Baum, Daniel, Dr.

Kontakt

Position

Leitung Arbeitsgruppe

Room

4005

Phone

+49 30 84185-293

E-Mail

Webseite

https://www.zib.de/members/baum

Birth name

Daniel Runge

Projects

Projects as Head

Data Processing Algorithms

The goal of this project is to provide an industry partner state-of-the-art advice on data processing algorithms. This comprises surface mesh processing algorithms, such...

Data Processing Algorithms

Segmentation and Quantitative Analysis of Cartilaginous Fish Skeletons

Unlike most other vertebrate animals, sharks and rays have skeletons made entirely of cartilage and not bone. In contrast to the cartilage in our knees, however, a shark...

Segmentation and Quantitative Analysis of Cartilaginous Fish Skeletons

Morphometric Analysis of the Para-Basisphenoid Complex of the Snake Genus Eirenis

Geometric morphometrics plays an important role in evolutionary studies. The state of the art in this field are landmark-based methods. Since landmarks usually need to be...

Morphometric Analysis of the Para-Basisphenoid Complex of the Snake Genus Eirenis

Reconstruction and Visualization of Anatomical Structures in Insects

High-resolution synchrotron μCT allows one to study insects in a non-destructive way. This is particularly important for rare specimens. Despite the non-destructive...

Reconstruction and Visualization of Anatomical Structures in Insects

Projects as Member

Transfer of Research Prototypes to the Commercial Visualization Systems Amira and Avizo (until 2012)

Amira and Avizo are professional software products for 3D visualization, geometry reconstruction and data analysis. The software has been designed and developed at the...

Transfer of Research Prototypes to the Commercial Visualization Systems Amira and Avizo (until 2012)

Image-Based Analysis of Pore and Particle Structures

The goal of this project is to develop an analysis environment for high-resolution CT scans of porous materials. This environment will integrate methods to compute the...

Image-Based Analysis of Pore and Particle Structures

Molecular Visualization

The understanding of biochemical processes requires the study of structure and dynamics of biomolecules of varying size. In these investigations vast amounts of data are...

Molecular Visualization

Publications

2025

Blobby is a synaptic active zone assembly protein required for memory in Drosophila Nature Communications, Vol.16, 2025 Janine Lützkendorf, Tanja Matkovic-Rachid, Sunbin Liu, Torsten Götz, Lili Gao, Oriane Turrel, Marta Maglione, Melanie Grieger, Sabrina Putignano, Niraja Ramesh, Tina Ghelani, Alexander Neumann, Niclas Gimber, Jan Schmoranzer, Anastasia Stawrakakis, Blaž Brence, Daniel Baum, Kai Ludwig, Martin Heine, Thorsten Mielke, Fan Liu, Alexander Walter, Markus Wahl, Stephan Sigrist BibTeX
DOI

Correlative light and electron microscopy reveals the fine circuit structure underlying evidence accumulation in larval zebrafish bioRxiv, 2025 (under review) Jonathan Boulanger-Weill, Florian Kaempf, Richard L. Schalek, Mariela Petkova, Sumit Kumar Vohra, Jay H. Savaliya, Yuelong Wu, Gregor F. P. Schuhknecht, Heike Naumann, Maren Eberle, Kim N. Kirchberger, Simone Rencken, Isaac H. Bianco, Daniel Baum, Filippo Del Bene, Florian Engert, Jeff W. Lichtman, Armin Bahl BibTeX
DOI

Improving the Identification of Layers in 3D Images of Ancient Papyrus using Artificial Neural Networks WACV 2025 workshop proceedings, 2025 (accepted for publication) Nicolas Klenert, Finn Schwoerer, Noushin Hajarolasvadi, Siloé Bournez, Tobias Arlt, Heinz-Eberhard Mahnke, Verena Lepper, Daniel Baum BibTeX

The helmeted hornbill casque is reinforced by a bundle of exceptionally thick, rod-like trabeculae Annals of the New York Academy of Sciences, 2025 VA Surapaneni, B Flaum, M Schindler, K Hayat, J Wölfer, D Baum, R Hu, TF Kong, M Doube, MN Dean BibTeX
DOI

2024

A Local Iterative Approach for the Extraction of 2D Manifolds from Strongly Curved and Folded Thin-Layer Structures IEEE Transactions on Visualization and Computer Graphics, 30(1), pp. 1260-1270, 2024 Nicolas Klenert, Verena Lepper, Daniel Baum BibTeX
DOI

A Ridge-based Approach for Extraction and Visualization of 3D Atmospheric Fronts 2024 IEEE Visualization and Visual Analytics (VIS), pp. 176-180, 2024 Anne Gossing, Andreas Beckert, Christoph Fischer, Nicolas Klenert, Vijay Natarajan, George Pacey, Thorwin Vogt, Marc Rautenhaus, Daniel Baum BibTeX
DOI

A Visual Interface for Exploring Hypotheses about Neural Circuits IEEE Transactions on Visualization and Computer Graphics, 30(7), pp. 3945-3958, 2024 (preprint available as ZIB-Report 23-07) Sumit Kumar Vohra, Philipp Harth, Yasuko Isoe, Armin Bahl, Haleh Fotowat, Florian Engert, Hans-Christian Hege, Daniel Baum PDF (ZIB-Report)
BibTeX
DOI

