometry Part A  
Here, we present a segmentation and cell tracking approach based on the premise that users know their data best -interpreting and using image features that are not accounted for in any a priori algorithm  ...  To study the process of morphogenesis, one often needs to collect and segment time-lapse images of living tissues to accurately track changing cellular morphology.  ...  Acknowledgments Research support acknowledgement: This work supported by the Human Frontier Science Program (RGP0021/2007C); National Science Foundation (IOB-0545679); and National Institutes of Health  ... 
doi:10.1002/cyto.a.22034 pmid:22411907 pmcid:PMC3331924 fatcat:ov6zudyglrforigdxljv4ykw6y

The Human Brain in Depth: How We See in 3D

Andrew E. Welchman
2016 Annual Review of Vision Science  
This work suggests that the dorsal visual cortex is strongly engaged by 3D information and is involved in integrating signals to represent the structure of viewed surfaces.  ...  Using brain imaging we are beginning to discover how different parts of the visual cortex support 3D perception by tracing different computations in the dorsal and ventral pathways.  ...  Third, disparity estimates need to be related to real world properties through some type of scaling operation.  ... 
doi:10.1146/annurev-vision-111815-114605 pmid:28532360 fatcat:sqiijpxmzvayhiu7yxyilhawcm

Topographic Representation of an Occluded Object and the Effects of Spatiotemporal Context in Human Early Visual Areas

Hiroshi Ban, Hiroki Yamamoto, Takashi Hanakawa, Shin-ichi Urayama, Toshihiko Aso, Hidenao Fukuyama, Yoshimichi Ejima
2013 Journal of Neuroscience  
Here, we provide functional magnetic resonance imaging (fMRI) evidence that the occluded portion of an object is indeed represented topographically in human V1 and V2.  ...  Although behavior, neurophysiological, and modeling studies have shown that occluded portions of objects may be completed at the early stage of visual processing, we have little knowledge on how and where  ...  However, an observer seeing the sequence of target rotation knows that the target is divided, and not occluded by the occluder.  ... 
doi:10.1523/jneurosci.1455-12.2013 pmid:24155304 pmcid:PMC6618442 fatcat:bcp5yvm25ffuvi623nxerp6vqa

PyNeval: A Python Toolbox for Evaluating Neuron Reconstruction Performance

Han Zhang, Chao Liu, Yifei Yu, Jianhua Dai, Ting Zhao, Nenggan Zheng
2022 Frontiers in Neuroinformatics  
We tested the toolbox on both synthetic data and real data to show its reliability and robustness.  ...  conveniently as far as we know.  ...  H., and Myers, E. W. (2010). V3d enables real-time 3d visualization and quantitative analysis of large-scale biological image data sets. Nat.  ... 
doi:10.3389/fninf.2021.767936 pmid:35153709 pmcid:PMC8831325 fatcat:dms6ciezpfarjknhwchrkzcrni

Deep Predictive Learning: A Comprehensive Model of Three Visual Streams [article]

Randall C. O'Reilly, Dean R. Wyatte, John Rohrlich
2017 arXiv   pre-print
and opportunistically partitioned to enable extraction of separable factors that drive the learning of further high-level abstractions.  ...  Our model self-organized systematic invariant object representations of 100 different objects from simple movies, accounts for a wide range of data, and makes many testable predictions.  ...  However, they require vast amounts of handlabeled image data, and are thus not plausible models of the largely self-organizing nature of human visual learning.  ... 
arXiv:1709.04654v1 fatcat:yfwcuiyjj5ggpcro7iblvt3zpi

Modeling & Analysis

2003 NeuroImage  
Another way is adding more data sets and assuming some parameters to have fixed values in all data sets.  ...  For example, initial results, based on biological motion data for a single subject, suggest that the mutual information between the fMRI and MEG data sets is maximal in the 5-15Hz band.  ...  Real and simluated data suggest that random field theory methods for low-df t images are quite conservative.  ... 
doi:10.1016/s1053-8119(05)70006-9 fatcat:zff2suxcofbxvetfrwfwcxi3zm

39th European Conference on Visual Perception (ECVP) 2016 Barcelona

2016 Perception  
To see if the visual cortex can perform this task in the real world we studied neurons in monkey cortical area V2 with static images of natural scenes.  ...  We show that via simple connectivity changes, Spike Processing Machines (SPMs) enable rotations, translations and scaling of the input visual field.  ...  Stimuli were images of real-world objects arranged into variable set size object arrays. The target is randomly present in half of trials.  ... 
doi:10.1177/0301006616671273 fatcat:el2dmsuk6zd25pedijucuexl5m

Reports on Energy Efficient Mobility -- Volume 2 [article]

Dirk Feßler, Maurice Kettner, Reiner Kriesten, Philipp Nenninger, Peter Offermann
2022 Zenodo  
Collection of papers documenting research at the Institute of Energy Efficient Mobility in 2021.  ...  This report is based on the associated project report.  ...  Acknowledgment This report is the short version of a student research project from the curriculum of the bachelor's degree program in automotive technology, allowing the participation of students in ongoing  ... 
doi:10.5281/zenodo.6373380 fatcat:kfvynjhii5crvkprlhjpqfizg4

Modelling Neuron Morphology: Automated Reconstruction from Microscopy Images [article]

The research in the various areas of neuroscience deals with advanced imaging techniques, collecting an increasing amounts of heterogeneous and complex data at different scales.  ...  Then, various methods and research lines have been investigated for the reconstruction of the whole dendritic arborization of each neuron, which is solved both in 2D and in 3D images. i  ...  V3D is a visualization tool for large-scale image datasets, supporting up to 5D rendering (spatially 3D over time and in multiple colors) of data that can be described as a graph (such as neuronal data  ... 
doi:10.15167/baglietto-silvia_phd2018-03-28 fatcat:tiebjdn3ozdhxj664vrbalju2a

Neural computation of depth from binocular disparity

Nuno Reis Goncalves, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository, Zoe Kourtzi, Andrew Welchman
Conversely, neural activity in downstream specialized areas is likely to be a more faithful correlate of depth perception.  ...  This dissertation focuses on the contributions of primary and dorsomedial visual cortex.  ...  I chose the 3D GRASE sequence for this reason. However, using 3D GRASE also imposes considerable restrictions on data acquisition and analysis.  ... 
doi:10.17863/cam.27049 fatcat:jq246y4lrfgsfadwjy6qddxgmu

Advances in Clinical Neuroscience & Rehabilitation

John Van Swieten, Sonia Rosso, Anish Bahra, Adnan Salman
His main area of research is into neurodegenerative and movement disorders, in particular parkinson's and Huntington's disease.  ...  He is also the university lecturer in Neurology at Cambridge where he continues to develop his clinical research into these diseases along with his basic research into brain repair using neural transplants  ...  Expression arrays can be utilised to answer fundamental biological questions; knowing when, where and to what extent a gene is expressed is central to understanding the biological role of its encoded protein  ... 
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