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Transfer Function design toolbox for full-color volume datasets

Martin Falk, Ingrid Hotz, Patric Ljung, Darren Treanor, Anders Ynnerman, Claes Lundstrom
2017 2017 IEEE Pacific Visualization Symposium (PacificVis)  
In this paper, we tackle the challenge of effective Transfer Function (TF) design for Direct Volume Rendering (DVR) of full-color datasets.  ...  The applicability of our TF design toolbox is demonstrated by volume ray casting challenging full-color volume data including the visible male cryosection dataset and examples from 3D histology.  ...  The Visible Human datasets are courtesy of National Library of Medicine and the Barrett's histology dataset was kindly provided by Dr. Marnix Jansen, UCLH and Barts, London, UK.  ... 
doi:10.1109/pacificvis.2017.8031591 dblp:conf/apvis/FalkHLTYL17 fatcat:mduh6q5smrc2nov7o7lamzvuqa

Interactive Exploration of 3D Scanned Baggage

Michael Traore, Christophe Hurter
2017 IEEE Computer Graphics and Applications  
While most existing systems use a combination of Direct Volume Rendering (DVR) technique and its corresponding Transfer Function (TF), we considered alternative interaction techniques to explore such datasets  ...  Final users were involved into the full design process and thus also validated the final tools.  ...  Transfer function edition Datasets such as two dimensional raster images or three dimensional voxel based representations are often processed for representation us-ing a transfer function (TF) defined  ... 
doi:10.1109/mcg.2017.10 pmid:28103542 fatcat:oduqkgccofavdlyuqn5mr57uey

PyMVPA: a Python Toolbox for Multivariate Pattern Analysis of fMRI Data

Michael Hanke, Yaroslav O. Halchenko, Per B. Sederberg, Stephen José Hanson, James V. Haxby, Stefan Pollmann
2009 Neuroinformatics  
Full-brain fMRI data were recorded with a volume repetition time of 2500 ms, thus, a stimulus block was covered by roughly 9 volumes.  ...  Utilization of the same classifier for both the sensitivity analysis and for the transfer error computation prevents us from re-training a classifier twice for the same dataset.  ... 
doi:10.1007/s12021-008-9041-y pmid:19184561 pmcid:PMC2664559 fatcat:hrvcqn7fgjae3k5favaifwsmym

BrainNet Viewer: A Network Visualization Tool for Human Brain Connectomics

Mingrui Xia, Jinhui Wang, Yong He, Peter Csermely
2013 PLoS ONE  
However, given the huge complexity of this methodology, toolboxes for graph-based network visualization are still lacking.  ...  The figure can be manipulated with certain interaction functions to display more detailed information.  ...  We thank Patrick Clark for helping revise our manual.  ... 
doi:10.1371/journal.pone.0068910 pmid:23861951 pmcid:PMC3701683 fatcat:tc7d3k72yff4dbjc3oiwqnq3am

Stepping into the Third Dimension

D. Feng, D. Marshburn, D. Jen, R. J. Weinberg, R. M. Taylor, A. Burette
2007 Journal of Neuroscience  
Although ImageSurfer is designed with fluorescent microscopy in mind, it is also effective for other types of data, including 3D datasets acquired by functional magnetic resonance imaging and EM tomography  ...  We also describe ImageSurfer, a new software package for volume visualization and data analysis.  ...  The assignment rule, or "transfer function," can be a linear (or nonlinear) function or an arbitrary table.  ... 
doi:10.1523/jneurosci.2846-07.2007 pmid:18032646 pmcid:PMC6673302 fatcat:oknyopjxrzbovponlt5qpi5ssm

MRIES: A Matlab Toolbox for Mapping the Responses to Intracranial Electrical Stimulation