CoDA: Interactive Segmentation and Morphological Analysis of Dendroid Structures Exemplified on Stony Cold-Water Corals 2024 Kira Schmitt, Jürgen Titschack, Daniel Baum BibTeX
arXiv

Comparative architecture of the tessellated boxfish (Ostracioidea) carapace Communications Biology, Vol.7, 2024 Lennart Eigen, Jan Wölfer, Daniel Baum, Mai-Lee Van Le, Daniel Werner, Mason N. Dean, John A. Nyakatura BibTeX
DOI

Data for Training the DeepOrientation Model: Simulated cryo-ET tomogram patches 2024 Noushin Hajarolasvadi, Daniel Baum BibTeX
DOI

Dissecting origins of wiring specificity in dense cortical connectomes bioRxiv, 2024 Philipp Harth, Daniel Udvary, Jan Boelts, Daniel Baum, Jakob H. Macke, Hans-Christian Hege, Marcel Oberlaender BibTeX
DOI

Growth of a tessellation: geometric rules for the development of stingray skeletal patterns Advanced Science, 11(48), 2024 (epub ahead of print) Binru Yang, David Knötel, Jana Ciecierska-Holmes, Jan Wölfer, Júlia Chaumel, Paul Zaslansky, Daniel Baum, Peter Fratzl, Mason N. Dean BibTeX
DOI

Helmeted hornbill cranial kinesis: balancing mobility and stability in a high-impact joint Anatomical Record, 2024 (accepted for publication) VA Surapaneni, B Flaum, M Schindler, K Hayat, J Wölfer, D Baum, R Hu, TF Kong, M Doube, MN Dean BibTeX

Multi-species community platform for comparative neuroscience in teleost fish bioRxiv, 2024 (under review, preprint available as ) Sumit Kumar Vohra, Kristian Herrera, Tinatini Tavhelidse-Suck, Simon Knoblich, Ali Seleit, Jonathan Boulanger-Weill, Sydney Chambule, Ariel Aspiras, Cristina Santoriello, Owen Randlett, Joachim Wittbrodt, Alexander Aulehla, Jeff W. Lichtman, Mark Fishman, Hans-Christian Hege, Daniel Baum, Florian Engert, Yasuko Isoe BibTeX
DOI

Shape-based Disease Grading via Functional Maps and Graph Convolutional Networks with Application to Alzheimer’s Disease BMC Medical Imaging, Vol.24, 2024 Julius Mayer, Daniel Baum, Felix Ambellan, Christoph von Tycowicz, for the Alzheimer’s Disease Neuroimaging Initiative BibTeX
DOI

2023

Automated segmentation of insect anatomy from micro-CT images using deep learning Natural Sciences, 3(4), 2023 Evropi Toulkeridou, Carlos Enrique Gutierrez, Daniel Baum, Kenji Doya, Evan P. Economo BibTeX
DOI

Dense Reconstruction of Elephant Trunk Musculature Current Biology, Vol.33, pp. 1-8, 2023 Luke L. Longren, Lennart Eigen, Ani Shubitidze, Oliver Lieschnegg, Daniel Baum, John A. Nyakatura, Thomas Hildebrandt, Michael Brecht BibTeX
DOI

Enhancing molecular visualization: Perceptual evaluation of line variables with application to uncertainty visualization Computers & Graphics, Vol.114, pp. 401-413, 2023 Anna Sterzik, Nils Lichtenberg, Michael Krone, Daniel Baum, Douglas W. Cunningham, Kai Lawonn BibTeX
DOI

Evolutionary traces of miniaturization in a giant – Comparative anatomy of brain and brain nerves in Bathochordaeus stygius (Tunicata, Appendicularia) Journal of Morphology, 284(7), 2023 Berit Zemann, Mai-Lee Van Le, Rob E. Sherlock, Daniel Baum, Kakani Katija, Thomas Stach BibTeX
DOI

High-throughput segmentation, data visualization, and analysis of sea star skeletal networks Journal of Structural Biology, 215(2), p. 107955, 2023 Lara Tomholt, Daniel Baum, Robert J. Wood, James C. Weaver BibTeX
DOI

Rapid Prototyping for Coordinated Views of Multi-scale Spatial and Abstract Data: A Grammar-based Approach Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM), 2023 Philipp Harth, Arco Bast, Jakob Troidl, Bjorge Meulemeester, Hanspeter Pfister, Johanna Beyer, Marcel Oberlaender, Hans-Christian Hege, Daniel Baum BibTeX
DOI

Segmentation of tooth enamel microstructure images using classical image processing and U-Net approaches Frontiers in Imaging, Vol.2, 2023 Giovani Bressan Fogalli, Sérgio Roberto Peres Line, Daniel Baum BibTeX
DOI

Serial-section electron tomography and quantitative analysis of the microtubule organization in 3D-reconstructed mitotic spindles Bio-protocol, 13(20), 2023 Robert Kiewisz, Daniel Baum, Thomas Müller-Reichert, Gunar Fabig BibTeX
DOI

