657
deu
reportzib
0
2001-10-21
2001-10-21
--
Anisotrope Materialmodellierung für den menschlichen Unterkiefer
Im Rahmen der biomechanischen Simulation knöcherner Organe ist die Frage nach einer befriedigenden Materialbeschreibung nach wie vor ungelöst. Computertomographische Datensätze liefern eine räumliche Verteilung der (Röntgen-)Dichte und ermöglichen damit eine gute Darstellung der individuellen Geometrie. Weiter können die verschiedenen Materialbestandteile des Knochens, Spongiosa und Kortikalis, voneinander getrennt werden. Aber die richtungsabängige Information der Materialanisotropie ist verloren. In dieser Arbeit wird ein Ansatz für eine anisotrope Materialbeschreibung vorgestellt, die es ermöglicht, den Einfluss der individuellen knöchernen Struktur auf das makroskopische Materialverhalten abzuschätzen.
01-31
658
urn:nbn:de:0297-zib-6574
Erschienen in: Die Methode der Finiten Elemente in der Biomechanik, Biomedizin und angrenzenden Gebieten, Workshop '01, Univ. Ulm, 23./24.7.2001
Cornelia Kober
Robert Sader
Hans-Florian Zeilhofer
Steffen Prohaska
Stefan Zachow
Peter Deuflhard
ZIB-Report
01-31
deu
uncontrolled
menschlicher Unterkiefer
deu
uncontrolled
Simulation mit der Methode der finiten Elemente
deu
uncontrolled
innerer Aufbau des Knochens
deu
uncontrolled
anisotrope Elastizität
Informatik, Informationswissenschaft, allgemeine Werke
Linear elasticity with initial stresses
ZIB Allgemein
Deuflhard, Peter
Prohaska, Steffen
Zachow, Stefan
https://opus4.kobv.de/opus4-zib/files/657/ZR-01-31.ps
https://opus4.kobv.de/opus4-zib/files/657/ZR-01-31.pdf
1103
2008
eng
reportzib
0
2008-12-12
2008-12-12
--
Dual Streamline Seeding - Method and Implementation
This work introduces a novel streamline seeding technique based on dual streamlines that are orthogonal to the vector field, instead of tangential. The greedy algorithm presented here produces a net of orthogonal streamlines that is iteratively refined resulting in good domain coverage and a high degree of continuity and uniformity. The algorithm is easy to implement and efficient, and it naturally extends to curved surfaces.
In dieser Arbeit wird eine neue Strategie zur Platzierung von Stromlinien vorgestellt. Hierzu werden zusätzliche duale Stromlinien verwendet, die --im Gegensatz zur üblichen Definition-- orthogonal zum Vektorfeld verlaufen. Der vorgestellte Greedy-Algorithmus berechnet ein Netz aus orthogonalen Stromlinien, welches iterativ verfeinert wird, was zu einer guten Abdeckung der Domäne und einer gleichmäßigen Verteilung der Stromlinien führt. Es handelt sich um einen einfach zu implementierenden und effizienten Algorithmus, der direkt auf gekrümmten Oberflächen anwendbar ist.
08-49
1438-0064
1141
urn:nbn:de:0297-zib-11032
Appeared in: Proceedings of the IEEE Pacific Visualization Symposium (P. Eades, T. Ertl und H.-W. Shen, Hg.), 2009, S. 9–16.
Olufemi Rosanwo
unknown unknown
Christoph Petz
Steffen Prohaska
Ingrid Hotz
Hans-Christian Hege
ZIB-Report
08-49
Datenverarbeitung; Informatik
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Hege, Hans-Christian
Prohaska, Steffen
FLOW-VIS
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/1103/DualSeeding.pdf
5091
deu
reportzib
0
--
2014-07-03
--
Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben
Kurzfassung. Durch die Alkalität des Betons wird Betonstahl dauerhaft vor
Korrosion geschützt. Infolge von Chlorideintrag kann dieser Schutz nicht länger
aufrechterhalten werden und führt zu Lochkorrosion. Die zerstörungsfreie Prüfung
von Stahlbetonproben mit 3D-CT bietet die Möglichkeit, eine Probe mehrfach
gezielt vorzuschädigen und den Korrosionsfortschritt zu untersuchen. Zur Quantifizierung
des Schädigungsgrades müssen die bei dieser Untersuchung anfallenden
großen Bilddaten mit Bildverarbeitungsmethoden ausgewertet werden. Ein wesentlicher
Schritt dabei ist die Segmentierung der Bilddaten, bei der zwischen Korrosionsprodukt
(Rost), Betonstahl (BSt), Beton, Rissen, Poren und Umgebung
unterschieden werden muss. Diese Segmentierung bildet die Grundlage für statistische
Untersuchungen des Schädigungsfortschritts. Hierbei sind die Änderung
der BSt-Geometrie, die Zunahme von Korrosionsprodukten und deren Veränderung
über die Zeit sowie ihrer räumlichen Verteilung in der Probe von Interesse. Aufgrund
der Größe der CT-Bilddaten ist eine manuelle Segmentierung nicht durchführbar,
so dass automatische Verfahren unabdingbar sind. Dabei ist insbesondere
die Segmentierung der Korrosionsprodukte in den Bilddaten ein schwieriges
Problem. Allein aufgrund der Grauwerte ist eine Zuordnung nahezu unmöglich,
denn die Grauwerte von Beton und Korrosionsprodukt unterscheiden sich kaum.
Eine formbasierte Suche ist nicht offensichtlich, da die Korrosionsprodukte in Beton
diffuse Formen haben.
Allerdings lässt sich Vorwissen über die Ausbreitung der Korrosionsprodukte
nutzen. Sie bilden sich in räumlicher Nähe des BSt (in Bereichen vorheriger
Volumenabnahme des BSt), entlang von Rissen sowie in Porenräumen, die direkt
am BSt und in dessen Nahbereich liegen. Davon ausgehend wird vor der
Korrosionsprodukterkennung zunächst eine BSt-Volumen-, Riss- und Porenerkennung
durchgeführt. Dieser in der Arbeit näher beschriebene Schritt erlaubt es, halbautomatisch
Startpunkte (Seed Points) für die Korrosionsprodukterkennung zu
finden. Weiterhin werden verschiedene in der Bildverarbeitung bekannte
Algorithmen auf ihre Eignung untersucht werden.
1438-0064
urn:nbn:de:0297-zib-50912
To appear in: DGZfP-Jahrestagung 2014 Konferenzband
Olaf Paetsch
Regine Kossick
Daniel Baum
Gino Ebell
Karsten Ehrig
Andreas Heyn
Dietmar Meinel
Steffen Prohaska
ZIB-Report
14-24
deu
uncontrolled
Beton
deu
uncontrolled
Korrosionserkennung
deu
uncontrolled
Bildverarbeitung
deu
uncontrolled
Computertomografie
eng
uncontrolled
concrete
eng
uncontrolled
corrosiondetection
eng
uncontrolled
image processing
eng
uncontrolled
computed tomography
Image processing
Visual Data Analysis
Baum, Daniel
Paetsch, Olaf
Prohaska, Steffen
BAM-CORROSION
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/5091/ZR-14-24.pdf
5129
2014
eng
261
278
18
incollection
Springer
0
--
--
--
The Segmentation of Microtubules in Electron Tomograms Using Amira
Mitosis: Methods and Protocols
10.1007/978-1-4939-0329-0_12
Methods in Molecular Biology
no
Stefanie Redemann
Steffen Prohaska
Britta Weber
Marit Möller
Jean-Marc Verbavatz
Anthony Hyman
Daniel Baum
Steffen Prohaska
Thomas Müller-Reichert
Visual Data Analysis
Image Analysis in Biology and Materials Science
Baum, Daniel
Prohaska, Steffen
MICROTUBULES
SPINDLE
Visual and Data-centric Computing
5130
2015
eng
other
0
--
--
--
NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases
bioRxiv preprint
10.1101/006346
no
appeared in Neuron https://doi.org/10.1016/j.neuron.2016.06.012
Marta Costa
Steffen Prohaska
Aaron D. Ostrovsky
James D. Manton
Steffen Prohaska
Gregory S.X.E. Jefferis
Visual Data Analysis
Image Analysis in Biology and Materials Science
Prohaska, Steffen
no-project
Visual and Data-centric Computing
6578
eng
reportzib
0
--
2017-11-14
--
Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage
Introduction – Many biological structures show recurring tiling patterns on one structural level or the other. Current image acquisition techniques are able to resolve those tiling patterns to allow quantitative analyses. The resulting image data, however, may contain an enormous number of elements. This renders manual image analysis infeasible, in particular when statistical analysis is to be conducted, requiring a larger number of image data to be analyzed. As a consequence, the analysis process needs to be automated to a large degree. In this paper, we describe a multi-step image segmentation pipeline for the automated segmentation of the calcified cartilage into individual tesserae from computed tomography images of skeletal elements of stingrays.
Methods – Besides applying state-of-the-art algorithms like anisotropic diffusion smoothing, local thresholding for foreground segmentation, distance map calculation, and hierarchical watershed, we exploit a graph-based representation for fast correction of the segmentation. In addition, we propose a new distance map that is computed only in the plane that locally best approximates the calcified cartilage. This distance map drastically improves the separation of individual tesserae. We apply our segmentation pipeline to hyomandibulae from three individuals of the round stingray (Urobatis halleri), varying both in age and size.
Results – Each of the hyomandibula datasets contains approximately 3000 tesserae. To evaluate the quality of the automated segmentation, four expert users manually generated ground truth segmentations of small parts of one hyomandibula. These ground truth segmentations allowed us to compare the segmentation quality w.r.t. individual tesserae. Additionally, to investigate the segmentation quality of whole skeletal elements, landmarks were manually placed on all tesserae and their positions were then compared to the segmented tesserae. With the proposed segmentation pipeline, we sped up the processing of a single skeletal element from days or weeks to a few hours.
1438-0064
urn:nbn:de:0297-zib-65785
David Knötel
David Knötel
Ronald Seidel
Steffen Prohaska
Mason N. Dean
Daniel Baum
ZIB-Report
17-62
eng
uncontrolled
micro-CT
eng
uncontrolled
image segmentation
eng
uncontrolled
2D distance map
eng
uncontrolled
hierarchical watershed
eng
uncontrolled
stingray
eng
uncontrolled
tesserae
eng
uncontrolled
biological tilings
eng
uncontrolled
Amira
Visual Data Analysis
Baum, Daniel
Knötel, David
Prohaska, Steffen
TESSERAE
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/6578/ZIB-Report_17-62.pdf
3611
2012
2012
eng
25
28
conferenceobject
Eurographics Association
Brighton, UK
0
--
--
--
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
10.2312/PE/VAST/VAST12S/025-028
http://diglib.eg.org/EG/DL/PE/VAST/VAST12S/025-028.pdf
yes
Marco Klindt
David Arnold
Steffen Prohaska
Jaime Kaminski
Daniel Baum
Franco Niccolucci
Hans-Christian Hege
Andre Stork
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Baum, Daniel
Hege, Hans-Christian
Klindt, Marco
Prohaska, Steffen
PERGAMON
Visual and Data-centric Computing
3612
2012
2012
eng
150
155
conferenceobject
Gesellschaft zur Förderung angewandter Informatik e.V.
