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Home Members Baum, Daniel, Dr.

Baum, Daniel, Dr.

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Contact

Position
Head of Research Group
Room
4005
Phone
+49 30 84185-293
Email
Email
Website
https://www.zib.de/members/baum
Birth name
Daniel Runge
Division
Mathematics of Complex Systems
Department
Visual and Data-Centric Computing
Group
Visual Data Analysis

Projects

Projects as Head

MATH+ AA1-20

Geometric Learning for Single-Cell RNA Velocity Modeling

Recent advances in Single-Cell RNA sequencing allow to infer both the gene expression of a cell and the so-called "velocity vector" initializing the changes in that...

Geometric Learning for Single-Cell RNA Velocity Modeling
RobustCircuit logo wide

RobustCircuit

RobustCircuit is a collaborative project of 13 research teams pursuing eight neurobiological projects at five different institutions. The goal of the project is to...

RobustCircuit
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CTcoral

CTcoral is a co­oper­a­tion pro­jet with the MARUM institute in Bremen.Con­tact per­son at MARUM: Jürgen TitschackFrame­work-form­ing cold-wa­ter cor­als (CWC) are im...

CTcoral
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A Soft-Correspondence Approach to Shape Analysis

Despite many advances, frameworks for geometric morphometry still rely on point-to-point correspondences between shapes, either explicitly in form of homologous landmarks...

A Soft-Correspondence Approach to Shape Analysis

Projects as Member

HPO

HPO-NAVI

The complexity of sustainably developing research software is still largely underrated and the question how to guarantee visibility and fair attribution of these efforts...

HPO-NAVI
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Visual Analysis of Energy Flows in Biomolecular Systems

Recent pulsed-laser experiments on molecular complexes yield a time-resolved picture of the energy transport through molecular complexes. The data shows the coupling...

Visual Analysis of Energy Flows in Biomolecular Systems
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Collaborative Data Analysis for Microscopy

In biological research, microscopy is a powerful tool to investigate morphological changes in tissues and cell cultures. Modern setups are able to produce 100000 and more...

Collaborative Data Analysis for Microscopy
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Comparative Zoology

The project is part of the so called 'Basisprojekt' Attention & Form within the DFG Cluster of Excellence 'Bild Wissen Gestaltung'. The aim of the project is to analyze...

Comparative Zoology

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
Functional models from limited data: a parametric and multimodal approach to anatomy and 3D kinematics of feeding in basking sharks (Cetorhinus maximus) Anatomical Record, 2025 (accepted for publication) Tairan Li, Mike Schindler, Martha Paskin, Venkata A. Surapaneni, Elliott Scott, Sabine Hauert, Nicholas Payne, David E. Cade, Jeremy A. Goldbogen, Frederik H. Mollen, Daniel Baum, Sean Hanna, Mason N. Dean BibTeX
Helmeted hornbill cranial kinesis: balancing mobility and stability in a high-impact joint The Anatomical Record, 2025 M Schindler, B Flaum, VA Surapaneni, K Hayat, J Wölfer, D Baum, R Hu, TF Kong, M Doube, MN Dean 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, 1544(1), pp. 78-91, 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
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
DOI
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
DOI
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
DOI
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
DOI
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
DOI
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)
BibTeX
DOI
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)
BibTeX
DOI
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
DOI
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
DOI
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
DOI
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)
BibTeX
DOI
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
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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