Simulation-based inference for efficient identification of generative models in computational connectomics PLOS Computational Biology, 19(9), 2023 (preprint available as ) Jan Boelts, Philipp Harth, Richard Gao, Daniel Udvary, Felipe Yanez, Daniel Baum, Hans-Christian Hege, Marcel Oberlaender, Jakob H. Macke BibTeX
DOI

2022

3D models related to the publication: Hide and seek shark teeth in Random Forests: Machine learning applied to Scyliorhinus canicula MorphoMuseuM, 2022 Fidji Berio, Yann Bayle, Sylvie Agret, Daniel Baum, Nicolas Goudemand, Mélanie Debiais-Thibaud BibTeX
DOI

A Kendall Shape Space Approach to 3D Shape Estimation from 2D Landmarks Computer Vision -- ECCV 2022, pp. 363-379, 2022 Martha Paskin, Mason Dean, Daniel Baum, Christoph von Tycowicz BibTeX
arXiv
DOI

A Kendall Shape Space Approach to 3D Shape Estimation from 2D Landmarks -- Source Code and Data 2022 Martha Paskin, Daniel Baum, Mason N. Dean, Christoph von Tycowicz BibTeX
DOI

A Soft-Correspondence Approach to Shape-based Disease Grading with Graph Convolutional Networks Proceedings of Machine Learning Research, pp. 85-95, Vol.194, 2022 Julius Mayer, Daniel Baum, Felix Ambellan, Christoph von Tycowicz PDF
BibTeX

A Stratification Matrix Viewer for Analysis of Neural Network Data Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM), 2022 Philipp Harth, Sumit Vohra, Daniel Udvary, Marcel Oberlaender, Hans-Christian Hege, Daniel Baum BibTeX
DOI

Active entanglement enables stochastic, topological grasping PNAS, 119(42), p. e2209819119, 2022 Kaitlyn P Becker, Clark Teeple, Nicholas Charles, Yeonsu Jung, Daniel Baum, James C Weaver, L. Mahadevan, Robert J Wood BibTeX
DOI

An Interactive Approach for Identifying Structure Definitions Computer Graphics Forum, 41(3), pp. 321-332, 2022 Natalia Mikula, Tom Dörffel, Daniel Baum, Hans-Christian Hege BibTeX
arXiv
DOI

Estimating 3D Shape of the Head Skeleton of Basking Sharks Using Annotated Landmarks on a 2D Image Master's thesis, Freie Universität Berlin, Daniel Baum, Christoph von Tycowicz, Mason N. Dean (Advisors), 2022 Martha Paskin PDF
BibTeX

Hide and seek shark teeth in Random Forests: Machine learning applied to Scyliorhinus canicula populations PeerJ - Aquatic Biology, p. 10:e13575, 2022 Fidji Berio, Yann Bayle, Daniel Baum, Nicolas Goudemand, Mélanie Debiais-Thibaud BibTeX
DOI

Large abdominal mechanoreceptive sense organs in small plant-dwelling insects Biology Letters, 18(4), 2022 Sarah Ehlers, Daniel Baum, Roland Mühlethaler, Hannelore Hoch, Peter Bräunig BibTeX
DOI

MCRS1 modulates the heterogeneity of microtubule minus-end morphologies in mitotic spindles Molecular Biology of the Cell, 34(1), 2022 Alejandra Laguillo-Diego, Robert Kiewisz, Carlos Martí-Gómez, Daniel Baum, Thomas Müller-Reichert, Isabelle Vernos BibTeX
DOI

Ontogeny of a tessellated surface: carapace growth of the longhorn cowfish Lactoria cornuta Journal of Anatomy, 241(3), pp. 565-580, 2022 Lennart Eigen, Daniel Baum, Mason N. Dean, Daniel Werner, Jan Wölfer, John A. Nyakatura BibTeX
DOI

Polyp-Cavity Segmentation of Cold-Water Corals guided by Ambient Occlusion and Ambient Curvature Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM), 2022 Kira Schmitt, Jürgen Titschack, Daniel Baum BibTeX
DOI

Three-dimensional structure of kinetochore-fibers in human mitotic spindles eLife, Vol.11, p. e75459, 2022 Robert Kiewisz, Gunar Fabig, William Conway, Daniel Baum, Daniel Needleman, Thomas Müller-Reichert BibTeX
DOI

Volumetric macromolecule identification in cryo-electron tomograms using capsule networks BMC Bioinformatics, 23(360), 2022 Noushin Hajarolasvadi, Vikram Sunkara, Sagar Khavnekar, Florian Beck, Robert Brandt, Daniel Baum BibTeX
DOI

2021

Automated segmentation of insect anatomy from micro-CT images using deep learning bioRxiv, 2021 Evropi Toulkeridou, Carlos Enrique Gutierrez, Daniel Baum, Kenji Doya, Evan P. Economo BibTeX
DOI

Revisiting the Jerash Silver Scroll: a new visual data analysis approach Digital Applications in Archaeology and Cultural Heritage, Vol.21, p. e00186, 2021 Daniel Baum, Felix Herter, John Møller Larsen, Achim Lichtenberger, Rubina Raja BibTeX
DOI

Segmentation of abdominal chordotonal organs based on semithin serial sections in the Rhododendron leafhopper Graphocephala fennahi (Cicadomorpha: Cicadellidae) 2021 Sarah Ehlers, Andreas Wessel, Daniel Baum BibTeX
DOI

Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography Journal of Microscopy, 284(1), pp. 25-44, 2021 Norbert Lindow, Florian Brünig, Vincent J. Dercksen, Gunar Fabig, Robert Kiewisz, Stefanie Redemann, Thomas Müller-Reichert, Steffen Prohaska, Daniel Baum BibTeX
DOI

Thin-Volume Visualization on Curved Domains Computer Graphics Forum, 40(3), pp. 147-157, 2021 Felix Herter, Hans-Christian Hege, Markus Hadwiger, Verena Lepper, Daniel Baum BibTeX
DOI

2020

4D imaging of lithium-batteries using correlative neutron and X-ray tomography with a virtual unrolling technique Nature Communications, Vol.11, p. 777, 2020 Ralf F. Ziesche, Tobias Arlt, Donal P. Finegan, Thomas M.M. Heenan, Alessandro Tengattini, Daniel Baum, Nikolay Kardjilov, Henning Markötter, Ingo Manke, Winfried Kockelmann, Dan J.L. Brett, Paul R. Shearing BibTeX
DOI

A comparative description of the mesosomal musculature in Sphecidae and Ampulicidae (Hymenoptera, Apoidea) using 3D techniques Deutsche Entomologische Zeitschrift, 67(1), pp. 51-67, 2020 Maraike Willsch, Frank Friedrich, Daniel Baum, Ivo Jurisch, Michael Ohl BibTeX
DOI

Co-aligned chondrocytes: Zonal morphological variation and structured arrangement of cell lacunae in tessellated cartilage Bone, Vol.134, p. 115264, 2020 (preprint available as ZIB-Report 20-04) Júlia Chaumel, Merlind Schotte, Joseph J. Bizzarro, Paul Zaslansky, Peter Fratzl, Daniel Baum, Mason N. Dean PDF (ZIB-Report)
BibTeX
DOI

D’Arcy W. Thompson’s Cartesian transformations: a critical evaluation Zoomorphology, Vol.139, pp. 293-308, 2020 Gerhard Scholtz, David Knötel, Daniel Baum BibTeX
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Image analysis pipeline for segmentation of a biological porosity network, the lacuno-canalicular system in stingray tesserae MethodsX, Vol.7, p. 100905, 2020 (preprint available as ZIB-Report 20-12) Merlind Schotte, Júlia Chaumel, Mason N. Dean, Daniel Baum PDF (ZIB-Report)
BibTeX
DOI

In-situ defect detection in laser powder bed fusion by using thermography and optical tomography – comparison to computed tomography Metals, 10(1), p. 103, 2020 Gunther Mohr, Simon J. Altenburg, Alexander Ulbricht, Philipp Heinrich, Daniel Baum, Christiane Maierhofer, Kai Hilgenberg BibTeX
DOI

Jerash Silver Scroll: Virtually Unfolded Volume figshare, 2020 Daniel Baum, Felix Herter, Verena Lepper BibTeX
DOI

Making spherical-harmonics-based Geometric Morphometrics (SPHARM) approachable for 3D images containing large cavity openings using Ambient Occlusion - a study using hermit crab claw shape variability Zoomorphology, Vol.139, pp. 421-432, 2020 (preprint available as ZIB-Report 20-09) Yannic Ege, Christian Foth, Daniel Baum, Christian S. Wirkner, Stefan Richter PDF (ZIB-Report)
BibTeX
DOI

Scattering and phase-contrast X-ray methods reveal damage to glass fibers in endodontic posts following dental bur trimming Dental Materials, 37(2), pp. 201-211, 2020 Ana Prates Soares, Daniel Baum, Bernhard Hesse, Andreas Kupsch, Bernd Müller, Paul Zaslansky BibTeX
DOI

Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography bioRxiv, 2020 Norbert Lindow, Florian Brünig, Vincent J. Dercksen, Gunar Fabig, Robert Kiewisz, Stefanie Redemann, Thomas Müller-Reichert, Steffen Prohaska, Daniel Baum BibTeX
DOI

Virtual unfolding of folded papyri Journal of Cultural Heritage, Vol.41, pp. 264-269, 2020 (preprint available as ZIB-Report 19-44) Heinz-Eberhard Mahnke, Tobias Arlt, Daniel Baum, Hans-Christian Hege, Felix Herter, Norbert Lindow, Ingo Manke, Tzulia Siopi, Eve Menei, Marc Etienne, Verena Lepper PDF (ZIB-Report)
BibTeX
DOI

2019

An Evaluation of Color Maps for Visual Data Exploration Science in Color: Visualizing Achromatic Knowledge, Bettina Bock von Wülfingen (Ed.), De Gruyter: Berlin, pp. 147-161, 2019 (preprint available as ZIB-Report 19-42) Daniel Baum PDF (ZIB-Report)
BibTeX

High-Throughput Segmentation of Tiled Biological Structures using Random-Walk Distance Transforms Integrative And Comparative Biology, 2019 (preprint available as ZIB-Report 19-33) Daniel Baum, James C. Weaver, Igor Zlotnikov, David Knötel, Lara Tomholt, Mason N. Dean PDF (ZIB-Report)
BibTeX
DOI

