Publication List

February 13th, 2013

A full list of my publications is available on the ZIB homepage.

Homberg et al. (2012), Automatic extraction and analysis of realistic pore structures from mCT data for pore space characterization of graded soil

September 12th, 2012

Ulrike Homberg, Daniel Baum, Steffen Prohaska, Ute Kalbe, and Karl Josef Witt. Automatic extraction and analysis of realistic pore structures from mCT data for pore space characterization of graded soil. In Proc. 6th Int. Conference on Scour and Erosion (ICSE-6), pages 66–73, 2012.

@inproceedings{Homberg:-2012-ICSE,
	Author = {Ulrike Homberg and Daniel Baum and Steffen Prohaska
        and Ute Kalbe and Karl Josef Witt},
	Booktitle = {Proc. 6th Int. Conference on Scour and Erosion
        (ICSE-6)},
	Pages = {66--73},
	Title = {Automatic Extraction and Analysis of Realistic Pore
        Structures from {$\mu$CT} Data for Pore Space Characterization
        of Graded Soil},
	Year = {2012}}

Weber et al. (2012), Automated tracing of microtubules in electron tomograms of plastic embedded samples of caenorhabditis elegans embryos

May 12th, 2012

Britta Weber, Garrett Greenan, Steffen Prohaska, Daniel Baum, Hans-Christian Hege, Thomas Müller-Reichert, Anthony A. Hyman, and Jean-Marc Verbavatz. Automated tracing of microtubules in electron tomograms of plastic embedded samples of caenorhabditis elegans embryos. Journal of Structural Biology, 178(2):129–138, 2012. 10.1016/j.jsb.2011.12.004.
[journal software]

@article{Weber:JOSB-2012-178-129----138,
	Author = {Britta Weber and Garrett Greenan and Steffen Prohaska
        and Daniel Baum and Hans-Christian Hege
        and Thomas M{\"u}ller-Reichert and Anthony A. Hyman
        and Jean-Marc Verbavatz},
	Journal = {Journal of Structural Biology},
	Number = {2},
	Pages = {129 -- 138},
	Title = {Automated tracing of microtubules in electron tomograms
        of plastic embedded samples of Caenorhabditis elegans embryos},
	Volume = {178},
	Year = {2012}}

Homberg et al. (2011), Describing and analyzing the dual structures of porous media

December 12th, 2011

Ulrike Homberg, Daniel Baum, and Steffen Prohaska. Describing and analyzing the dual structures of porous media. In Proc. 3D-Microstructure Meeting, pages 24–25, 2011.

@inproceedings{Homberg:2011--24,
	Author = {Ulrike Homberg and Daniel Baum and Steffen Prohaska},
	Booktitle = {Proc. {3D}-Microstructure Meeting},
	Pages = {24--25},
	Title = {Describing and Analyzing the Dual Structures of Porous
        Media},
	Year = {2011}}

Ehrig et al. (2011), Comparison of crack detection methods for analyzing damage processes in concrete with computed tomography

December 12th, 2011

Karsten Ehrig, Jürgen Goebbels, Dietmar Meinel, Olaf Paetsch, Steffen Prohaska, and Valentin Zobel. Comparison of crack detection methods for analyzing damage processes in concrete with computed tomography. In Proc. Int. Symp. Digital Industrial Radiology and Computed Tomography, 2011.
[pdf]

@inproceedings{Ehrig:2011,
	Author = {Karsten Ehrig and J{\"u}rgen Goebbels
        and Dietmar Meinel and Olaf Paetsch and Steffen Prohaska
        and Valentin Zobel},
	Booktitle = {Proc. Int. Symp. Digital Industrial Radiology
        and Computed Tomography},
	Title = {Comparison of Crack Detection Methods for Analyzing
        Damage Processes in Concrete with Computed Tomography},
	Year = {2011}}

Streicher et al. (2011), 3-D-Visualisierung von Radar- und Ultraschallecho-Daten mit ZIBAmira

December 12th, 2011

Doreen Streicher, Olaf Paetsch, Robert Seiler, Steffen Prohaska, Martin Krause, and Christian Boller. 3-D-Visualisierung von Radar- und Ultraschallecho-Daten mit ZIBAmira. In Proc. DGZfP-Jahrestagung 2011, 2011.
[pdf]

@inproceedings{Streicher:2011,
	Author = {Doreen Streicher and Olaf Paetsch and Robert Seiler
        and Steffen Prohaska and Martin Krause and Christian Boller},
	Booktitle = {Proc. {DGZfP}-{J}ahrestagung 2011},
	Title = {3-{D}-{V}isualisierung von {R}adar- und
        {U}ltraschallecho-{D}aten mit {ZIBAmira}},
	Year = {2011}}