Volmerstraße 3, 12489 Berlin
0
--
--
--
iCon.text – a customizable iPad app for kiosk applications in museum exhibitions
EVA 2012 Berlin
urn:nbn:de:0297-zib-17731
no
Marco Klindt
Daniel Baum
Steffen Prohaska
Hans-Christian Hege
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Baum, Daniel
Hege, Hans-Christian
Klindt, Marco
Prohaska, Steffen
PERGAMON
Visual and Data-centric Computing
3877
2005
2005
eng
820
830
9-12
56
article
0
--
--
--
Quantification of spatial structure of human proximal tibial bone biopsies using 3D measures of complexity
Acta Astronautica
10.1016/j.actaastro.2005.01.007
Peter Saparin
Jesper Thomsen
Steffen Prohaska
Alexei Zaikin
Jürgen Kurths
Hans-Christian Hege
Wolfgang Gowin
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
3924
2003
2003
eng
7
conferenceobject
Banff, Alberta, Canada
0
--
--
--
A Virtual Laboratory for Assessment of Bone Biopsies
14th IAA Humans in Space Symposium
Steffen Prohaska
Hans-Christian Hege
Michael Giehl
Wolfgang Gowin
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
3884
2004
2004
eng
463
41
article
0
--
--
--
3-D reconstruction of tumor vascular networks
J. Vas. Res.
Steffen Prohaska
Matthew Dreher
Mark Dewhirst
Ashutosh Chilkoti
Axel Pries
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Prohaska, Steffen
Visual and Data-centric Computing
3885
2004
2004
eng
345
352
conferenceobject
Austin, Texas
0
--
--
--
Interactive exploration of large remote micro-CT scans
Proc. IEEE Visualization 2004
10.1109/VIS.2004.51
Steffen Prohaska
Andrei Hutanu
Ralf Kähler
Hans-Christian Hege
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
3886
2004
2004
eng
89
92
conferenceobject
Arlington, Virginia
0
--
--
--
Skeletonization by blocks for large 3D datasets: Application to brain microcirculation
IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI'04)
10.1109/ISBI.2004.1398481
Céline Fouard
Grégoire Malandain
Steffen Prohaska
Malte Westerhoff
Francis Cassot
Christophe Mazel
Didier Asselot
Jean-Pierre Marc-Vergnes
Visual Data Analysis
Image Analysis in Biology and Materials Science
Prohaska, Steffen
Visual and Data-centric Computing
3887
2004
2004
eng
conferenceobject
Toulouse, France
0
--
--
--
Squelettisation par blocs pour des grands volumes de données 3D
Reconnaissance des Formes et Intelligence Artificielle (RFIA 2004)
Céline Fouard
Grégoire Malandain
Steffen Prohaska
Malte Westerhoff
Francis Cassot
Christophe Mazel
Didier Asselot
Jean-Pierre Marc-Vergnes
Visual Data Analysis
Image Analysis in Biology and Materials Science
Prohaska, Steffen
Visual and Data-centric Computing
3946
2002
2002
eng
29
36
conferenceobject
IEEE Computer Society Press
Boston MA, USA
IEEE Computer Society
0
--
--
--
Fast Visualization of Plane-Like Structures in Voxel Data
Proceedings of IEEE Visualization 2002
10.1109/VISUAL.2002.1183753
Steffen Prohaska
Robert J. Moorhead
Hans-Christian Hege
Markus Gross
Kenneth I. Joy
Visual Data Analysis
Image Analysis in Biology and Materials Science
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
3956
2002
2002
eng
conferenceobject
Kanazawa University
Kanazawa City, Ishikawa, Japan
0
--
--
--
From Image Data to Three-Dimensional Models - Case Studies on the Impact of 3D Patient Models
Proceedings of the Japan Korea Computer Graphics Conference 2002
Hans-Christian Hege
Hartmut Schirmacher
Malte Westerhoff
Hans Lamecker
Steffen Prohaska
Stefan Zachow
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Therapy Planning
Hege, Hans-Christian
Lamecker, Hans
Prohaska, Steffen
Zachow, Stefan
MATHEON-F2
Visual and Data-centric Computing
3957
2002
2002
eng
171
172
9 (1)
article
0
--
--
--
Visual Analysis of Trabecular Bone Structure
Journal of Gravitational Physiology
Steffen Prohaska
Hans-Christian Hege
Michael Giehl
Wolfgang Gowin
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
3958
2002
2002
eng
other
0
--
--
--
Regional Structural Skeletal Discordance Assessed by Measures of Complexity
Wolfgang Gowin
Peter Saparin
Dieter Felsenberg
Jürgen Kurths
Alexei Zaikin
Steffen Prohaska
Hans-Christian Hege
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
3959
2002
2002
eng
175
176
9
article
0
--
--
--
Bone Modeling and Structural Measures of Complexity
Journal of Gravitational Physiology
10.1016/j.actaastro.2005.01.007
Alexei Zaikin
Peter Saparin
Steffen Prohaska
Jürgen Kurths
Wolfgang Gowin
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Prohaska, Steffen
Visual and Data-centric Computing
3960
2002
2002
eng
26
73
article
0
--
--
--
Femoral Neck Fractures: Reasons for the Most Common Location of Fractures
Acta Orthop. Scand. (Suppl. 304)
Wolfgang Gowin
Peter Saparin
Steffen Prohaska
Hans-Christian Hege
Dieter Felsenberg
Visual Data Analysis
Image Analysis in Biology and Materials Science
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
3925
2003
2003
eng
conferenceobject
Banff, Alberta, Canada
0
--
--
--
Quantification of Changes in Spatial Structure of Human Bone Biopsies Using 3D Measures of Complexity
14th IAA Humans in Space Symposium
Peter Saparin
Wolfgang Gowin
Alexei Zaikin
Jesper Thomsen
Steffen Prohaska
Hans-Christian Hege
Jürgen Kurths
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
3927
2003
2003
eng
conferenceobject
Berlin-Adlershof
0
--
--
--
Interactive Visualization to Support Quantification of Bone Biopsies
2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’
Steffen Prohaska
Hans-Christian Hege
Michael Giehl
Wolfgang Gowin
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
3928
2003
2003
eng
conferenceobject
Berlin-Adlershof
0
--
--
--
Quantification of changes in human bone structure at different skeletal locations using measures of complexity
2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’
Peter Saparin
Wolfgang Gowin
Alexei Zaikin
Steffen Prohaska
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Prohaska, Steffen
Visual and Data-centric Computing
3932
2003
2003
eng
conferenceobject
Berlin-Adlershof
0
--
--
--
Architectural Reasons for the Femoral Neck Fracture Location
2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’
Wolfgang Gowin
Peter Saparin
Steffen Prohaska
Hans-Christian Hege
Stefan Belle
Dieter Felsenberg
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
3933
2003
2003
eng
conferenceobject
Berlin-Adlershof
0
--
--
--
2D and 3D bone modelling for analysis of changes in the bone architecture and for evaluation of structural measures.
2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’
Alexei Zaikin
Peter Saparin
Steffen Prohaska
Jürgen Kurths
Wolfgang Gowin
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Prohaska, Steffen
Visual and Data-centric Computing
3934
2003
2003
eng
conferenceobject
Berlin-Adlershof
0
--
--
--
Comparison between Static Histomorphometric Measures Conducted by Traditionally 2D Histomorphometry and 3D μ-CT in Human Tibial Biopsies
2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’
Jesper Thomsen
Bruno Koller
Andreas Laib
Steffen Prohaska
Michael Giehl
Wolfgang Gowin
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Prohaska, Steffen
Visual and Data-centric Computing
3906
2004
2004
eng
145
150
conferenceobject
Sendai, Japan
0
--
--
--
Distributed visualization and analysis of fluid dynamics data
Proc. Fourth International Symposium on Advanced Fluid Information and Transdisciplinary Fluid Integration
Hans-Christian Hege
Tino Weinkauf
Steffen Prohaska
Andrei Hutanu
Visual Data Analysis
Image Analysis in Biology and Materials Science
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
3653
2012
2012
eng
135
144
177
article
0
--
--
--
Automated segmentation of electron tomograms for a quantitative description of actin filament networks
Journal of Structural Biology
10.1016/j.jsb.2011.08.012
yes
Alexander Rigort
David Günther
Reiner Hegerl
Daniel Baum
Britta Weber
Steffen Prohaska
Ohad Medalia
Wolfgang Baumeister
Hans-Christian Hege
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Baum, Daniel
Hege, Hans-Christian
Prohaska, Steffen
MICROTUBULES
Visual and Data-centric Computing
3636
2012
2012
eng
345
352
conferenceobject
0
--
--
--
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)
yes
Ulrike Homberg
Daniel Baum
Steffen Prohaska
Ute Kalbe
Karl Josef Witt
Visual Data Analysis
Image Analysis in Biology and Materials Science
Baum, Daniel
Prohaska, Steffen
PORESPACE
Visual and Data-centric Computing
3643
2012
2012
eng
129
138
2
178
article
0
--
--
--
Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos
Journal of Structural Biology
10.1016/j.jsb.2011.12.004
http://www.sciencedirect.com/science/article/pii/S1047847711003509
yes
Britta Weber
Garrett Greenan
Steffen Prohaska
Daniel Baum
Hans-Christian Hege
Thomas Müller-Reichert
Anthony Hyman
Jean-Marc Verbavatz
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Baum, Daniel
Hege, Hans-Christian
Prohaska, Steffen
MICROTUBULES
SPINDLE
Visual and Data-centric Computing
3652
2011
2011
eng
16125
16138
45
31
article
0
--
--
--
Large-scale automated histology in the pursuit of connectomes
Journal of Neuroscience
10.1523/JNEUROSCI.4077-11.2011
http://www.zib.de/prohaska/docs/Kleinfeld_JNS_Connectomes_2011.pdf
yes
David Kleinfeld
Arjun Bharioke
Pablo Blinder
David Bock
Kevin Briggman
Dmitri Chklovskii
Winfried Denk
Moritz Helmstaedter
John Kaufhold
Wei-Chung Lee
Hanno Meyer
Kristina Micheva
Marcel Oberlaender
Steffen Prohaska
R. Reid
Stephen Smith
Shinya Takemura
Philbert Tsai
Bert Sakmann
Visual Data Analysis
Image Analysis in Biology and Materials Science
Prohaska, Steffen
ENTIRE-MOUSE-BRAIN
Visual and Data-centric Computing
3709
2010
2010
eng
943
952
29
article
0
--
--
--
Accelerated Visualization of Dynamic Molecular Surfaces
Comput. Graph. Forum
10.1111/j.1467-8659.2009.01693.x
yes
Norbert Lindow
Daniel Baum
Steffen Prohaska
Hans-Christian Hege
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Baum, Daniel
Hege, Hans-Christian
Lindow, Norbert
Prohaska, Steffen
MOL-ANALYSIS
Visual and Data-centric Computing
3710
2010
2010
eng
198
208
6327
conferenceobject
Springer
0
--
--
--
TADD: A Computational Framework for Data Analysis Using Discrete Morse Theory
Mathematical Software - ICMS 2010
10.1007/978-3-642-15582-6_35
Lecture Notes in Computer Science
yes
Jan Reininghaus
David Günther
Ingrid Hotz
Steffen Prohaska
Hans-Christian Hege
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Vergleichende Visualisierung
Hege, Hans-Christian
Prohaska, Steffen
CVT
Visual and Data-centric Computing
3712
2010
2010
eng
1003
1012
29
article
0
--
--
--
Effective Techniques to Visualize Filament-Surface Relationships
Comput. Graph. Forum
yes
http://www.zib.de/visual-publications/sources/src-2010/Kuss_EuroVis2010.pdf
Anja Kuß
Maria Gensel
Björn Meyer
Vincent J. Dercksen
Steffen Prohaska
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Prohaska, Steffen
Neuro
DIGINEURO
Visual and Data-centric Computing
3607
2014
2014
eng
235
248
incollection
Springer
0
--
--
--
Definition, Extraction, and Validation of Pore Structures in Porous Materials
Topological Methods in Data Analysis and Visualization III
Theory, Algorithms, and Applications
10.1007/978-3-319-04099-8_15
yes
urn:nbn:de:0297-zib-42510
Ulrike Homberg
Peer-Timo Bremer
Daniel Baum
Ingrid Hotz
Alexander Wiebel
Valerio Pascucci
Steffen Prohaska
Ronald Peikert
Hans-Christian Hege
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Baum, Daniel
Hege, Hans-Christian
Prohaska, Steffen
BAM-ASPHALT
PORESPACE
Visual and Data-centric Computing
3739
2009
2009
eng
9
16
conferenceobject
Beijing, China
0
--
--
--
Dual Streamline Seeding
Proceedings of the IEEE Pacific Visualization Symposium
urn:nbn:de:0297-zib-11032
yes
Olufemi Rosanwo
Peter Eades
Christoph Petz
Thomas Ertl
Steffen Prohaska
Han-Wei Shen
Ingrid Hotz
Hans-Christian Hege
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Hege, Hans-Christian
Prohaska, Steffen
FLOW-VIS
Visual and Data-centric Computing
3747
2009
2009
eng
37
52
21
conferenceobject
0
--
--
--
Determining Geometric Grain Structure from X-Ray Micro-Tomograms of Gradated Soil
Workshop Internal Erosion
Schriftenreihe Geotechnik
no
Ulrike Homberg
Richard Binner
Steffen Prohaska
Vincent J. Dercksen
Anja Kuß
Ute Kalbe
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Prohaska, Steffen
PORESPACE
Visual and Data-centric Computing
5809
2015
eng
conferenceobject
0
--
--
--
3D Corrosion Detection in Time-dependent CT Images of Concrete
In civil engineering, the corrosion of steel reinforcements in structural elements of concrete bares a risk of
stability-reduction, mainly caused by the exposure to chlorides. 3D computed tomography (CT) reveals the inner
structure of concrete and allows one to investigate the corrosion with non-destructive testing methods. To carry
out such investigations, specimens with a large artificial crack and an embedded steel rebar have been
manufactured. 3D CT images of those specimens were acquired in the original state. Subsequently three cycles
of electrochemical pre-damaging together with CT imaging were applied. These time series have been evaluated
by means of image processing algorithms to segment and quantify the corrosion products. Visualization of the
results supports the understanding of how corrosion propagates into cracks and pores. Furthermore, pitting of
structural elements can be seen without dismantling. In this work, several image processing and visualization
techniques are presented that have turned out to be particularly effective for the visualization and segmentation
of corrosion products. Their combination to a workflow for corrosion analysis is the main contribution of this
work.