Kaijia Sun, Haixiang Wang, Yunxian Bai, Wenjing Zhou, Liang Wang
2021 Frontiers in Neuroscience  
However, automated processing of CCEP datasets and visualization of connectivity results remain challenging for researchers and clinicians.  ...  MRIES integrates the processing pipeline of the CCEP datasets and various methods for connectivity calculation based on low- and high-frequency signals with stimulation artifacts removed.  ...  However, this toolbox did not provide an integrated function including various calculation methods that were important for comparing different indicators in the same dataset.  ... 
doi:10.3389/fnins.2021.652841 pmid:34194294 pmcid:PMC8236813 fatcat:4cs5xsqiynht3hynhq5kc7izqa

Anatomical Volume Visualization with Weighted Distance Fields [article]

Thomas Kerwin, Brad Hittle, Han-Wei Shen, Don Stredney, Gregory Wiet
2010 Eurographics Workshop on Visual Computing for Biomedicine  
We describe the use of the weighted distance transform (WDT) to enhance applications designed for volume visualization of segmented anatomical datasets.  ...  We obtain real-time interaction with the volume by calculating the WDT on the graphics card.  ...  In general, the weighted distance transform can be used for a wide number of effects to improve anatomical visualization.  ... 
doi:10.2312/vcbm/vcbm10/117-124 fatcat:jbdtrnu77jfg3m3o4wzygyeqee

eConnectome: A MATLAB toolbox for mapping and imaging of brain functional connectivity

Bin He, Yakang Dai, Laura Astolfi, Fabio Babiloni, Han Yuan, Lin Yang
2011 Journal of Neuroscience Methods  
Graphical user interfaces were designed for interactive and intuitive use of the toolbox.  ...  Granger causality measures such as Directed Transfer Function and adaptive Directed Transfer Function were implemented to estimate the directional interactions of brain functional networks, over the scalp  ...  Acknowledgments We are grateful to Christopher Wilke for useful discussions and Yunfeng Lu for assistance in the testing of eConnectome software.  ... 
doi:10.1016/j.jneumeth.2010.11.015 pmid:21130115 pmcid:PMC3244474 fatcat:zopwwskqxzcm7n56vywkrbhh64

Design and Evaluation of Interactive Proofreading Tools for Connectomics

Daniel Haehn, Seymour Knowles-Barley, Mike Roberts, Johanna Beyer, Narayanan Kasthuri, Jeff W. Lichtman, Hanspeter Pfister
2014 IEEE Transactions on Visualization and Computer Graphics  
Split, merge and adjust functionality enables multiple users to correct the labeling of neurons in a collaborative fashion. Color-coded structures can be explored in 2D and 3D.  ...  We designed a between-subjects experiment and asked non-experts to proofread neurons in a publicly available connectomics dataset.  ...  ACKNOWLEDGMENTS We would like to thank Steffen Kirchhoff for his input.  ... 
doi:10.1109/tvcg.2014.2346371 pmid:26356960 fatcat:m2ujx6cwqvg4xfnqzfmbplpnmm

Real-Time fMRI Pattern Decoding and Neurofeedback Using FRIEND: An FSL-Integrated BCI Toolbox

João R. Sato, Rodrigo Basilio, Fernando F. Paiva, Griselda J. Garrido, Ivanei E. Bramati, Patricia Bado, Fernanda Tovar-Moll, Roland Zahn, Jorge Moll, Essa Yacoub
2013 PLoS ONE  
The package integrates routines for image preprocessing in real-time, ROI-based feedback (single-ROI BOLD level and functional connectivity) and brain decoding-based feedback using SVM.  ...  In addition, a user-defined visual neurofeedback module allows users to easily design and run fMRI neurofeedback experiments using ROI-based or multivariate classification approaches.  ...  Acknowledgements The authors are thankful to Ricardo de Oliveira Souza, Sebastian Höefle, Debora Lima, Theo Marins and Julie Weingartner for their contributions, including helpful discussions on earlier  ... 
doi:10.1371/journal.pone.0081658 pmid:24312569 pmcid:PMC3847114 fatcat:efkr5ako55cqfmjk4yjyragjsa

Unfold: an integrated toolbox for overlap correction, non-linear modeling, and regression-based EEG analysis