Interactive Visualization of RNA and DNA Structures IEEE Transactions on Visualization and Computer Graphics, 25(1), pp. 967-976, 2019 (preprint available as ZIB-Report 18-33) Norbert Lindow, Daniel Baum, Morgan Leborgne, Hans-Christian Hege PDF (ZIB-Report)
BibTeX
DOI

Muscle internal structure revealed by contrast-enhanced μCT and fibre recognition: The hindlimb extensors of an arboreal and a fossorial squirrel Mammalian Biology, Vol.99, pp. 71-80, 2019 John Nyakatura, Roxane Baumgarten, Daniel Baum, Heiko Stark, Dionisios Youlatos BibTeX
DOI

2018

Ambient occlusion – a powerful algorithm to segment shell and skeletal intrapores in computed tomography data Computers and Geosciences, Vol.115, pp. 75-87, 2018 (preprint available as ZIB-Report 18-14) Jürgen Titschack, Daniel Baum, Kei Matsuyama, Karin Boos, Claudia Färber, Wolf-Achim Kahl, Karsten Ehrig, Dietmar Meinel, Carmen Soriano, Stuart R. Stock PDF (ZIB-Report)
BibTeX
DOI

Atomic Accessibility Radii for Molecular Dynamics Analysis Workshop on Molecular Graphics and Visual Analysis of Molecular Data, 2018, ISBN: 978-3-03868-061-1 (preprint available as ZIB-Report 18-18) Norbert Lindow, Daniel Baum, Hans-Christian Hege PDF (ZIB-Report)
BibTeX
DOI

Dust and gas emission from cometary nuclei: the case of comet 67P/Churyumov-Gerasimenko Advances in Physics: X, 3(1), p. 1404436, 2018 (preprint available as ZIB-Report 17-78) Tobias Kramer, Matthias Noack, Daniel Baum, Hans-Christian Hege, Eric J. Heller PDF (ZIB-Report)
BibTeX
DOI

Global and Local Mesh Morphing for Complex Biological Objects from microCT Data Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM), pp. 179-183, 2018 (preprint available as ZIB-Report 18-53) David Knötel, Carola Becker, Gerhard Scholtz, Daniel Baum PDF (ZIB-Report)
BibTeX
DOI

2017

Adapting trabecular structures for 3D printing: an image processing approach based on µCT data Biomedical Physics & Engineering Express, 3(3), 2017 (preprint available as ZIB-Report 17-26) Ulrike Homberg, Daniel Baum, Steffen Prohaska, Jens Günster, Stefanie Krauß-Schüler PDF (ZIB-Report)
BibTeX
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Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage PLOS ONE, 2017 (preprint available as ZIB-Report 17-62) David Knötel, Ronald Seidel, Steffen Prohaska, Mason N. Dean, Daniel Baum PDF (ZIB-Report)
BibTeX
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Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage (Supplementary Material) 2017 David Knötel, Ronald Seidel, Paul Zaslansky, Steffen Prohaska, Mason N. Dean, Daniel Baum BibTeX
DOI

Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies Computer Graphics Forum, 36(3), pp. 329-339, 2017 (preprint available as ZIB-Report 17-16) Amal Aboulhassan, Ronell Sicat, Daniel Baum, Olga Wodo, Markus Hadwiger PDF (ZIB-Report)
BibTeX
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Revealing hidden text in rolled and folded papyri Applied Physics A, 123(3), p. 171, 2017 (preprint available as ZIB-Report 17-02) Daniel Baum, Norbert Lindow, Hans-Christian Hege, Verena Lepper, Tzulia Siopi, Frank Kutz, Kristin Mahlow, Heinz-Eberhard Mahnke PDF (ZIB-Report)
BibTeX
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2016

Biological strategies for fatique and wear avoidance: lessons from stingray skeletons and teeth Poster, Tomography for Scientific Advancement symposium (ToScA), 2016 Mason N. Dean, Ahmed Hosny, Ronald Seidel, Daniel Baum BibTeX

Cavity and Pore Segmentation in 3D Images with Ambient Occlusion EuroVis 2016 - Short Papers, 2016 (preprint available as ZIB-Report 16-17) Daniel Baum, Jürgen Titschack PDF (ZIB-Report)
BibTeX
DOI

Long-term macrobioerosion in the Mediterranean Sea assessed by micro-computed tomography Biogeosciences, 13(11), pp. 3461-3474, 2016 Claudia Färber, Jürgen Titschack, Christine H. L. Schönberg, Karsten Ehrig, Karin Boos, Daniel Baum, Bernd Illerhaus, Ulla Asgaard, Richard G. Bromley, André Freiwald, Max Wisshak BibTeX
DOI

Mediterranean cold-water corals - an important regional carbonate factory? The Depositional Record, 2(1), pp. 74-96, 2016 Jürgen Titschack, Hiske G. Fink, Daniel Baum, Claudia Wienberg, Dierk Hebbeln, André Freiwald BibTeX
DOI

To build a shark: 3D tiling laws of tessellated cartilage Abstract in Integrative and Comparative Biology; conference Society of Integrative and Comparative Biology annual meeting, January 3-7, 2016, Portland, USA, Vol.56 (suppl 1), 2016 Mason N. Dean, R. Seidel, David Knötel, K. Lyons, Daniel Baum, James C. Weaver, Peter Fratzl BibTeX