DIR-2015 Proceedings
http://www.ndt.net/events/DIR2015/app/content/Paper/36_Paetsch.pdf
no
Olaf Paetsch
Olaf Paetsch
Daniel Baum
Steffen Prohaska
Karsten Ehrig
Dietmar Meinel
Gino Ebell
Visual Data Analysis
Baum, Daniel
Paetsch, Olaf
Prohaska, Steffen
BAM-CORROSION
Visual and Data-centric Computing
4251
2013
eng
reportzib
0
2013-09-19
2013-09-19
--
Definition, Extraction, and Validation of Pore Structures in Porous Materials
An intuitive and sparse representation of the void space of porous materials supports the efficient analysis and visualization of interesting qualitative and quantitative parameters of such materials. We introduce definitions of the elements of this void space, here called pore space, based on its distance function, and present methods to extract these elements using the extremal structures of the distance function. The presented methods are implemented by an image processing pipeline that determines pore centers, pore paths and pore constrictions. These pore space elements build a graph that represents the topology of the pore space in a compact way. The representations we derive from μCT image data of realistic soil specimens enable the computation of many statistical parameters and, thus, provide a basis for further visual analysis and application-specific developments. We introduced parts of our pipeline in previous work. In this chapter, we present additional details and compare our results with the analytic computation of the pore space elements for a sphere packing in order to show the correctness of our graph computation.
1438-0064
urn:nbn:de:0297-zib-42510
no
Appeared in: Topological Methods in Data Analysis and Visualization III
Ulrike Homberg
Ulrike Homberg
Daniel Baum
Alexander Wiebel
Steffen Prohaska
Hans-Christian Hege
ZIB-Report
13-56
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Baum, Daniel
Hege, Hans-Christian
Prohaska, Steffen
PORESPACE
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/4251/ZR-13-56.pdf
6400
eng
reportzib
0
--
2017-05-15
--
Adapting trabecular structures for 3D printing: an image processing approach based on µCT data
Materials with a trabecular structure notably combine advantages such as lightweight, reasonable strength, and permeability for fluids. This combination of advantages is especially interesting for tissue engineering in trauma surgery and orthopedics. Bone-substituting scaffolds for instance are designed with a trabecular structure in order to allow cell migration for bone ingrowth and vascularization. An emerging and recently very popular technology to produce such complex, porous structures is 3D printing. However, several technological aspects regarding the scaffold architecture, the printable resolution, and the feature size have to be considered when fabricating scaffolds for bone tissue replacement and regeneration.
Here, we present a strategy to assess and prepare realistic trabecular structures for 3D printing using image analysis with the aim of preserving the structural elements. We discuss critical conditions of the printing system and present a 3-stage approach to adapt a trabecular structure from $\mu$CT data while incorporating knowledge about the printing system. In the first stage, an image-based extraction of solid and void structures is performed, which results in voxel- and graph-based representations of the extracted structures. These representations not only allow us to quantify geometrical properties such as pore size or strut geometry and length. But, since the graph represents the geometry and the topology of the initial structure, it can be used in the second stage to modify and adjust feature size, volume and sample size in an easy and consistent way. In the final reconstruction stage, the graph is then converted into a voxel representation preserving the topology of the initial structure. This stage generates a model with respect to the printing conditions to ensure a stable and controlled voxel placement during the printing process.
1438-0064
urn:nbn:de:0297-zib-64004
no
Appeared in: Biomedical Physics & Engineering Express
Ulrike Homberg
Ulrike Homberg
Daniel Baum
Steffen Prohaska
Jens Günster
Stefanie Krauß-Schüler
ZIB-Report
17-26
eng
uncontrolled
trabecular structures
eng
uncontrolled
image-based analysis
eng
uncontrolled
additive manufacturing
eng
uncontrolled
printability
Visual Data Analysis
Baum, Daniel
Prohaska, Steffen
BAM-3D-PRINTING
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/6400/ZIB-Report_17-26.pdf
6417
2017
2017
eng
15288
8
article
0
2017-05-11
2017-05-11
--
C. elegans chromosomes connect to centrosomes by anchoring into the spindle network
The mitotic spindle ensures the faithful segregation of chromosomes. Here we combine the first large-scale serial electron tomography of whole mitotic spindles in early C. elegans embryos with live-cell imaging to reconstruct all microtubules in 3D and identify their plus- and minus-ends. We classify them as kinetochore (KMTs), spindle (SMTs) or astral microtubules (AMTs) according to their positions, and quantify distinct properties of each class. While our light microscopy and mutant studies show that microtubules are nucleated from the centrosomes, we find only a few KMTs directly connected to the centrosomes. Indeed, by quantitatively analysing several models of microtubule growth, we conclude that minus-ends of KMTs have selectively detached and depolymerized from the centrosome. In toto, our results show that the connection between centrosomes and chromosomes is mediated by an anchoring into the entire spindle network and that any direct connections through KMTs are few and likely very transient.
Nature Communications
10.1038/ncomms15288
yes
Stefanie Redemann
Norbert Lindow
Johannes Baumgart
Norbert Lindow
Michael Shelley
Ehssan Nazockdast
Andrea Kratz
Steffen Prohaska
Jan Brugués
Sebastian Fürthauer
Thomas Müller-Reichert
Visual Data Analysis
Kratz, Andrea
Lindow, Norbert
Prohaska, Steffen
SPINDLE
Visual and Data-centric Computing
6422
2017
eng
3
3
article
IOP Publishing
0
--
--
--
Adapting trabecular structures for 3D printing: an image processing approach based on µCT data
Materials with a trabecular structure notably combine advantages such as lightweight, reasonable strength, and permeability for fluids. This combination of advantages is especially interesting for tissue engineering in trauma surgery and orthopedics. Bone-substituting scaffolds for instance are designed with a trabecular structure in order to allow cell migration for bone ingrowth and vascularization. An emerging and recently very popular technology to produce such complex, porous structures is 3D printing. However, several technological aspects regarding the scaffold architecture, the printable resolution, and the feature size have to be considered when fabricating scaffolds for bone tissue replacement and regeneration.
Here, we present a strategy to assess and prepare realistic trabecular structures for 3D printing using image analysis with the aim of preserving the structural elements. We discuss critical conditions of the printing system and present a 3-stage approach to adapt a trabecular structure from $\mu$CT data while incorporating knowledge about the printing system. In the first stage, an image-based extraction of solid and void structures is performed, which results in voxel- and graph-based representations of the extracted structures. These representations not only allow us to quantify geometrical properties such as pore size or strut geometry and length. But, since the graph represents the geometry and the topology of the initial structure, it can be used in the second stage to modify and adjust feature size, volume and sample size in an easy and consistent way. In the final reconstruction stage, the graph is then converted into a voxel representation preserving the topology of the initial structure. This stage generates a model with respect to the printing conditions to ensure a stable and controlled voxel placement during the printing process.
Biomedical Physics & Engineering Express
10.1088/2057-1976/aa7611
yes
urn:nbn:de:0297-zib-64004
Ulrike Homberg
Ulrike Homberg
Daniel Baum
Steffen Prohaska
Jens Günster
Stefanie Krauß-Schüler
Visual Data Analysis
Image Analysis in Biology and Materials Science
Baum, Daniel
Prohaska, Steffen
BAM-3D-PRINTING
Visual and Data-centric Computing
6305
eng
reportzib
0
--
2017-04-07
--
The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration
Surface structuring of titanium-based implants with appropriate nanotopographies can significantly modulate their impact on the biological behavior of cells populating these implants. Implant assisted bone tissue repair and regeneration require functional adhesion and expansion of bone progenitors. The surface nanotopography of implant materials used to support bone healing and its effect on cell behavior, in particular cell adhesion, spreading, expansion, and motility, is still not clearly understood. The aim of this study is to investigate preosteoblast proliferation, adhesion, morphology, and migration on different titanium materials with similar surface chemistry, but distinct nanotopographical features. Sonochemical treatment and anodic oxidation were employed to fabricate disordered – mesoporous titania (TMS), and ordered – titania nanotubular (TNT) topographies respectively. The morphological evaluation revealed a surface dependent shape, thickness, and spreading of cells owing to different adherence behavior. Cells were polygonal-shaped and well-spread on glass and TMS, but displayed an elongated fibroblast-like morphology on TNT surfaces. The cells on glass however, were much flatter than on nanostructured surfaces. Both nanostructured surfaces impaired cell adhesion, but TMS was more favorable for cell growth due to its support of cell attachment and spreading in contrast to TNT. Quantitative wound healing assay in combination with live-cell imaging revealed that cells seeded on TMS surfaces migrated in close proximity to neighboring cells and less directed when compared to the migratory behavior on other surfaces. The results indicate distinctly different cell adhesion and migration on ordered and disordered titania nanotopographies, providing important information that could be used in optimizing titanium-based scaffold design to foster bone tissue growth and repair.
1438-0064
urn:nbn:de:0297-zib-63053
10.1002/adhm.201601244
Appeared in: Advanced Healthcare Materials
Yulia Zhukova
Marc Osterland
Christian Hiepen
Petra Knaus
Marc Osterland
Steffen Prohaska
John W. C. Dunlop
Peter Fratzl
Ekaterina V. Skorb
ZIB-Report
17-06
BIOLOGY AND OTHER NATURAL SCIENCES
Visual Data Analysis
Prohaska, Steffen
FU-Images
Cellmigration
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/6305/zibreport_with_submitted_manuscript.pdf
5029
2014
deu
article
0
--
--
--
Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben
DGZfP-Jahrestagung 2014 Konferenzband
http://jt2014.dgzfp.de/portals/jt2014/BB/di1c3.pdf
yes
urn:nbn:de:0297-zib-50912
Olaf Paetsch
Olaf Paetsch
Daniel Baum
Steffen Prohaska
Karsten Ehrig
Gino Ebell
Dietmar Meinel
Andreas Heyn
Visual Data Analysis
Baum, Daniel
Paetsch, Olaf
Prohaska, Steffen
BAM-CORROSION
Visual and Data-centric Computing
6631
2017
eng
article
0
--
--
--
Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage
Introduction – Many biological structures show recurring tiling patterns on one structural level or the other. Current image acquisition techniques are able to resolve those tiling patterns to allow quantitative analyses. The resulting image data, however, may contain an enormous number of elements. This renders manual image analysis infeasible, in particular when statistical analysis is to be conducted, requiring a larger number of image data to be analyzed. As a consequence, the analysis process needs to be automated to a large degree. In this paper, we describe a multi-step image segmentation pipeline for the automated segmentation of the calcified cartilage into individual tesserae from computed tomography images of skeletal elements of stingrays.
Methods – Besides applying state-of-the-art algorithms like anisotropic diffusion smoothing, local thresholding for foreground segmentation, distance map calculation, and hierarchical watershed, we exploit a graph-based representation for fast correction of the segmentation. In addition, we propose a new distance map that is computed only in the plane that locally best approximates the calcified cartilage. This distance map drastically improves the separation of individual tesserae. We apply our segmentation pipeline to hyomandibulae from three individuals of the round stingray (Urobatis halleri), varying both in age and size.
Results – Each of the hyomandibula datasets contains approximately 3000 tesserae. To evaluate the quality of the automated segmentation, four expert users manually generated ground truth segmentations of small parts of one hyomandibula. These ground truth segmentations allowed us to compare the segmentation quality w.r.t. individual tesserae. Additionally, to investigate the segmentation quality of whole skeletal elements, landmarks were manually placed on all tesserae and their positions were then compared to the segmented tesserae. With the proposed segmentation pipeline, we sped up the processing of a single skeletal element from days or weeks to a few hours.
