J. Ahrens, B. Geveci, and C. Law, Paraview: An end-user tool for large-data visualization. The Visualization Handbook, pp.717-731, 2005.

H. Bhatia, A. G. Gyulassy, V. Lordi, J. E. Pask, V. Pascucci et al., Topoms: Comprehensive topological exploration for molecular and condensed-matter systems, J. of Comp. Chem, 2018.
DOI : 10.1002/jcc.25181

S. Biasotti, D. Giorgio, M. Spagnuolo, and B. Falcidieno, Reeb graphs for shape analysis and applications, Theoretical Computer Science, vol.392, issue.1-3, 2008.
DOI : 10.1016/j.tcs.2007.10.018
URL : https://doi.org/10.1016/j.tcs.2007.10.018

P. Bremer, G. Weber, J. Tierny, V. Pascucci, M. Day et al., Interactive Exploration and Analysis of Large-Scale Simulations Using Topology-Based Data Segmentation, IEEE Transactions on Visualization and Computer Graphics, vol.17, issue.9, 2011.
DOI : 10.1109/TVCG.2010.253
URL : https://hal.archives-ouvertes.fr/hal-01211172

H. Carr, J. Snoeyink, and U. Axen, Computing contour trees in all dimensions, Computational Geometry, vol.24, issue.2, 2000.
DOI : 10.1016/S0925-7721(02)00093-7
URL : https://doi.org/10.1016/s0925-7721(02)00093-7

H. Carr, J. Snoeyink, and M. Van-de-panne, Simplifying flexible isosurfaces using local geometric measures, IEEE Visualization 2004, 2004.
DOI : 10.1109/VISUAL.2004.96
URL : http://vis.computer.org/vis2004/DVD/vis/papers/carr.pdf

F. Chen, H. Obermaier, H. Hagen, B. Hamann, J. Tierny et al., Topology analysis of time-dependent multi-fluid data using the Reeb graph, Computer Aided Geometric Design, vol.30, issue.6, 2013.
DOI : 10.1016/j.cagd.2012.03.019

L. De-floriani, U. Fugacci, F. Iuricich, and P. Magillo, Morse complexes for shape segmentation and homological analysis: discrete models and algorithms, Computer Graphics Forum, vol.32, issue.3, 2015.
DOI : 10.1017/CBO9780511546945

H. Edelsbrunner and J. Harer, Computational Topology: An Introduction, 2009.
DOI : 10.1090/mbk/069

G. Favelier, C. Gueunet, and J. Tierny, Visualizing ensembles of viscous fingers, IEEE SciVis Contest, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01359694

D. Guenther, R. Alvarez-boto, J. Contreras-garcia, J. Piquemal, and J. Tierny, Characterizing Molecular Interactions in Chemical Systems, IEEE Transactions on Visualization and Computer Graphics, vol.20, issue.12, 2014.
DOI : 10.1109/TVCG.2014.2346403
URL : https://hal.archives-ouvertes.fr/hal-01146475

C. Gueunet, P. Fortin, J. Jomier, and J. Tierny, Contour forests: Fast multi-threaded augmented contour trees, 2016 IEEE 6th Symposium on Large Data Analysis and Visualization (LDAV), 2016.
DOI : 10.1109/LDAV.2016.7874333
URL : https://hal.archives-ouvertes.fr/hal-01355328

C. Gueunet, P. Fortin, J. Jomier, and J. Tierny, Task-based augmented merge trees with Fibonacci heaps, 2017 IEEE 7th Symposium on Large Data Analysis and Visualization (LDAV), 2017.
DOI : 10.1109/LDAV.2017.8231846
URL : https://hal.archives-ouvertes.fr/hal-01575019

A. Gyulassy, P. Bremer, R. Grout, H. Kolla, J. Chen et al., Stability of Dissipation Elements: A Case Study in Combustion, Computer Graphics Forum, vol.608, issue.10, 2014.
DOI : 10.1017/S0022112008002139