Understanding the Tiling Rules of the Tessellated Mineralized Endoskeleton of Sharks and Rays Poster, Euro Bio-inspired Materials 2016, Potsdam, Germany, February 22 - 25, 2016, 2016 David Knötel, Ronald Seidel, Ahmed Hosny, Paul Zaslansky, James C. Weaver, Daniel Baum, Mason N. Dean BibTeX

Virtual Access to Hidden Texts – Study of Ancient Papyri Eighth Joint BER II and BESSY II User Meeting, Dec 7-9, 2016, Berlin, Germany, 2016 Tobias Arlt, Norbert Lindow, Daniel Baum, Andre Hilger, Ingo Mahnke, Hans-Christian Hege, Verena Lepper, Tzulia Siopi, Heinz.Eberhard Mahnke BibTeX

Visual Analysis of Biomolecular Cavities: State of the Art Computer Graphics Forum, 35(3), pp. 527-551, 2016 (preprint available as ZIB-Report 16-42) Michael Krone, Barbora Kozlíková, Norbert Lindow, Marc Baaden, Daniel Baum, Julius Parulek, Hans-Christian Hege, Ivan Viola PDF (ZIB-Report)
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Visualization of Biomolecular Structures: State of the Art Revisited Computer Graphics Forum, 36(8), pp. 178-204, 2016 Barbora Kozlíková, Michael Krone, Martin Falk, Norbert Lindow, Marc Baaden, Daniel Baum, Ivan Viola, Julius Parulek, Hans-Christian Hege BibTeX
DOI

2015

3D Corrosion Detection in Time-dependent CT Images of Concrete DIR-2015 Proceedings, 2015 Olaf Paetsch, Daniel Baum, Steffen Prohaska, Karsten Ehrig, Dietmar Meinel, Gino Ebell BibTeX

A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials Computer Graphics Forum, 34(3), pp. 401-410, 2015 (preprint available as ZIB-Report 15-20) Amal Aboulhassan, Daniel Baum, Olga Wodo, Baskar Ganapathysubramanian, Aram Amassian, Markus Hadwiger PDF (ZIB-Report)
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Aggradation and carbonate accumulation of Holocene Norwegian cold-water coral reefs Sedimentology, 62(7), pp. 1873-1898, 2015 Jürgen Titschack, Daniel Baum, Ricardo De Pol-Holz, Matthias López Correa, Nina Forster, Sascha Flögel, Dierk Hebbeln, André Freiwald BibTeX
DOI

Ambient occlusion - a powerful algorithm to segment skeletal intrapores and gastral cavities in dendrophyllid cold-water corals Poster, 31st IAS Meeting of Sedimentology, 2015, June 22-25, Kraków, Poland, 2015 Jürgen Titschack, Daniel Baum BibTeX

Homogeneous dust emission and jet structure near active cometary nuclei: the case of 67P/Churyumov-Gerasimenko 2015 Tobias Kramer, Matthias Noack, Daniel Baum, Hans-Christian Hege, Eric J. Heller BibTeX
arXiv

Membrane Protein Structure, Function and Dynamics: A Perspective from Experiments and Theory Journal of Membrane Biology, 248(4), pp. 611-640, 2015 Zoe Cournia, Toby W. Allen, Ioan Andricioaei, Bruno Antonny, Daniel Baum, Grace Brannigan, Nicolae-Viorel Buchete, Jason T. Deckman, Lucie Delemotte, Coral del Val, Ran Friedman, Paraskevi Gkeka, Hans-Christian Hege, Jérôme Hénin, Marina A. Kasimova, Antonios Kolocouris, Michael L. Klein, Syma Khalid, Joanne Lemieux, Norbert Lindow, Mahua Roy, Jana Selent, Mounir Tarek, Florentina Tofoleanu, Stefano Vanni, Sinisa Urban, David J. Wales, Jeremy C. Smith, Ana-Nicoleta Bondar BibTeX
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Registering 2D and 3D Imaging Data of Bone during Healing Connective Tissue Research, 56(2), pp. 133-143, 2015 (preprint available as ZIB-Report 15-01) Rebecca M. Hoerth, Daniel Baum, David Knötel, Steffen Prohaska, Bettina M. Willie, Georg Duda, Hans-Christian Hege, Peter Fratzl, Wolfgang Wagermaier PDF (ZIB-Report)
BibTeX
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Segmentation of the Tessellated Mineralized Endoskeleton of Sharks and Rays Poster, Tomography for Scientific Advancement symposium (ToScA), Manchester, UK, September 3 - 4, 2015, 2015 David Knötel, Ronald Seidel, James C. Weaver, Daniel Baum, Mason N. Dean BibTeX

Two new species of erect Bryozoa (Gymnolaemata: Cheilostomata) and the application of non-destructive imaging methods for quantitative taxonomy Zootaxa, 4020(1), pp. 81-100, 2015 Kei Matsuyama, Jürgen Titschack, Daniel Baum, André Freiwald BibTeX
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Visualization of Biomolecular Structures: State of the Art EuroVis 2015 STARS Proceedings, pp. 61-81, 2015 (preprint available as ZIB-Report 15-63) Barbora Kozlikova, Michael Krone, Norbert Lindow, Martin Falk, Marc Baaden, Daniel Baum, Ivan Viola, Julius Parulek, Hans-Christian Hege PDF (ZIB-Report)
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2014