PLOS ONE
10.1371/journal.pone.0188018
yes
urn:nbn:de:0297-zib-65785
https://doi.org/10.12752/4.DKN.1.0
David Knötel
David Knötel
Ronald Seidel
Steffen Prohaska
Mason N. Dean
Daniel Baum
Visual Data Analysis
Image Analysis in Biology and Materials Science
Baum, Daniel
Knötel, David
Prohaska, Steffen
TESSERAE
Visual and Data-centric Computing
6652
2017
eng
researchdata
0
--
--
--
Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage (Supplementary Material)
Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data. In particular, sections from hyomandibulae harvested from specimens of round stingray Urobatis halleri, donated from another study (DOI: 10.1002/etc.2564). Specimens were from sub-adults/adults collected by beach seine from collection sites in San Diego and Seal Beach, California, USA. The hyomandibulae were mounted in clay, sealed in ethanol-humidified plastic tubes and scanned with a Skyscan 1172 desktop μCT scanner (Bruker μCT, Kontich, Belgium) in association with another study (DOI: 10.1111/joa.12508). Scans for all samples were performed with voxel sizes of 4.89 μm at 59 kV source voltage and 167 μA source current, over 360◦ sample 120 rotation. For our segmentations, the datasets were resampled to a voxel size of 9.78 μm to reduce the size of the images and speed up processing. In addition, the processed data that was generated with the visualization software Amira with techniques described in the related publication based on the mentioned specimens.
10.12752/4.DKN.1.0
Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data.
Dataset
San Diego and Seal Beach, California, USA
Urobatis halleri
2017
The data was processed with the visualization software Amira. See http://www.zib.de/software/tesserae-segmentation for information about Amira and how to download the Amira extension package created for this publication. See https://github.com/zibamira/tesserae-segmentation.git for the source code of the Amira extension package.
http://www.zib.de/ext-data/2017_Knoetel_PLOSONE-Supplementary-Material.zip
https://doi.org/10.1371/journal.pone.0188018
David Knötel
David Knötel
Ronald Seidel
Paul Zaslansky
Steffen Prohaska
Mason N. Dean
Daniel Baum
Visual Data Analysis
Image Analysis in Biology and Materials Science
Baum, Daniel
Knötel, David
Prohaska, Steffen
TESSERAE
Visual and Data-centric Computing
6656
eng
reportzib
0
--
2018-02-01
--
Quantification of Three-Dimensional Spindle Architecture
Mitotic and meiotic spindles are microtubule-based structures to faithfully segregate chromosomes. Electron tomography is currently the method of choice to analyze the three-dimensional architecture of both types of spindles. Over the years, we have developed methods and software for automatic segmentation and stitching of microtubules in serial sections for large-scale reconstructions. Three-dimensional reconstruction of microtubules, however, is only the first step towards biological insight. The second step is the analysis of the structural data to derive measurable spindle properties. Here, we present a comprehensive set of techniques to quantify spindle parameters. These techniques provide quantitative analyses of specific microtubule classes and are applicable to a variety of tomographic reconstructions of spindles from different organisms.
1438-0064
urn:nbn:de:0297-zib-66562
Norbert Lindow
Norbert Lindow
Stefanie Redemann
Gunar Fabig
Thomas Müller-Reichert
Steffen Prohaska
ZIB-Report
18-07
Visual Data Analysis
Lindow, Norbert
Prohaska, Steffen
SPINDLE
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/6656/zib-report-final.pdf
6202
2017
eng
article
0
2017-03-30
2017-03-30
--
The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration
Surface structuring of titanium-based implants with appropriate nanotopographies can significantly modulate their impact on the biological behavior of cells populating these implants. Implant assisted bone tissue repair and regeneration require functional adhesion and expansion of bone progenitors. The surface nanotopography of implant materials used to support bone healing and its effect on cell behavior, in particular cell adhesion, spreading, expansion, and motility, is still not clearly understood. The aim of this study is to investigate preosteoblast proliferation, adhesion, morphology, and migration on different titanium materials with similar surface chemistry, but distinct nanotopographical features. Sonochemical treatment and anodic oxidation were employed to fabricate disordered – mesoporous titania (TMS), and ordered – titania nanotubular (TNT) topographies respectively. The morphological evaluation revealed a surface dependent shape, thickness, and spreading of cells owing to different adherence behavior. Cells were polygonal-shaped and well-spread on glass and TMS, but displayed an elongated fibroblast-like morphology on TNT surfaces. The cells on glass however, were much flatter than on nanostructured surfaces. Both nanostructured surfaces impaired cell adhesion, but TMS was more favorable for cell growth due to its support of cell attachment and spreading in contrast to TNT. Quantitative wound healing assay in combination with live-cell imaging revealed that cells seeded on TMS surfaces migrated in close proximity to neighboring cells and less directed when compared to the migratory behavior on other surfaces. The results indicate distinctly different cell adhesion and migration on ordered and disordered titania nanotopographies, providing important information that could be used in optimizing titanium-based scaffold design to foster bone tissue growth and repair.
Advanced Healthcare Materials
10.1002/adhm.201601244
yes
urn:nbn:de:0297-zib-63053
Yulia Zhukova
Marc Osterland
Christian Hiepen
Petra Knaus
Marc Osterland
Steffen Prohaska
John W. C. Dunlop
Peter Fratzl
Ekaterina V. Skorb
Visual Data Analysis
Prohaska, Steffen
FU-Images
Cellmigration
Visual and Data-centric Computing
6232
2017
eng
100645J
100645J-13
10064
conferenceobject
0
--
--
--
Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography
The goal of quantitative photoacoustic tomography (qPAT) is to recover maps of the chromophore distributions from multiwavelength images of the initial pressure. Model-based inversions that incorporate the physical processes underlying the photoacoustic (PA) signal generation represent a promising approach. Monte-Carlo models of the light transport are computationally expensive, but provide accurate fluence distributions predictions, especially in the ballistic and quasi-ballistic regimes. Here, we focus on the inverse problem of 3D qPAT of blood oxygenation and investigate the application of the Monte-Carlo method in a model-based inversion scheme. A forward model of the light transport based on the MCX simulator and acoustic propagation modeled by the k-Wave toolbox was used to generate a PA image data set acquired in a tissue phantom over a planar detection geometry. The combination of the optical and acoustic models is shown to account for limited-view artifacts. In addition, the errors in the fluence due to, for example, partial volume artifacts and absorbers immediately adjacent to the region of interest are investigated. To accomplish large-scale inversions in 3D, the number of degrees of freedom is reduced by applying image segmentation to the initial pressure distribution to extract a limited number of regions with homogeneous optical parameters. The absorber concentration in the tissue phantom was estimated using a coordinate descent parameter search based on the comparison between measured and modeled PA spectra. The estimated relative concentrations using this approach lie within 5 % compared to the known concentrations. Finally, we discuss the feasibility of this approach to recover the blood oxygenation from experimental data.
Proc. of SPIE, Photons Plus Ultrasound: Imaging and Sensing 2017
10.1117/12.2251945
Proc. of SPIE
no
urn:nbn:de:0297-zib-62318
Bernhard Kaplan
Bernhard Kaplan
Jens Buchmann
Steffen Prohaska
Jan Laufer
Visual Data Analysis
Prohaska, Steffen
dfg-photom
Visual and Data-centric Computing
6268
2017
eng
1006416
1006416-8
10064
conferenceobject
0
--
--
--
Experimental validation of a Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography
Quantitative photoacoustic tomography (qPAT) aims to extract physiological parameters, such as blood oxygen saturation (sO2), from measured multi-wavelength image data sets. The challenge of this approach lies in the inherently nonlinear fluence distribution in the tissue, which has to be accounted for by using an appropriate model, and the large scale of the inverse problem. In addition, the accuracy of experimental and scanner-specific parameters, such as the wavelength dependence of the incident fluence, the acoustic detector response, the beam profile and divergence, needs to be considered. This study aims at quantitative imaging of blood sO2, as it has been shown to be a more robust parameter compared to absolute concentrations. We propose a Monte-Carlo–based inversion scheme in conjunction with a reduction in the number of variables achieved using image segmentation. The inversion scheme is experimentally validated in tissue-mimicking phantoms consisting of polymer tubes suspended in a scattering liquid. The tubes were filled with chromophore solutions at different concentration ratios. 3-D multi-spectral image data sets were acquired using a Fabry-Perot based PA scanner. A quantitative comparison of the measured data with the output of the forward model is presented. Parameter estimates of chromophore concentration ratios were found to be within 5 % of the true values.
Proc. of SPIE, Photons Plus Ultrasound: Imaging and Sensing
10.1117/12.2252359
Proc. of SPIE
no
Jens Buchmann
Bernhard Kaplan
Bernhard Kaplan
Steffen Prohaska
Jan Laufer
Visual Data Analysis
Prohaska, Steffen
dfg-photom
Visual and Data-centric Computing
5968
2016
eng
293
311
2
91
article
0
--
--
--
NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases
Neural circuit mapping is generating datasets of tens of thousands of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1,052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types, including searching neurons against transgene expression patterns. Finally, we show that NBLAST is effective with data from other invertebrates and zebrafish.
Neuron
10.1016/j.neuron.2016.06.012
yes
urn:nbn:de:0297-zib-59672
appeared also as bioRxiv preprint https://doi.org/10.1101/006346
Marta Costa
Steffen Prohaska
James D. Manton
Aaron D. Ostrovsky
Steffen Prohaska
Gregory S.X.E. Jefferis
Visual Data Analysis
Prohaska, Steffen
no-project
Visual and Data-centric Computing
5841
2015
eng
poster
0
--
--
--
Single Cell Tracking in Phase-Contrast Microscopy
In this work, we developed an automatic algorithm to analyze cell migration in chemotaxis assays, based on phase-contrast time-lapse microscopy. While manual approaches are still widely used in recent publications, our algorithm is able to track hundreds of single cells per frame. The extracted paths are analysed with traditional geometrical approaches as well as diffusion-driven Markov state models (MSM). Based on these models, a detailed view on spatial and temporal effects is possible.
Using our new approach on experimental data, we are able to distinguish between directed migration (e.g. towards a VEGF gradient) and random migration without favored direction. A calculation of the committor probabilities reveals that cells of the whole image area are more likely to migrate directly towards the VEGF than away from it during the first four hours. However, in absence of a chemoattractant, cells migrate more likely to their nearest image border. These conclusions are supported by the spatial mean directions.
In a next step, the cell-cell interaction during migration and the migration of cell clusters will be analyzed. Furthermore, we want to observe phenotypical changes during migration based on fluorescence microscopy and machine learning.
The algorithm is part of a collaborative platform which brings the experimental expertise of scientists from life sciences and the analytical knowledge of computer scientists together. This platform is built using web-based technologies with a responsive real-time user interface. All data, including raw and metadata as well as the accompanying results, will be stored in a secure and scalable compute cluster. The compute cluster provides sufficient space and computational power for modern image-based experiments and their analyses. Specific versions of data and results can be tagged to keep immutable records for archival.