A. Gyulassy, P. T. Bremer, B. Hamann, and V. Pascucci, A Practical Approach to Morse-Smale Complex Computation: Scalability and Generality, IEEE Transactions on Visualization and Computer Graphics, vol.14, issue.6, 2008.
DOI : 10.1109/TVCG.2008.110
URL : http://www.cs.jhu.edu/~misha/ReadingSeminar/Papers/Gyulassy08.pdf

A. Gyulassy, D. Guenther, J. A. Levine, J. Tierny, and V. Pascucci, , 2014.

A. Gyulassy, A. Knoll, K. Lau, B. Wang, P. Bremer et al., Interstitial and Interlayer Ion Diffusion Geometry Extraction in Graphitic Nanosphere Battery Materials, IEEE Transactions on Visualization and Computer Graphics, vol.22, issue.1, 2015.
DOI : 10.1109/TVCG.2015.2467432

A. Gyulassy, V. Natarajan, M. Duchaineau, V. Pascucci, E. Bringa et al., Topologically Clean Distance Fields, IEEE Transactions on Visualization and Computer Graphics, vol.13, issue.6, 2007.
DOI : 10.1109/TVCG.2007.70603

C. Heine, H. Leitte, M. Hlawitschka, F. Iuricich, L. De-floriani et al., A Survey of Topology-based Methods in Visualization, Computer Graphics Forum, vol.11, issue.4, 2016.
DOI : 10.1109/TVCG.2005.67

J. Kasten, J. Reininghaus, I. Hotz, and H. Hege, Two-Dimensional Time-Dependent Vortex Regions Based on the Acceleration Magnitude, IEEE Transactions on Visualization and Computer Graphics, vol.17, issue.12, 2011.
DOI : 10.1109/TVCG.2011.249

D. E. Laney, P. Bremer, A. Mascarenhas, P. Miller, and V. Pascucci, Understanding the Structure of the Turbulent Mixing Layer in Hydrodynamic Instabilities, IEEE Transactions on Visualization and Computer Graphics, vol.12, issue.5, 2006.
DOI : 10.1109/TVCG.2006.186

J. Lukasczyk, G. Aldrich, M. Steptoe, G. Favelier, C. Gueunet et al., Viscous Fingering: A Topological Visual Analytic Approach, Physical Modeling for Virtual Manufacturing Systems and Processes, 2017.
DOI : 10.4028/www.scientific.net/AMM.869.9
URL : https://hal.archives-ouvertes.fr/hal-01547523

S. Parsa, A deterministic o(m log m) time algorithm for the reeb graph, Symp. on Comp. Geom, 2012.
DOI : 10.1145/2261250.2261289

V. Pascucci, G. Scorzelli, P. T. Bremer, and A. Mascarenhas, Robust on-line computation of Reeb graphs: simplicity and speed, ACM Trans. on Graph, 2007.
DOI : 10.1145/1239451.1239509

V. Pascucci, X. Tricoche, H. Hagen, and J. Tierny, Topological Methods in Data Analysis and Visualization: Theory, Algorithms and Applications, 2010.
DOI : 10.1007/978-3-642-15014-2

E. Santos, J. Tierny, A. Khan, B. Grimm, L. Lins et al., Enabling Advanced Visualization Tools in a Web-Based Simulation Monitoring System, 2009 Fifth IEEE International Conference on e-Science, 2009.
DOI : 10.1109/e-Science.2009.57
URL : https://hal.archives-ouvertes.fr/hal-01211179

N. Shivashankar, P. Pranav, V. Natarajan, R. Van-de-weygaert, E. P. Bos et al., Felix: A Topology Based Framework for Visual Exploration of Cosmic Filaments, IEEE Transactions on Visualization and Computer Graphics, vol.22, issue.6, 2016.
DOI : 10.1109/TVCG.2015.2452919
URL : http://arxiv.org/pdf/1508.00737

B. S. Sohn and C. L. Bajaj, Time-varying contour topology, IEEE Transactions on Visualization and Computer Graphics, vol.12, issue.1, 2006.
DOI : 10.1109/TVCG.2006.16
URL : http://europepmc.org/articles/pmc2703823?pdf=render