Advanced computed tomography analyses of cold-water coral mound cores: new insights into mound formation processes Poster, 19th International Sedimentological Congress, Geneva, Switzerland, 2014, August 18 - 22, 2014 Jürgen Titschack, Daniel Baum BibTeX

Automated stitching of microtubule centerlines across serial electron tomograms PLoS ONE, p. e113222, 2014 (preprint available as ZIB-Report 14-41) Britta Weber, Erin M. Tranfield, Johanna L. Höög, Daniel Baum, Claude Antony, Tony Hyman, Jean-Marc Verbavatz, Steffen Prohaska PDF (ZIB-Report)
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Definition, Extraction, and Validation of Pore Structures in Porous Materials Topological Methods in Data Analysis and Visualization III, pp. 235-248, Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, Ronald Peikert (Eds.), Springer, 2014 (preprint available as ZIB-Report 13-56) Ulrike Homberg, Daniel Baum, Alexander Wiebel, Steffen Prohaska, Hans-Christian Hege PDF (ZIB-Report)
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Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben DGZfP-Jahrestagung 2014 Konferenzband, 2014 (preprint available as ZIB-Report 14-24) Olaf Paetsch, Daniel Baum, Steffen Prohaska, Karsten Ehrig, Gino Ebell, Dietmar Meinel, Andreas Heyn PDF
PDF (ZIB-Report)
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Ligand Excluded Surface: A New Type of Molecular Surface IEEE Transactions on Visualization and Computer Graphics, 20(12), pp. 2486-2495, 2014 (preprint available as ZIB-Report 14-27) Norbert Lindow, Daniel Baum, Hans-Christian Hege PDF (ZIB-Report)
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Material and structural characterization of mineralized elasmobranch cartilage – lessons in repeated tiling patterns in mechanically loaded 3D objects Poster, Tomography for Scientific Advancement symposium (ToScA), London, UK, September 1 - 3, 2014, 2014 Ronald Seidel, David Knötel, Daniel Baum, James C. Weaver, Mason N. Dean BibTeX

Non-Sexual Abdominal Appendages in Adult Insects Challenge a 300 Million Year Old Bauplan Current Biology, 24(1), pp. R16-R17, 2014 Hannelore Hoch, Andreas Wessel, Manfred Asche, Daniel Baum, Felix Beckmann, Peter Bräunig, Karsten Ehrig, Roland Mühlethaler, Heinrich Riesemeier, Andreas Staude, Björn Stelbrink, Ekkehard Wachmann, Phyllis Weintraub, Benjamin Wipfler, Carsten Wolff, Mathias Zilch BibTeX
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The Potential of Surface-based Geometric Morphometrics for Evolutionary Studies: An Example using Dwarf Snakes (Eirenis) Abstract in DigitalSpecimen 2014, 2014 Daniel Baum, Kristin Mahlow, Hans Lamecker, Stefan Zachow, Johannes Müller, Hans-Christian Hege BibTeX

The Segmentation of Microtubules in Electron Tomograms Using Amira Mitosis: Methods and Protocols, pp. 261-278, Springer, 2014 Stefanie Redemann, Britta Weber, Marit Möller, Jean-Marc Verbavatz, Anthony Hyman, Daniel Baum, Steffen Prohaska, Thomas Müller-Reichert BibTeX
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2013

3-D-Visualisierung und statistische Analyse von Rissen in mit Computer-Tomographie untersuchten Betonproben Tagungsband der DGZfP Jahrestagung 2013, 2013 Olaf Paetsch, Daniel Baum, David Breßler, Karsten Ehrig, Dietmar Meinel, Steffen Prohaska PDF
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Anisotropic Sampling of Planar and Two-Manifold Domains for Texture Generation and Glyph Distribution Transactions on Visualization and Computer Graphics (TVCG), Vol.19, pp. 1782-1794, 2013 Andrea Kratz, Daniel Baum, Ingrid Hotz BibTeX
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Exploring cavity dynamics in biomolecular systems BMC Bioinformatics, Vol.14, 2013 Norbert Lindow, Daniel Baum, Ana-Nicoleta Bondar, Hans-Christian Hege BibTeX
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2012

Automated 3D Crack Detection for Analyzing Damage Processes in Concrete with Computed Tomography Proceedings of Conference on Industrial Computed Tomography, pp. 321-330, 2012 Olaf Paetsch, Daniel Baum, Karsten Ehrig, Dietmar Meinel, Steffen Prohaska BibTeX

Automated segmentation of electron tomograms for a quantitative description of actin filament networks Journal of Structural Biology, Vol.177, pp. 135-144, 2012 Alexander Rigort, David Günther, Reiner Hegerl, Daniel Baum, Britta Weber, Steffen Prohaska, Ohad Medalia, Wolfgang Baumeister, Hans-Christian Hege BibTeX
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Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos Journal of Structural Biology, 178(2), pp. 129-138, 2012 Britta Weber, Garrett Greenan, Steffen Prohaska, Daniel Baum, Hans-Christian Hege, Thomas Müller-Reichert, Anthony Hyman, Jean-Marc Verbavatz BibTeX
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Automatic Extraction and Analysis of Realistic Pore Structures from µCT Data for Pore Space Characterization of Graded Soil Proceedings of the 6th International Conference on Scour and Erosion (ICSE-6), pp. 345-352, 2012 Ulrike Homberg, Daniel Baum, Steffen Prohaska, Ute Kalbe, Karl Josef Witt BibTeX