EMBL Symposium 2015 - Seeing is Believing - Imaging the Processes of Life
no
Marc Osterland
Marc Osterland
Andreas Benn
Steffen Prohaska
Christof Schütte
Visual Data Analysis
Prohaska, Steffen
Schütte, Christof
MODAL-MedLab
FU-Images
MODAL-Gesamt
Cellmigration
Visual and Data-centric Computing
4576
2011
eng
conferenceobject
0
--
--
--
Osteocytes number and volume in osteoporotic and in healthy bone biopsies analysed using Synchrotron CT: a pilot study
Proc. ISB 2011
yes
Zully Ritter
Steffen Prohaska
Steffen Prohaska
R. Brand
A. Friedmann
Hans-Christian Hege
Jürgen Goebbels
Dieter Felsenberg
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
4579
2011
deu
conferenceobject
0
--
--
--
3-D-Visualisierung von Radar- und Ultraschallecho-Daten mit ZIBAmira
Proc. DGZfP-Jahrestagung 2011
no
Doreen Streicher
Olaf Paetsch
Olaf Paetsch
Robert Seiler
Steffen Prohaska
Martin Krause
Christian Boller
Visual Data Analysis
Paetsch, Olaf
Prohaska, Steffen
BAM-ECHOBETONVIZ
Visual and Data-centric Computing
3666
2012
2012
eng
15
29
incollection
Springer
0
--
--
--
Efficient Computation of a Hierarchy of Discrete 3D Gradient Vector Fields
Topological Methods in Data Analysis and Visualization II
10.1007/978-3-642-23175-9_2
Mathematics and Visualization
yes
David Günther
Ronny Peikert
Jan Reininghaus
Helwig Hauser
Steffen Prohaska
Hamish Carr
Tino Weinkauf
Hans-Christian Hege
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Vergleichende Visualisierung
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
3760
2008
2008
eng
177
184
conferenceobject
0
--
--
--
Ontology-Based Visualization of Hierarchical Neuroanatomical Structures
Proceedings of the Eurographics Workshop on Visual Computing for Biomedicine VCBM 2008
Anja Kuß
Steffen Prohaska
Björn Meyer
Jürgen Rybak
Hans-Christian Hege
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Hege, Hans-Christian
Prohaska, Steffen
DIGINEURO
Visual and Data-centric Computing
3766
2008
2008
eng
93
105
conferenceobject
Magdeburg, Germany
0
--
--
--
Near-Wall Flow Visualization in Flattened Surface Neighborhoods
Proc. Simulation and Visualization 2008
http://www.simvis.org/Tagung2008/sv-proceedings.html
Christoph Petz
Steffen Prohaska
Leonid Goubergrits
Ulrich Kertzscher
Hans-Christian Hege
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Hege, Hans-Christian
Prohaska, Steffen
FLOW-VIS
Visual and Data-centric Computing
3767
2008
2008
eng
735
742
3
27
article
Eindhoven, Netherlands
0
--
--
--
Extraction of feature Lines on surface meshes based on discrete Morse theory
Computer Graphics Forum
10.1111/j.1467-8659.2008.01202.x
Jan Sahner
Britta Weber
Hans Lamecker
Steffen Prohaska
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Lamecker, Hans
Prohaska, Steffen
MATHEON-F2
Visual and Data-centric Computing
3748
2009
2009
eng
53
60
21
conferenceobject
0
--
--
--
Modelling and Analysis of Particle and Pore Structures in Soils
Workshop Internal Erosion
Schriftenreihe Geotechnik
no
Tobias Mehlhorn
Steffen Prohaska
Ulrike Homberg
Volker Slowik
Visual Data Analysis
Image Analysis in Biology and Materials Science
Prohaska, Steffen
PORESPACE
Visual and Data-centric Computing
3749
2009
2009
eng
29
35
21
conferenceobject
0
--
--
--
Conditions for Suffosive Erosion Phemomena in Soils – Concept and Approach
Workshop Internal Erosion
Schriftenreihe Geotechnik
no
Olivier Semar
Richard Binner
Ulrike Homberg
Ute Kalbe
Tobias Mehlhorn
Steffen Prohaska
Volker Slowik
Karl Josef Witt
Visual Data Analysis
Image Analysis in Biology and Materials Science
Prohaska, Steffen
PORESPACE
Visual and Data-centric Computing
3694
2010
2010
eng
267
274
conferenceobject
0
--
--
--
Image-Error-Based Level of Detail for Landscape Visualization
Proc. VMV 2010
yes
Malte Clasen
Steffen Prohaska
Visual Data Analysis
Image Analysis in Biology and Materials Science
Prohaska, Steffen
Visual and Data-centric Computing
3679
2011
2011
eng
24
25
conferenceobject
0
--
--
--
Describing and Analyzing the Dual Structures of Porous Media
Proc. 3D-Microstructure Meeting
yes
Ulrike Homberg
Frank Mücklich
Daniel Baum
Philipp Slussallek
Steffen Prohaska
Katja Schladitz
Visual Data Analysis
Image Analysis in Biology and Materials Science
Baum, Daniel
Prohaska, Steffen
PORESPACE
Visual and Data-centric Computing
3680
2011
2011
eng
conferenceobject
0
--
--
--
Fast Tracing of Microtubule Centerlines in Electron Tomograms
BioVis 2011 Abstracts, 1st IEEE Symposium on Biological Data Visualization
yes
Britta Weber
Marit Möller
Jean-Marc Verbavatz
Daniel Baum
Hans-Christian Hege
Steffen Prohaska
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Baum, Daniel
Hege, Hans-Christian
Prohaska, Steffen
SPINDLE
Visual and Data-centric Computing
3682
2011
2011
eng
conferenceobject
0
--
--
--
Comparison of Crack Detection Methods for Analyzing Damage Processes in Concrete with Computed Tomography
International Symposium on Digital Industrial Radiology and Computed Tomography
no
Karsten Ehrig
Jürgen Goebbels
Dietmar Meinel
Olaf Paetsch
Steffen Prohaska
Valentin Zobel
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Paetsch, Olaf
Prohaska, Steffen
BAM-RISSBETON
Visual and Data-centric Computing
3733
2009
2009
eng
863
870
3
28
article
0
--
--
--
Hierarchical Vortex Regions in Swirling Flow
Computer Graphics Forum
yes
Christoph Petz
Jens Kasten
Steffen Prohaska
Hans-Christian Hege
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Hege, Hans-Christian
Prohaska, Steffen
FLOW-VIS
Visual and Data-centric Computing
3734
2009
2009
eng
971
974
conferenceobject
IEEE press
Boston, USA
0
--
--
--
Automatic alignment of stacks of filament data
Proc. IEEE International Symposium on Biomedical Imaging
yes
http://www.zib.de/visual-publications/sources/src-2009/DercksenFilamentAlign2009final.pdf
Vincent J. Dercksen
Britta Weber
David Günther
Marcel Oberlaender
Steffen Prohaska
Hans-Christian Hege
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Hege, Hans-Christian
Prohaska, Steffen
MICROTUBULES
Neuro
Visual and Data-centric Computing
3724
2009
2009
eng
conferenceobject
0
--
--
--
Using Ontologies for the Visualization of Hierarchical Neuroanatomical Structures
Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics
10.3389/conf.neuro.11.2009.08.017
no
Anja Kuß
Steffen Prohaska
Jürgen Rybak
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Prohaska, Steffen
DIGINEURO
Visual and Data-centric Computing
4385
2012
2012
deu
conferenceobject
0
--
--
--
Vergleich automatischer 3D-Risserkennungsmethoden für die quantitative Analyse der Schadensentwicklung in Betonproben mit Computer-Tomographie
Tagungsband der DACH Jahrestagung 2012
No
http://www.ndt.net/article/dgzfp2012/papers/mo2b2.pdf
Olaf Paetsch
Daniel Baum
Karsten Ehrig
Dietmar Meinel
Steffen Prohaska
Visual Data Analysis
Image Analysis in Biology and Materials Science
Baum, Daniel
Paetsch, Olaf
Prohaska, Steffen
BAM-RISSBETON
Visual and Data-centric Computing
4386
2013
2013
deu
conferenceobject
0
--
--
--
3-D-Visualisierung und statistische Analyse von Rissen in mit Computer-Tomographie untersuchten Betonproben
Tagungsband der DGZfP Jahrestagung 2013
No
http://www.ndt.net/article/dgzfp2013/papers/poster12.pdf
Olaf Paetsch
Daniel Baum
David Breßler
Karsten Ehrig
Dietmar Meinel
Steffen Prohaska
Visual Data Analysis
Image Analysis in Biology and Materials Science
Baum, Daniel
Paetsch, Olaf
Prohaska, Steffen
BAM-RISSBETON
Visual and Data-centric Computing
4387
2012
2012
eng
321
330
conferenceobject
0
--
--
--
Automated 3D Crack Detection for Analyzing Damage Processes in Concrete with Computed Tomography
Proceedings of Conference on Industrial Computed Tomography
No
Olaf Paetsch
Daniel Baum
Karsten Ehrig
Dietmar Meinel
Steffen Prohaska
Visual Data Analysis
Image Analysis in Biology and Materials Science
Baum, Daniel
Paetsch, Olaf
Prohaska, Steffen
BAM-RISSBETON
Visual and Data-centric Computing
3700
2010
2010
eng
45
1
5
article
1
--
--
--
Opportunities and challenges for digital morphology
Biology Direct
10.1186/1745-6150-5-45
yes
Alexander Ziegler
Malte Ogurreck
Thomas Steinke
Felix Beckmann
Steffen Prohaska
Andreas Ziegler
Visual Data Analysis
Distributed Algorithms and Supercomputing
Image Analysis in Biology and Materials Science
Prohaska, Steffen
Steinke, Thomas
Visual and Data-centric Computing
3704
2010
2010
eng
397
407
conferenceobject
American Society of Civil Engineers (ASCE)
0
--
--
--
Identification of Descriptive Parameters of the Soil Pore Structure using Experiments and CT Data
Proceedings of the 5th International Conference on Scour and Erosion (ICSE-5)
yes
Richard Binner
Ulrike Homberg
Steffen Prohaska
Ute Kalbe
Karl Josef Witt
Visual Data Analysis
Image Analysis in Biology and Materials Science
Prohaska, Steffen
PORESPACE
Visual and Data-centric Computing
3812
2006
2006
eng
1004
1010
22(8)
article
0
--
--
--
Distributed and collaborative visualization of large data sets using high-speed networks
Future Generation Comp. Syst
10.1016/j.future.2006.03.026
Andrei Hutanu
Gabrielle Allen
Stephen Beck
Petr Holub
Hartmut Kaiser
Archit Kulshrestha
Milos Liska
Jon MacLaren
Ludek Matyska
Ravi Paruchuri
Steffen Prohaska
Edward Seidel
Brygg Ullmer
Shalini Venkataraman
Visual Data Analysis
Image Analysis in Biology and Materials Science
Prohaska, Steffen
Visual and Data-centric Computing
3814
2006
2006
eng
103
110
10
conferenceobject
0
--
--
--
Interaktive Visualisierung und Datenanalyse: Herausforderungen durch wachsende Datenmengen
Kartographische Schriften
Steffen Prohaska
Visual Data Analysis
Image Analysis in Biology and Materials Science
Prohaska, Steffen
Visual and Data-centric Computing
3868
2005
2005
eng
241
246
48 (2)
article
0
--
--
--
Towards distributed visualization and analysis of large flow data
JSME International Journal, Series B
Hans-Christian Hege
Tino Weinkauf
Steffen Prohaska
Andrei Hutanu
Visual Data Analysis
Image Analysis in Biology and Materials Science
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
3869
2005
2005
eng
336
339
conferenceobject
Tsukuba, Japan
0
--
--
--
Fast cross-sectional display of large data sets
IAPR Conference on Machine Vision Applications
http://www.zib.de/visual-publications/sources/src-2005/Paper175FastCrossSectionalDisplay_v4.pdf
Vincent J. Dercksen
Steffen Prohaska
Hans-Christian Hege
Visual Data Analysis
Image Analysis in Biology and Materials Science
Hege, Hans-Christian
Prohaska, Steffen
BIC-GH
Visual and Data-centric Computing
3848
2005
2005
eng
175
182
conferenceobject
Minneapolis, USA
0
--
--
--
Visualization of time-dependent remote adaptive mesh refinement data
Proc. IEEE Visualization 2005
10.1109/VISUAL.2005.1532793
Ralf Kähler
Steffen Prohaska
Andrei Hutanu
Hans-Christian Hege
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Hege, Hans-Christian
Prohaska, Steffen
Visual and Data-centric Computing
3850
2005
2005
eng
171
179
218
article
0
--
--
--
Stereological measures of trabecular bone structure: Comparison of 3D micro computed tomography with 2D histological sections in human proximal tibial bone biopsies
Journal of Microscopy
Jesper Thomsen
Andreas Laib
Bruno Koller
Steffen Prohaska
L. Mosekilde
Wolfgang Gowin
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Prohaska, Steffen
Visual and Data-centric Computing
3833
2006
2006
eng
15
32
13
article
0
--
--
--
A novel three-dimensional computer assisted method for a quantitative study of microvascular networks of the human cerebral cortex
Microcirculation
Francis Cassot
Frederic Lauwers
Céline Fouard
Steffen Prohaska
Valerie Lauwer-Cances
Visual Data Analysis
Image Analysis in Biology and Materials Science
Prohaska, Steffen
Visual and Data-centric Computing
3834
2006
2006
eng
1319
1328
10
25
article
0
--
--
--
Blockwise processing applied to brain micro-vascular network study
IEEE Transactions on Medical Imaging
10.1109/TMI.2006.880670
Céline Fouard
Grégoire Malandain
Steffen Prohaska
Malte Westerhoff
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Prohaska, Steffen
Visual and Data-centric Computing
3837
2005
2005
eng
2995
3009
15(9)
article
0
--
--
--
Modeling resorption in 2D-CT and 3D μ-CT bone images
Int. J. of Bif. and Chaos
Alexei Zaikin
Peter Saparin
Jürgen Kurths
Steffen Prohaska
Wolfgang Gowin
Visual Data Analysis
Image Analysis in Biology and Materials Science
Therapy Planning
Prohaska, Steffen
Visual and Data-centric Computing
3851
2005
2005
eng
17
22
conferenceobject
0
--
--
--
Remote data access for interactive visualization
13th Annual Mardi Gras Conference: Frontiers of Grid Applications and Technologies
Steffen Prohaska
Andrei Hutanu
Visual Data Analysis
Image Analysis in Biology and Materials Science
Prohaska, Steffen
Visual and Data-centric Computing
5266
2014
eng
e113222
article
0
--
--
--
Automated stitching of microtubule centerlines across serial electron tomograms
PLoS ONE
10.1371/journal.pone.0113222
yes
urn:nbn:de:0297-zib-52958
Britta Weber
Steffen Prohaska
Erin M. Tranfield
Johanna L. Höög
Daniel Baum
Claude Antony
Tony Hyman
Jean-Marc Verbavatz
Steffen Prohaska
Visual Data Analysis
Image Analysis in Biology and Materials Science
Baum, Daniel
Prohaska, Steffen
MICROTUBULES
SPINDLE
Visual and Data-centric Computing
7792
2020
eng
e50988
9
article
0
--
--
--
Sperm-specific meiotic chromosome segregation in C. elegans
eLife
10.7554/eLife.50988
yes
2020-03-08
Gunar Fabig
Steffen Prohaska
Robert Kiewisz
Norbert Lindow
James A. Powers
Vanessa Cota
Luis J. Quintanilla
Jan Brugués
Steffen Prohaska
Diana S. Chu
Thomas Müller-Reichert
Visual Data Analysis
Image Analysis in Biology and Materials Science
Lindow, Norbert
Prohaska, Steffen
SPINDLE
Visual and Data-centric Computing
7542
2020
eng
100157
17
article
0
2020-01-08
--
--
Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms
Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies.