Benedikt V. Ehinger, Olaf Dimigen
2019 PeerJ  
The toolbox is modular, compatible with EEGLAB and can handle even large datasets efficiently.  ...  It also includes advanced options for regularization and the use of temporal basis functions (e.g., Fourier sets).  ...  The unfold toolbox includes a function to remove artifactual intervals from the design matrix before fitting the model.  ... 
doi:10.7717/peerj.7838 pmid:31660265 pmcid:PMC6815663 fatcat:ubr3iz6fzvek3ixfzksmwck3uq

The PhysIO Toolbox for Modeling Physiological Noise in fMRI Data

Lars Kasper, Steffen Bollmann, Andreea O. Diaconescu, Chloe Hutton, Jakob Heinzle, Sandra Iglesias, Tobias U. Hauser, Miriam Sebold, Zina-Mary Manjaly, Klaas P. Pruessmann, Klaas E. Stephan
2017 Journal of Neuroscience Methods  
For volumes exceeding these thresholds, the toolbox creates additional stick regressors (1 for the affected volume, 0 for all others), which absorb any variance from a single motioncompromised volume (  ...  The respiratory phase, ϕ resp , is derived using an equalized-histogram transfer function (Glover et al., 2000) , accounting for the differing breathing amplitudes in each cycle (Fig.  ... 
doi:10.1016/j.jneumeth.2016.10.019 pmid:27832957 fatcat:tdf3pj6kzrbtjfdoaqqdxeclo4

Connexel visualization: a software implementation of glyphs and edge-bundling for dense connectivity data using brainGL

Joachim Böttger, Ralph Schurade, Estrid Jakobsen, Alexander Schaefer, Daniel S. Margulies
2014 Frontiers in Neuroscience  
The tools have been implemented as part of brainGL, an extensive open-source software for the interactive exploration of structural and functional brain data.  ...  Drawing full connectivity graphs can result in depictions that, rather than illustrating connectivity patterns in more detail, obfuscate patterns owing to the data density.  ...  ACKNOWLEDGMENTS We would like to thank Natacha Mendes for contributions during the preparation of the manuscript.  ... 
doi:10.3389/fnins.2014.00015 pmid:24624052 pmcid:PMC3941704 fatcat:lpfd4oumfjb3fguk2jvnph7h6y

TRENTOOL: A Matlab open source toolbox to analyse information flow in time series data with transfer entropy

Michael Lindner, Raul Vicente, Viola Priesemann, Michael Wibral
2011 BMC Neuroscience  
Transfer entropy (TE) is a measure for the detection of directed interactions. Transfer entropy is an information theoretic implementation of Wiener's principle of observational causality.  ...  TRENTOOL is implemented as a MATLAB toolbox and available under an open source license (GPL v3). For the use with neural data TRENTOOL seamlessly integrates with the popular FieldTrip toolbox.  ...  We designed TRENTOOL as an open source toolbox, because this gives maximum control to users and developers.  ... 
doi:10.1186/1471-2202-12-119 pmid:22098775 pmcid:PMC3287134 fatcat:oqyfsscomfbdbgt6hrgq4toha4

Interactive Tools for Scientific and Medical Illustration Composition [article]

Bill Andrews, Stefan Bruckner, Wei Chen, Carlos D. Correa, David S. Ebert, Mario Costa Sousa, Ivan Viola
2008 Eurographics State of the Art Reports  
In the last part of the tutorial we present techniques for deforming volumes in various ways inspired by traditional illustration techniques such as the depiction of surgical procedures.  ...  Next, we introduce the importance of intuitive interaction for illustrative visualization describing sketch-based approaches as an intuitive way of manipulating and exploring volumetric datasets.  ...  Process Hierarchical Transfer Functions Usually transfer functions control (color, opacity) They can also be used to control parameters/contribution of the effects Design multiple transfer functions  ... 
doi:10.2312/egt.20081056 fatcat:wnwbzcbj2nfthoe37hlp6ijfd4
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