Conveying Archaeological Contexts to Museum Visitors: Case Study Pergamon Exhibition VAST12: The 13th International Symposium on Virtual Reality, Archaeology and Intelligent Cultural Heritage - Short Papers, David Arnold, Jaime Kaminski, Franco Niccolucci, Andre Stork (Eds.), pp. 25-28, 2012 Marco Klindt, Steffen Prohaska, Daniel Baum, Hans-Christian Hege BibTeX
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Dynamic Channels in Biomolecular Systems: Path Analysis and Visualization Proceedings of IEEE Symposium on Biological Data Visualization (biovis’12), pp. 99-106, 2012 Norbert Lindow, Daniel Baum, Ana-Nicoleta Bondar, Hans-Christian Hege BibTeX
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Interactive Rendering of Materials and Biological Structures on Atomic and Nanoscopic Scale Computer Graphics Forum, 31(3), pp. 1325-1334, 2012 Norbert Lindow, Daniel Baum, Hans-Christian Hege BibTeX
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Perceptually Linear Parameter Variations Computer Graphics Forum, 31(2), pp. 535-544, 2012 Norbert Lindow, Daniel Baum, Hans-Christian Hege BibTeX
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Vergleich automatischer 3D-Risserkennungsmethoden für die quantitative Analyse der Schadensentwicklung in Betonproben mit Computer-Tomographie Tagungsband der DACH Jahrestagung 2012, 2012 Olaf Paetsch, Daniel Baum, Karsten Ehrig, Dietmar Meinel, Steffen Prohaska PDF
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iCon.text – a customizable iPad app for kiosk applications in museum exhibitions EVA 2012 Berlin, pp. 150-155, 2012 (preprint available as ZIB-Report 13-07) Marco Klindt, Daniel Baum, Steffen Prohaska, Hans-Christian Hege PDF (ZIB-Report)
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2011

Describing and Analyzing the Dual Structures of Porous Media Proc. 3D-Microstructure Meeting, Frank Mücklich, Philipp Slussallek, Katja Schladitz (Eds.), pp. 24-25, 2011 Ulrike Homberg, Daniel Baum, Steffen Prohaska BibTeX

Fast Tracing of Microtubule Centerlines in Electron Tomograms BioVis 2011 Abstracts, 1st IEEE Symposium on Biological Data Visualization, 2011 Britta Weber, Marit Möller, Jean-Marc Verbavatz, Daniel Baum, Hans-Christian Hege, Steffen Prohaska BibTeX

Voronoi-Based Extraction and Visualization of Molecular Paths IEEE Transactions on Visualization and Computer Graphics, 17(12), pp. 2025-2034, 2011 Norbert Lindow, Daniel Baum, Hans-Christian Hege BibTeX
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2010

Accelerated Visualization of Dynamic Molecular Surfaces Comput. Graph. Forum, Vol.29, pp. 943-952, 2010 Norbert Lindow, Daniel Baum, Steffen Prohaska, Hans-Christian Hege BibTeX
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2007

A Point-Based Algorithm for Multiple 3D Surface Alignment of Drug-Sized Molecules Doctoral thesis, Freie Universität Berlin, Peter Deuflhard, Joachim Selbig (Advisors), 2007 Daniel Baum PDF
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2006

A Point-matching based algorithm for 3D surface alignment of drug-sized molecules Computational Life Sciences II, Second International Symposium, CompLife 2006, Cambridge (UK), Sept. 2006, pp. 183-193, Vol.4216, Lecture Notes in Bioinformatics, 2006 Daniel Baum, Hans-Christian Hege BibTeX
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2005

Multiple semi-flexible 3D superposition of drug-sized molecules Computational Life Sciences: First International Symposium, CompLife 2005, pp. 198-207, Vol.3695, Lecture Notes on Computer Science, 2005 (preprint available as ZIB-Report 04-52) Daniel Baum PDF (ZIB-Report)
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2004

Finding All Maximal Cliques of a Family of Induced Subgraphs ZIB-Report 03-53 Daniel Baum PDF
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2002

Visualizing Dynamic Molecular Conformations Proceedings of IEEE Visualization 2002, Robert J. Moorhead, Markus Gross, Kenneth I. Joy (Eds.), pp. 235-242, 2002 Johannes Schmidt-Ehrenberg, Daniel Baum, Hans-Christian Hege BibTeX
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2001

Visually stunning - Molecular conformations The Biochemist, 23(5), pp. 22-26, 2001 Johannes Schmidt-Ehrenberg, Daniel Baum, Hans-Christian Hege BibTeX

1999

Algorithms and Methods for the Visualization of Molecular Surfaces and Interfaces Master's thesis, Humboldt-Universität zu Berlin, Fachbereich für Informatik (W. Reisig) and ZIB (H.-C. Hege), 1999 Daniel Runge BibTeX