Photoacoustics
10.1016/j.pacs.2019.100157
yes
2019-12-05
urn:nbn:de:0297-zib-75416
Jens Buchmann
Steffen Prohaska
Bernhard Kaplan
Samuel Powell
Steffen Prohaska
Jan Laufer
Visual Data Analysis
Prohaska, Steffen
dfg-photom
Visual and Data-centric Computing
7952
2020
eng
article
0
2020-05-28
--
--
Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography
We present a software-assisted workflow for the alignment and matching of filamentous structures across a 3D stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labor. The software tool was developed to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite the problems related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time consuming. Furthermore, an interactive visualization of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialized, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. The key to our solution is a careful design of the visualization and interaction tools for each processing step to guarantee real-time response, and an optimized workflow that efficiently guides the user through datasets.
bioRxiv
10.1101/2020.05.28.120899
no
bioRxiv
2020-05-28
Norbert Lindow
Daniel Baum
Florian Brünig
Vincent J. Dercksen
Gunar Fabig
Robert Kiewisz
Stefanie Redemann
Thomas Müller-Reichert
Steffen Prohaska
Daniel Baum
Visual Data Analysis
Image Analysis in Biology and Materials Science
Baum, Daniel
Prohaska, Steffen
MODAL-MedLab
SPINDLE
MODAL-Gesamt
Visual and Data-centric Computing
6796
2018
eng
1027
1038.e4
7
28
article
0
2018-03-15
--
--
Live Observation of Two Parallel Membrane Degradation Pathways at Axon Terminals
Neurons are highly polarized cells that require continuous turnover of membrane proteins at axon terminals to develop, function, and survive. Yet, it is still unclear whether membrane protein degradation requires transport back to the cell body or whether degradation also occurs locally at the axon terminal, where live observation of sorting and degradation has remained a challenge. Here, we report direct observation of two cargo-specific membrane protein degradation mechanisms at axon terminals based on a live-imaging approach in intact Drosophila brains.
We show that different acidification-sensing cargo probes are sorted into distinct classes of degradative ‘‘hub’’ compartments for synaptic vesicle proteins and plasma membrane proteins at axon terminals. Sorting and degradation of the two cargoes in the separate hubs are molecularly distinct. Local sorting of synaptic vesicle proteins for degradation at the axon terminal is, surprisingly, Rab7 independent,
whereas sorting of plasma membrane proteins is Rab7 dependent. The cathepsin-like protease CP1 is specific to synaptic vesicle hubs, and its delivery requires the vesicle SNARE neuronal synaptobrevin. Cargo separation only occurs at the axon terminal, whereas degradative compartments at the cell body are mixed. These data show that at least two local, molecularly distinct pathways sort membrane cargo for degradation specifically at the axon terminal, whereas degradation can occur both at the terminal and en route to the cell body.
Current Biology
10.1016/j.cub.2018.02.032
yes
Eugene Jennifer Jin
Marc Osterland
Ferdi Ridvan Kiral
Mehmet Neset Ozel
Lara Sophie Burchardt
Marc Osterland
Daniel Epstein
Heike Wolfenberg
Steffen Prohaska
Peter Robin Hiesinger
Visual Data Analysis
Prohaska, Steffen
FU-Images
GC-Dynamics
Visual and Data-centric Computing
7373
eng
reportzib
0
--
2019-11-28
--
Semi-automatic Stitching of Serial Section Image Stacks with Filamentous Structures
In this paper, we present a software-assisted workflow for the alignment and matching of filamentous structures across a stack of 3D serial image sections. This is achieved by a combination of automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. This is supported by a quality assessment that visualizes regions that have been already inspected and, thus, allows a trade-off between quality and manual labor.
The software tool was developed in collaboration with biologists who investigate microtubule-based spindles during cell division. To quantitatively understand the structural organization of such spindles, a 3D reconstruction of the numerous microtubules is essential. Each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The sections then need to be stitched, i.e. non-rigidly aligned; and the microtubules need to be traced in each section and connected across section boundaries. Experiments led to the conclusion that automatic methods for stitching alone provide only an incomplete solution to practical analysis needs. Automatic methods may fail due to large physical distortions, a low signal-to-noise ratio of the images, or other unexpected experimental difficulties. In such situations, semi-automatic validation and correction is required to rescue as much information as possible to derive biologically meaningful results despite of some errors related to data collection.
Since the correct stitching is visually not obvious due to the number of microtubules (up to 30k) and their dense spatial arrangement, these are difficult tasks. Furthermore, a naive inspection of each microtubule is too time consuming. In addition, interactive visualization is hampered by the size of the image data (up to 100 GB). Based on the requirements of our collaborators, we present a practical solution for the semi-automatic stitching of serial section image stacks with filamentous structures.
1438-0064
urn:nbn:de:0297-zib-73739
false
true
Creative Commons - CC BY - Namensnennung 4.0 International
Norbert Lindow
Norbert Lindow
Florian Brünig
Vincent J. Dercksen
Gunar Fabig
Robert Kiewisz
Stefanie Redemann
Thomas Müller-Reichert
Steffen Prohaska
ZIB-Report
19-30
Visual Data Analysis
Lindow, Norbert
Prohaska, Steffen
SPINDLE
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/7373/zib-report-19-30-v1.pdf
7300
2019
eng
066001
6
24
article
0
--
--
--
3D quantitative photoacoustic tomography using an adjoint radiance Monte Carlo model and gradient descent
Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Grüneisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori.
Journal of Biomedical Optics
10.1117/1.JBO.24.6.066001
yes
2019-04-24
urn:nbn:de:0297-zib-72995
Jens Buchmann
Steffen Prohaska
Bernhard Kaplan
Samuel Powell
Steffen Prohaska
Jan Laufer
Visual Data Analysis
Prohaska, Steffen
dfg-photom
Visual and Data-centric Computing
6937
2018
eng
45
64
145
bookpart
Academic Press
0
--
--
--
Quantification of three-dimensional spindle architecture
Mitotic and meiotic spindles are microtubule-based structures to faithfully segregate chromosomes. Electron tomography is currently the method of choice to analyze the three-dimensional (3D) architecture of both types of spindles. Over the years, we have developed methods and software for automatic segmentation and stitching of microtubules in serial sections for large-scale reconstructions. 3D reconstruction of microtubules, however, is only the first step toward biological insight. The second step is the analysis of the structural data to derive measurable spindle properties. Here, we present a comprehensive set of techniques to quantify spindle parameters. These techniques provide quantitative analyses of specific microtubule classes and are applicable to a variety of tomographic reconstructions of spindles from different organisms.
Methods in Cell Biology Part B
10.1016/bs.mcb.2018.03.012
0091-679X
no
urn:nbn:de:0297-zib-66562
Norbert Lindow
Norbert Lindow
Stefanie Redemann
Florian Brünig
Gunar Fabig
Thomas Müller-Reichert
Steffen Prohaska
Visual Data Analysis
Lindow, Norbert
Prohaska, Steffen
SPINDLE
Visual and Data-centric Computing
6985
eng
reportzib
0
--
2018-08-07
--
A switch in microtubule orientation during C. elegans meiosis
In oocytes of many organisms, meiotic spindles form in the absence of centrosomes [1–5]. Such female meiotic spindles have a pointed appearance in metaphase with microtubules focused at acentrosomal spindle poles. At anaphase, the microtubules of acentrosomal spindles then transition to an inter- chromosomal array, while the spindle poles disappear. This transition is currently not understood. Previous studies have focused on this inter- chromosomal microtubule array and proposed a pushing model to drive chromosome segregation [6, 7]. This model includes an end-on orientation of microtubules with chromosomes. Alternatively, chromosomes were thought to associate along bundles of microtubules [8, 9]. Starting with metaphase, this second model proposed a pure lateral chromosome-to-microtubule association up to the final meiotic stages of anaphase. Here we applied large-scale electron tomography [10] of staged C. elegans oocytes in meiosis to analyze the orientation of microtubules in respect to chromosomes. We show that microtubules at metaphase I are primarily oriented laterally to the chromosomes and that microtubules switch to an end-on orientation during progression through anaphase. We further show that this switch in microtubule orientation involves a kinesin-13 microtubule depolymerase, KLP-7, which removes laterally associated microtubules around chromosomes. From this we conclude that both lateral and end-on modes of microtubule-to-chromosome orientations are successively used in C. elegans oocytes to segregate meiotic chromosomes.
1438-0064
urn:nbn:de:0297-zib-69855
Norbert Lindow
Stefanie Redemann
Ina Lantzsch
Norbert Lindow
Steffen Prohaska
Martin Srayko
Thomas Müller-Reichert
ZIB-Report
18-34
Visual Data Analysis
Lindow, Norbert
Prohaska, Steffen
SPINDLE
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/6985/zib-report-v1.pdf
6986
2018
eng
article
0
--
--
--
A switch in microtubule orientation during C. elegans meiosis
In oocytes of many organisms, meiotic spindles form in the absence
of centrosomes [1–5]. Such female meiotic spindles have a pointed appearance in metaphase with microtubules focused at acentrosomal spindle poles. At anaphase, the microtubules of acentrosomal spindles then transition to an inter- chromosomal array, while the spindle poles disappear. This transition is currently not understood. Previous studies have focused on this inter- chromosomal microtubule array and proposed a pushing model to drive chromosome segregation [6, 7]. This model includes an end-on orientation of microtubules with chromosomes. Alternatively, chromosomes were thought to associate along bundles of microtubules [8, 9]. Starting with metaphase, this second model proposed a pure lateral chromosome-to-microtubule association up to the final meiotic stages of anaphase. Here we applied large-scale electron tomography [10] of staged C. elegans oocytes in meiosis to analyze the orientation of microtubules in respect to chromosomes. We show that microtubules at metaphase I are primarily oriented laterally to the chromosomes and that microtubules switch to an end-on orientation during progression through anaphase. We further show that this switch in microtubule orientation involves a kinesin-13 microtubule depolymerase, KLP-7, which removes laterally associated microtubules around chromosomes. From this we conclude that both lateral and end-on modes of microtubule-to-chromosome orientations are successively used in C. elegans oocytes to segregate meiotic chromosomes.
Current Biology
10.1016/j.cub.2018.07.012
0960-9822
yes
2018-07-05
urn:nbn:de:0297-zib-69855
Stefanie Redemann
Norbert Lindow
Ina Lantzsch
Norbert Lindow
Steffen Prohaska
Martin Srayko
Thomas Müller-Reichert
Visual Data Analysis
Lindow, Norbert
Prohaska, Steffen
SPINDLE
Visual and Data-centric Computing
8264
2021
eng
e58903
10
article
0
--
--
--
Microtubule reorganization during female meiosis in C. elegans
Most female meiotic spindles undergo striking morphological changes while transitioning from metaphase to anaphase. The ultra-structure of meiotic spindles, and how changes to this structure correlate with such dramatic spindle rearrangements remains largely unknown. To address this, we applied light microscopy, large-scale electron tomography and mathematical modeling of female meiotic \textit{Caenorhabditis elegans} spindles. Combining these approaches, we find that meiotic spindles are dynamic arrays of short microtubules that turn over within seconds. The results show that the metaphase to anaphase transition correlates with an increase in microtubule numbers and a decrease in their average length. Detailed analysis of the tomographic data revealed that the microtubule length changes significantly during the metaphase-to-anaphase transition. This effect is most pronounced for microtubules located within 150 nm of the chromosome surface. To understand the mechanisms that drive this transition, we developed a mathematical model for the microtubule length distribution that considers microtubule growth, catastrophe, and severing. Using Bayesian inference to compare model predictions and data, we find that microtubule turn-over is the major driver of the spindle reorganizations. Our data suggest that in metaphase only a minor fraction of microtubules, those closest to the chromosomes, are severed. The large majority of microtubules, which are not in close contact with chromosomes, do not undergo severing. Instead, their length distribution is fully explained by growth and catastrophe. This suggests that the most prominent drivers of spindle rearrangements are changes in nucleation and catastrophe rate. In addition, we provide evidence that microtubule severing is dependent on katanin.
eLife
10.7554/eLife.58903
yes
publish
Ina Lantzsch
Steffen Prohaska
Che-Hang Yu
Yu-Zen Chen
Vitaly Zimyanin
Hossein Yazdkhasti
Norbert Lindow
Erik Szentgyoergyi
Ariel M Pani
Steffen Prohaska
Martin Srayko
Sebastian Fürthauer
Stefanie Redemann
Lindow, Norbert
Prohaska, Steffen
SPINDLE
Visual and Data-centric Computing
7299
eng
reportzib
0
--
2019-04-25
--
3D quantitative photoacoustic tomography using an adjoint radiance Monte Carlo model and gradient descent
Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Grüneisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori.