M. Soler, M. Plainchault, B. Conche, and J. Tierny, Topologically Controlled Lossy Compression, 2018 IEEE Pacific Visualization Symposium (PacificVis), 2018.
DOI : 10.1109/PacificVis.2018.00015
URL : https://hal.archives-ouvertes.fr/hal-01703832

T. Sousbie, The persistent cosmic web and its filamentary structure - I. Theory and implementation, Monthly Notices of the Royal Astronomical Society, vol.0, issue.10, 2011.
DOI : 10.1109/ISVD.2010.24
URL : https://academic.oup.com/mnras/article-pdf/414/1/384/3811918/mnras0414-0384.pdf

D. M. Thomas and V. Natarajan, Multiscale Symmetry Detection in Scalar Fields by Clustering Contours, IEEE Transactions on Visualization and Computer Graphics, vol.20, issue.12, 2014.
DOI : 10.1109/TVCG.2014.2346332
URL : http://drona.csa.iisc.ernet.in/~vijayn/research/papers/SymmetryViaContourClusteringSCIVIS2014.pdf

J. Tierny, Topological Data Analysis for Scientific Visualization, 2018.
DOI : 10.1007/978-3-319-71507-0
URL : https://hal.archives-ouvertes.fr/tel-01310926

J. Tierny, J. Daniels, L. G. Nonato, V. Pascucci, and C. Silva, Interactive Quadrangulation with Reeb Atlases and Connectivity Textures, IEEE Transactions on Visualization and Computer Graphics, vol.18, issue.10, 2012.
DOI : 10.1109/TVCG.2011.270
URL : https://hal.archives-ouvertes.fr/hal-01211169

J. Tierny, G. Favelier, J. A. Levine, C. Gueunet, and M. Michaux, The Topology ToolKit, IEEE Transactions on Visualization and Computer Graphics, vol.24, issue.1, 2017.
DOI : 10.1109/TVCG.2017.2743938
URL : https://hal.archives-ouvertes.fr/hal-01499905

J. Tierny, A. Gyulassy, E. Simon, and V. Pascucci, Loop surgery for volumetric meshes: Reeb graphs reduced to contour trees, IEEE Transactions on Visualization and Computer Graphics, vol.15, issue.6, 2009.
DOI : 10.1109/TVCG.2009.163
URL : https://hal.archives-ouvertes.fr/hal-01211176

J. Tierny and V. Pascucci, Generalized Topological Simplification of Scalar Fields on Surfaces, IEEE Transactions on Visualization and Computer Graphics, vol.18, issue.12, 2012.
DOI : 10.1109/TVCG.2012.228
URL : https://hal.archives-ouvertes.fr/hal-01206877

J. Tierny, J. Vandeborre, and M. Daoudi, Partial 3D Shape Retrieval by Reeb Pattern Unfolding, Computer Graphics Forum, vol.24, issue.1, pp.41-55, 2009.
DOI : 10.1515/9781400881802
URL : https://hal.archives-ouvertes.fr/hal-00662254

W. Usher and Q. Wu, Topo-Vol: Topology guided volume exploration. https://github

M. Van-kreveld, R. Van-oostrum, C. Bajaj, V. Pasucci, and D. Schikore, Contour trees and small seed sets for isosurface traversal, Proceedings of the thirteenth annual symposium on Computational geometry , SCG '97, 1997.
DOI : 10.1145/262839.269238

A. Vintescu, F. Dupont, G. Lavoué, P. Memari, and J. Tierny, Conformal factor persistence for fast hierarchical cone extraction, Eurographics, p.2017
URL : https://hal.archives-ouvertes.fr/hal-01508966

G. Weber, P. Bremer, H. Carr, and A. Gyulassy, Scalar topology in visual data analysis, IEEE VIS Tutorials, 2009.

G. Weber, S. E. Dillard, H. Carr, V. Pascucci, and B. Hamann, Topology-Controlled Volume Rendering, IEEE Transactions on Visualization and Computer Graphics, vol.13, issue.2, 2007.
DOI : 10.1109/TVCG.2007.47
URL : https://cloudfront.escholarship.org/dist/prd/content/qt6bt8m788/qt6bt8m788.pdf