1438-0064
urn:nbn:de:0297-zib-72995
10.1117/1.JBO.24.6.066001
Appeared in: Journal of Biomedical Optics, 24, p. 066001, 2019
Jens Buchmann
Steffen Prohaska
Bernhard Kaplan
Samuel Powell
Steffen Prohaska
Jan Laufer
ZIB-Report
19-16
eng
uncontrolled
quantitative photoacoustic imaging
eng
uncontrolled
blood oxygen saturation
eng
uncontrolled
inverse problem
eng
uncontrolled
model-based inversion
eng
uncontrolled
Monte Carlo
eng
uncontrolled
spectral unmixing
Computer Applications
INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY
NUMERICAL ANALYSIS
Visual Data Analysis
Prohaska, Steffen
dfg-photom
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/7299/zibreport-19-16_v1.pdf
7541
eng
reportzib
0
--
2019-12-10
--
Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms
Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies.
1438-0064
urn:nbn:de:0297-zib-75416
10.1016/j.pacs.2019.100157
Photoacoustics 17:100157, 2020
Jens Buchmann
Steffen Prohaska
Bernhard Kaplan
Samuel Powell
Steffen Prohaska
Jan Laufer
ZIB-Report
19-60
eng
uncontrolled
quantitative photoacoustic imaging
eng
uncontrolled
blood oxygen saturation
eng
uncontrolled
inverse problem
eng
uncontrolled
model-based inversion
eng
uncontrolled
Monte Carlo
eng
uncontrolled
spectral unmixing
Computer Applications
INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY
NUMERICAL ANALYSIS
Visual Data Analysis
Prohaska, Steffen
dfg-photom
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/7541/zibreport-19-60_v1.pdf
1097
2007
eng
doctoralthesis
0
--
2007-08-17
2007-07-18
Skeleton-based visualization of massive voxel objects with network-like architecture
Skelettbasierte Visualisierung großer Voxel-Objekte mit netzwerkartiger Architektur
This work introduces novel internal and external memory algorithms for computing voxel skeletons of massive voxel objects with complex network-like architecture and for converting these voxel skeletons to piecewise linear geometry, that is triangle meshes and piecewise straight lines. The presented techniques help to tackle the challenge of visualizing and analyzing 3d images of increasing size and complexity, which are becoming more and more important in, for example, biological and medical research. Section 2.3.1 contributes to the theoretical foundations of thinning algorithms with a discussion of homotopic thinning in the grid cell model. The grid cell model explicitly represents a cell complex built of faces, edges, and vertices shared between voxels. A characterization of pairs of cells to be deleted is much simpler than characterizations of simple voxels were before. The grid cell model resolves topologically unclear voxel configurations at junctions and locked voxel configurations causing, for example, interior voxels in sets of non-simple voxels. A general conclusion is that the grid cell model is superior to indecomposable voxels for algorithms that need detailed control of topology. Section 2.3.2 introduces a noise-insensitive measure based on the geodesic distance along the boundary to compute two-dimensional skeletons. The measure is able to retain thin object structures if they are geometrically important while ignoring noise on the object's boundary. This combination of properties is not known of other measures. The measure is also used to guide erosion in a thinning process from the boundary towards lines centered within plate-like structures. Geodesic distance based quantities seem to be well suited to robustly identify one- and two-dimensional skeletons. Chapter 6 applies the method to visualization of bone micro-architecture. Chapter 3 describes a novel geometry generation scheme for representing voxel skeletons, which retracts voxel skeletons to piecewise linear geometry per dual cube. The generated triangle meshes and graphs provide a link to geometry processing and efficient rendering of voxel skeletons. The scheme creates non-closed surfaces with boundaries, which contain fewer triangles than a representation of voxel skeletons using closed surfaces like small cubes or iso-surfaces. A conclusion is that thinking specifically about voxel skeleton configurations instead of generic voxel configurations helps to deal with the topological implications. The geometry generation is one foundation of the applications presented in Chapter 6. Chapter 5 presents a novel external memory algorithm for distance ordered homotopic thinning. The presented method extends known algorithms for computing chamfer distance transformations and thinning to execute I/O-efficiently when input is larger than the available main memory. The applied block-wise decomposition schemes are quite simple. Yet it was necessary to carefully analyze effects of block boundaries to devise globally correct external memory variants of known algorithms. In general, doing so is superior to naive block-wise processing ignoring boundary effects. Chapter 6 applies the algorithms in a novel method based on confocal microscopy for quantitative study of micro-vascular networks in the field of microcirculation.
Die vorliegende Arbeit führt I/O-effiziente Algorithmen und Standard-Algorithmen zur Berechnung von Voxel-Skeletten aus großen Voxel-Objekten mit komplexer, netzwerkartiger Struktur und zur Umwandlung solcher Voxel-Skelette in stückweise-lineare Geometrie ein. Die vorgestellten Techniken werden zur Visualisierung und Analyse komplexer drei-dimensionaler Bilddaten, beispielsweise aus Biologie und Medizin, eingesetzt. Abschnitt 2.3.1 leistet mit der Diskussion von topologischem Thinning im Grid-Cell-Modell einen Beitrag zu den theoretischen Grundlagen von Thinning-Algorithmen. Im Grid-Cell-Modell wird ein Voxel-Objekt als Zellkomplex dargestellt, der aus den Ecken, Kanten, Flächen und den eingeschlossenen Volumina der Voxel gebildet wird. Topologisch unklare Situationen an Verzweigungen und blockierte Voxel-Kombinationen werden aufgelöst. Die Charakterisierung von Zellpaaren, die im Thinning-Prozess entfernt werden dürfen, ist einfacher als bekannte Charakterisierungen von so genannten "Simple Voxels". Eine wesentliche Schlussfolgerung ist, dass das Grid-Cell-Modell atomaren Voxeln überlegen ist, wenn Algorithmen detaillierte Kontrolle über Topologie benötigen. Abschnitt 2.3.2 präsentiert ein rauschunempfindliches Maß, das den geodätischen Abstand entlang der Oberfläche verwendet, um zweidimensionale Skelette zu berechnen, welche dünne, aber geometrisch bedeutsame, Strukturen des Objekts rauschunempfindlich abbilden. Das Maß wird im weiteren mit Thinning kombiniert, um die Erosion von Voxeln auf Linien zuzusteuern, die zentriert in plattenförmigen Strukturen liegen. Maße, die auf dem geodätischen Abstand aufbauen, scheinen sehr geeignet zu sein, um ein- und zwei-dimensionale Skelette bei vorhandenem Rauschen zu identifizieren. Eine theoretische Begründung für diese Beobachtung steht noch aus. In Abschnitt 6 werden die diskutierten Methoden zur Visualisierung von Knochenfeinstruktur eingesetzt. Abschnitt 3 beschreibt eine Methode, um Voxel-Skelette durch kontrollierte Retraktion in eine stückweise-lineare geometrische Darstellung umzuwandeln, die als Eingabe für Geometrieverarbeitung und effizientes Rendering von Voxel-Skeletten dient. Es zeigt sich, dass eine detaillierte Betrachtung der topologischen Eigenschaften eines Voxel-Skeletts einer Betrachtung von allgemeinen Voxel-Konfigurationen für die Umwandlung zu einer geometrischen Darstellung überlegen ist. Die diskutierte Methode bildet die Grundlage für die Anwendungen, die in Abschnitt 6 diskutiert werden. Abschnitt 5 führt einen I/O-effizienten Algorithmus für Thinning ein. Die vorgestellte Methode erweitert bekannte Algorithmen zur Berechung von Chamfer-Distanztransformationen und Thinning so, dass diese effizient ausführbar sind, wenn die Eingabedaten den verfügbaren Hauptspeicher übersteigen. Der Einfluss der Blockgrenzen auf die Algorithmen wurde analysiert, um global korrekte Ergebnisse sicherzustellen. Eine detaillierte Analyse ist einer naiven Zerlegung, die die Einflüsse von Blockgrenzen vernachlässigt, überlegen. In Abschnitt 6 wird, aufbauend auf den I/O-effizienten Algorithmen, ein Verfahren zur quantitativen Analyse von Mikrogefäßnetzwerken diskutiert.
1134
urn:nbn:de:kobv:517-opus-14888
http://opus.kobv.de/ubp/volltexte/2007/1488/
Steffen Prohaska
Steffen Prohaska
Jürgen Döllner
deu
uncontrolled
Visualisierung
deu
uncontrolled
Bilddatenanalyse
deu
uncontrolled
Skelettberechnung
deu
uncontrolled
Geometrieerzeugung
deu
uncontrolled
I/O-effiziente Algorithmen
eng
uncontrolled
visualization
eng
uncontrolled
image data analysis
eng
uncontrolled
skeletonization
eng
uncontrolled
geometry generation
eng
uncontrolled
external memory algorithms
Datenverarbeitung; Informatik
LIFE AND MEDICAL SCIENCES
Computational Geometry and Object Modeling
Applications
Feature Measurement
Image Representation
Dissertationen
Visual Data Analysis
Prohaska, Steffen
Visual and Data-centric Computing
Universität Potsdam
https://opus4.kobv.de/opus4-zib/files/1097/prohaska_diss_lowres.pdf
5967
eng
reportzib
0
--
2016-06-15
--
NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases
Neural circuit mapping is generating datasets of 10,000s of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches.
We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types including searching neurons against transgene expression patterns. Finally we show that NBLAST is effective with data from other invertebrates and zebrafish.
1438-0064
urn:nbn:de:0297-zib-59672
10.1016/j.neuron.2016.06.012
appeared also as bioRxiv preprint http://dx.doi.org/10.1101/006346 and in revised form in Neuron
Marta Costa
Steffen Prohaska
James D. Manton
Aaron D. Ostrovsky
Steffen Prohaska
Gregory S.X.E. Jefferis
ZIB-Report
16-34
eng
uncontrolled
neuroinformatics
eng
uncontrolled
NBLAST
eng
uncontrolled
neuron similarity
eng
uncontrolled
cell type
eng
uncontrolled
clustering
Computer Applications
INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY
COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)
BIOLOGY AND OTHER NATURAL SCIENCES
Visual Data Analysis
Prohaska, Steffen
no-project
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/5967/zibreport-16-34_v1.pdf
1425
2011
eng
reportzib
0
2011-11-05
2011-11-05
--
Level of Detail for Trees Using Clustered Ellipsoids
We present a level of detail method for trees based on ellipsoids and lines. We leverage the Expectation Maximization algorithm with a Gaussian Mixture Model to create a hierarchy of high-quality leaf clusterings, while the branches are simplified using agglomerative bottom-up clustering to preserve the connectivity. The simplification runs in a preprocessing step and requires no human interaction. For a fly by over and through a scene of 10k trees, our method renders on average at 40 ms/frame, up to 6 times faster than billboard clouds with comparable artifacts.
1438-0064
11-41
urn:nbn:de:0297-zib-14251
no
Malte Clasen
Steffen Prohaska
Philip Paar
Steffen Prohaska
ZIB-Report
11-41
eng
uncontrolled
level of detail
eng
uncontrolled
rendering
eng
uncontrolled
natural scene
eng
uncontrolled
Gaussian mixture model
Computing Methodologies
INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY
NUMERICAL ANALYSIS
COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)
Visual Data Analysis
Image Analysis in Biology and Materials Science
Prohaska, Steffen
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/1425/zibreport.pdf
6231
2017
eng
reportzib
0
--
2017-03-24
--
Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography
The goal of quantitative photoacoustic tomography (qPAT) is to recover maps of the chromophore distributions from multiwavelength images of the initial pressure. Model-based inversions that incorporate the physical processes underlying the photoacoustic (PA) signal generation represent a promising approach. Monte-Carlo models of the light transport are computationally expensive, but provide accurate fluence distributions predictions, especially in the ballistic and quasi-ballistic regimes. Here, we focus on the inverse problem of 3D qPAT of blood oxygenation and investigate the application of the Monte-Carlo method in a model-based inversion scheme. A forward model of the light transport based on the MCX simulator and acoustic propagation modeled by the k-Wave toolbox was used to generate a PA image data set acquired in a tissue phantom over a planar detection geometry. The combination of the optical and acoustic models is shown to account for limited-view artifacts. In addition, the errors in the fluence due to, for example, partial volume artifacts and absorbers immediately adjacent to the region of interest are investigated. To accomplish large-scale inversions in 3D, the number of degrees of freedom is reduced by applying image segmentation to the initial pressure distribution to extract a limited number of regions with homogeneous optical parameters. The absorber concentration in the tissue phantom was estimated using a coordinate descent parameter search based on the comparison between measured and modeled PA spectra. The estimated relative concentrations using this approach lie within 5 % compared to the known concentrations. Finally, we discuss the feasibility of this approach to recover the blood oxygenation from experimental data.
1438-0064
urn:nbn:de:0297-zib-62318
10.1117/12.2251945
Appeared in: Proc. SPIE 10064, Photons Plus Ultrasound: Imaging and Sensing 2017, 100645J (March 23, 2017)
Bernhard Kaplan
Bernhard Kaplan
Jan Laufer
Steffen Prohaska
Jens Buchmann
ZIB-Report
17-04
eng
uncontrolled
quantitative photoacoustic tomography
eng
uncontrolled
model-based inversion
eng
uncontrolled
oxygen saturation
eng
uncontrolled
chromophore concentration
eng
uncontrolled
photoacoustic imaging
eng
uncontrolled
Monte Carlo methods for light transport
eng
uncontrolled
boundary conditions
eng
uncontrolled
coordinate search
Computer Applications
INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY
COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)
Visual Data Analysis
Prohaska, Steffen
dfg-photom
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/6231/zib_report_qpat.pdf
1773
2013
eng
reportzib
0
2013-12-02
2013-12-02
--
iCon.text – a customizable iPad app for kiosk applications in museum exhibitions
We present iCon.text, a kiosk platform for the iPad centered around artefacts, whose content and layout can be tailored without programming skills for specific museum exhibitions. The central metaphor to access information is a virtual postcard with one front and a customizable number of back sides that provide details about exhibits to museum visitors in textual and image form. Back sides can link to others cards. Access to these postcards is possible through one or more navigation views that can be navigated to from a navigation bar.
The entry point to the application is designed as a multitouch interactive pile of cards in a playful manner that allows visitors of any age an easy approach to the presentation and interaction metaphor. To directly access a certain postcard, a mosaic view can be uitilized to provide an overview about all available exhibits. A category view groups postcards into themes. Locating artefacts on a zoomable map or exhibition floor plan allows for conveying information about spatial contexts between different objects and their location. Furthermore, contexts can be illustrated with a two stage view comprising an overview and corresponding detail views to provide further insights into the spatial, temporal, and thematic contexts of artefacts. The application scaffolding allows the design of bilingual presentations to support exhibitions with an international audience. The logo of the presenting institution or exhibition can be incorporated to display the the kiosk's corporate design branding and to access an imprint or further informations. Usage is logged into files to provide a basis for extracting statistical information about the usage.
The details about the exhibits are presented as images and as such impose no limit to the design choices made by the content provider or exhibition designer.
The application (enhanced with a panoramic view) has been integrated successfully into a large special exhibition about the ancient city of Pergamon 2011/2012 at the Pergamon Museum Berlin within the interdisciplinary project "Berlin Sculpture Network".
1438-0064
urn:nbn:de:0297-zib-17731
Appeared in: EVA , Berlin Nov. 2012, pp. 150-155. Gesellschaft zur Förderung angewandter Informatik
no
Marco Klindt
Marco Klindt
Daniel Baum
Steffen Prohaska
Hans-Christian Hege
ZIB-Report
13-07
eng
uncontrolled
HCI
eng
uncontrolled
Cultural Heritage
eng
uncontrolled
Kiosk application
eng
uncontrolled
iPad
Multimedia Information Systems
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Baum, Daniel
Hege, Hans-Christian
Klindt, Marco
Prohaska, Steffen
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/1773/ZIB-Report-13-07.pdf
5295
eng
reportzib
0
--
2014-10-28
--
Automated stitching of microtubule centerlines across serial electron tomograms
Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed with a probabilistic variant of the iterative closest points algorithm, which we extended to handle the orientation of lines by introducing a periodic random variable to the probabilistic formulation. 3) Endpoint correspondence is established by formulating a matching problem in terms of a Markov random field and computing the best matching with belief propagation. Belief propagation is not generally guaranteed to converge to a minimum. We show how convergence can be achieved, nonetheless, with minimal manual input. In addition to stitching microtubule centerlines, the correspondence is also applied to transform and merge the electron tomograms. We applied the proposed methods to samples from the mitotic spindle in C. elegans, the meiotic spindle in X. laevis, and sub-pellicular microtubule arrays in T. brucei. The methods were able to stitch microtubules across section boundaries in good agreement with experts’ opinions for the spindle samples. Results, however, were not satisfactory for the microtubule arrays. For certain experiments, such as an analysis of the spindle, the proposed methods can replace manual expert tracing and thus enable the analysis of microtubules over long distances with reasonable manual effort.
1438-0064
urn:nbn:de:0297-zib-52958
10.1371/journal.pone.0113222
published in PLoS ONE
Britta Weber
Steffen Prohaska
Erin M. Tranfield
Johanna L. Höög
Daniel Baum
Claude Antony
Tony Hyman
Jean-Marc Verbavatz
Steffen Prohaska
ZIB-Report
14-41
eng
uncontrolled
electron tomography
eng
uncontrolled
microtubules
eng
uncontrolled
serial sectioning
eng
uncontrolled
image analysis
eng
uncontrolled
geometry reconstruction
eng
uncontrolled
image and geometry alignment
eng
uncontrolled
point correspondence
Applications
Biology and genetics (REVISED)
Cell processes
PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX)
COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)
BIOLOGY AND OTHER NATURAL SCIENCES
Visual Data Analysis
Image Analysis in Biology and Materials Science
Baum, Daniel
Prohaska, Steffen
MICROTUBULES
SPINDLE
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/5295/zibreport-14-41_v1.pdf
5342
2015
eng
reportzib
0
--
2015-01-19
--
Registering 2D and 3D Imaging Data of Bone during Healing
Purpose/Aims of the Study: Bone’s hierarchical structure can be visualized using a variety of methods. Many techniques, such as light and electron microscopy generate two-dimensional (2D) images, while micro computed tomography (μCT) allows a direct representation of the three-dimensional (3D) structure. In addition, different methods provide complementary structural information, such as the arrangement of organic or inorganic compounds. The overall aim of the present study is to answer bone research questions by linking information of different 2D and 3D imaging techniques. A great challenge in combining different methods arises from the fact that they usually reflect different characteristics of the real structure.
Materials and Methods: We investigated bone during healing by means of μCT and a couple of 2D methods. Backscattered electron images were used to qualitatively evaluate the tissue’s calcium content and served as a position map for other experimental data. Nanoindentation and X-ray scattering experiments were performed to visualize mechanical and structural properties. Results: We present an approach for the registration of 2D data in a 3D μCT reference frame, where scanning electron microscopies serve as a methodic link. Backscattered electron images are perfectly suited for registration into μCT reference frames, since both show structures based on the same physical principles. We introduce specific registration tools that have been developed to perform the registration process in a semi-automatic way.
Conclusions: By applying this routine, we were able to exactly locate structural information (e.g. mineral particle properties) in the 3D bone volume. In bone healing studies this will help to better understand basic formation, remodeling and mineralization processes.
1438-0064
urn:nbn:de:0297-zib-53426
no
Appeared in: Connective Tissue Research, 56(2)
Rebecca M. Hoerth
Daniel Baum
Daniel Baum
David Knötel
Steffen Prohaska
Bettina M. Willie
Georg Duda
Hans-Christian Hege
Peter Fratzl
Wolfgang Wagermaier
ZIB-Report
15-01
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Image Analysis in Biology and Materials Science
Baum, Daniel
Hege, Hans-Christian
Knötel, David
Prohaska, Steffen
BONE-HEALING
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/5342/ZR-15-01.pdf
7439
eng
reportzib
0
--
2019-08-14
--
Serial synapse formation through filopodial competition for synaptic seeding factors
Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses.
1438-0064
urn:nbn:de:0297-zib-74397
10.1016/j.devcel.2019.06.014
Appeared in: Developmental Cell, 50(4), pp. 447-461, 2019
M. Neset Özel
Josephine Brummer
Abhishek Kulkarni
Amr Hasan
Josephine Brummer
Marian Moldenhauer
Ilsa-Maria Daumann
Heike Wolfenberg
Vincent J. Dercksen
F. Ridvan Kiral
Martin Weiser
Steffen Prohaska
Max von Kleist
Peter Robin Hiesinger
ZIB-Report
19-45
eng
uncontrolled
filopodia
eng
uncontrolled
growth cone dynamics
eng
uncontrolled
brain wiring
eng
uncontrolled
2-photon microscopy
eng
uncontrolled
model
Computing Methodologies
Computer Applications
INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY
PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX)
COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)
BIOLOGY AND OTHER NATURAL SCIENCES
Numerical Mathematics
Visual Data Analysis
Prohaska, Steffen
Weiser, Martin
FU-Images
GC-Dynamics
BrainWiring
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/7439/zibreport-19-45_v1.pdf
7129
2019
eng
447
461
4
50
article
0
--
--
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Serial synapse formation through filopodial competition for synaptic seeding factors
Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses.
Developmental Cell
10.1016/j.devcel.2019.06.014
yes
appeared also as bioRxiv preprint https://doi.org/10.1101/506378
2019-06-21
urn:nbn:de:0297-zib-74397
Mehmet Neset Ozel
Steffen Prohaska
Abhishek Kulkarni
Amr Hasan
Josephine Brummer
Marian Moldenhauer
Ilsa-Maria Daumann
Heike Wolfenberg
Vincent J. Dercksen
Ferdi Ridvan Kiral
Martin Weiser
Steffen Prohaska
Max von Kleist
Peter Robin Hiesinger
Numerical Mathematics
Visual Data Analysis
Prohaska, Steffen
Weiser, Martin
FU-Images
GC-Dynamics
BrainWiring
Visual and Data-centric Computing
8238
2021
eng
25
44
1
284
article
0
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2021-06-10
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Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography
We present a software-assisted workflow for the alignment and matching of filamentous structures across a three-dimensional (3D) stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After the computation of an initial automatic matching, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labor. The software tool was developed in an interdisciplinary collaboration between computer scientists and cell biologists to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite dealing with imperfect data related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time-consuming. Furthermore, an interactive visualization of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialized, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. To the best of our knowledge, it is the only currently available tool which is able to process data of the type and size presented here. The key to our solution is a careful design of the visualization and interaction tools for each processing step to guarantee real-time response, and an optimized workflow that efficiently guides the user through datasets. The final solution presented here is the result of an iterative process with tight feedback loops between the involved computer scientists and cell biologists.
Journal of Microscopy
10.1111/jmi.13039
yes
Journal of Microscopy
2021-06-02
publish
Norbert Lindow
Daniel Baum
Florian Brünig
Vincent J. Dercksen
Gunar Fabig
Robert Kiewisz
Stefanie Redemann
Thomas Müller-Reichert
Steffen Prohaska
Daniel Baum
Baum, Daniel
Lindow, Norbert
Prohaska, Steffen
SPINDLE
Visual and Data-centric Computing
5318
2015
2015
eng
133
143
11
2
56
article
Taylor & Francis
0
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Registering 2D and 3D Imaging Data of Bone during Healing
Connective Tissue Research
10.3109/03008207.2015.1005210
yes
urn:nbn:de:0297-zib-53426
Daniel Baum
Rebecca M. Hoerth
Daniel Baum
David Knötel
Steffen Prohaska
Bettina M. Willie
Georg Duda
Hans-Christian Hege
Peter Fratzl
Wolfgang Wagermaier
Visual Data Analysis
Baum, Daniel
Hege, Hans-Christian
Knötel, David
Prohaska, Steffen
BONE-HEALING
Visual and Data-centric Computing