Weber et al. (2011), Fast tracing of microtubule centerlines in electron tomograms

December 12th, 2011

Britta Weber, Marit Möller, Jean-Marc Verbavatz, Daniel Baum, Hans-Christian Hege, and Steffen Prohaska. Fast tracing of microtubule centerlines in electron tomograms. In IEEE Symposium on Biological Data Visualization, 2011.
[pdf]

@inproceedings{Weber:2011,
	Author = {Britta Weber and Marit M{\"o}ller
        and Jean-Marc Verbavatz and Daniel Baum and Hans-Christian Hege
        and Steffen Prohaska},
	Booktitle = {IEEE Symposium on Biological Data Visualization},
	Title = {Fast Tracing of Microtubule Centerlines in Electron
        Tomograms},
	Year = {2011}}

Clasen et al. (2011), Level of detail for trees using clustered ellipsoids

December 12th, 2011

Malte Clasen, Philip Paar, and Steffen Prohaska. Level of detail for trees using clustered ellipsoids. Technical Report 11-41, ZIB, Takustr.7, 14195 Berlin, 2011.
[pdf]

@techreport{Clasen:2011,
	Address = {Takustr.7, 14195 Berlin},
	Author = {Malte Clasen and Philip Paar and Steffen Prohaska},
	Institution = {ZIB},
	Number = {11-41},
	Title = {Level of Detail for Trees Using Clustered Ellipsoids},
	Year = {2011}}

Should I sign the Research Without Walls pledge?

October 22nd, 2011

Slashdot thinks that the Research Without Walls pledge could be a tipping point for open access CS research.

Kleinfeld et al. (2011), Large-scale automated histology in the pursuit of connectomes

October 22nd, 2011

David Kleinfeld, Arjun Bharioke, Pablo Blinder, Davi D. Bock, Kevin L. Briggman, Dmitri B. Chklovskii, Winfried Denk, Moritz Helmstaedter, John P. Kaufhold, Wei-Chung Allen Lee, Hanno S. Meyer, Kristina D. Micheva, Marcel Oberlaender, Steffen Prohaska, R. Clay Reid, Stephen J. Smith, Shinya Takemura, Philbert S. Tsai, and Bert Sakmann. Large-scale automated histology in the pursuit of connectomes. The Journal of Neuroscience, 31(45): 16125–16138, 2011. 10.1523/JNEUROSCI.4077-11.2011.
[preprint journal]


@article{Kleinfeld:JNS-2011,
	Author = {Kleinfeld, David and Bharioke, Arjun and Blinder, Pablo
        and Bock, Davi D. and Briggman, Kevin L. and Chklovskii, Dmitri B.
        and Denk, Winfried and Helmstaedter, Moritz and Kaufhold, John P.
        and Lee, Wei-Chung Allen and Meyer, Hanno S.
        and Micheva, Kristina D. and Oberlaender, Marcel
        and Prohaska, Steffen and Reid, R. Clay and Smith, Stephen J.
        and Takemura, Shinya and Tsai, Philbert S. and Sakmann, Bert},
	Journal = {The Journal of Neuroscience},
	Number = {45},
	Pages = {16125-16138},
	Title = {Large-Scale Automated Histology in the Pursuit of Connectomes},
	Volume = {31},
	Year = {2011},
        doi={10.1523/JNEUROSCI.4077-11.2011}
}

Rigort et al. (2011), Automated segmentation of electron tomograms for a quantitative description of actin filament networks

October 21st, 2011

Alexander Rigort, David Günther, Reiner Hegerl, Daniel Baum, Britta Weber, Steffen Prohaska, Ohad Medalia, Wolfgang Baumeister, and Hans-Christian Hege. Automated segmentation of electron tomograms for a quantitative description of actin filament networks. J Struct Biol, 178:135–144, Sep 2011. 10.1016/j.jsb.2011.08.012.
[article, software]

@article{Rigort:JSB-2011,
	Author = {Rigort, Alexander and G{\"u}nther, David and Hegerl, Reiner and
        Baum, Daniel and Weber, Britta and Prohaska, Steffen and
        Medalia, Ohad and Baumeister, Wolfgang and Hege, Hans-Christian},
	Journal = {J Struct Biol},
	Pages = {135--144},
	Volume = {178},
	Month = {Sep},
	Title = {Automated segmentation of electron tomograms for a quantitative
        description of actin filament networks},
	Year = {2011},
        Doi = {10.1016/j.jsb.2011.08.012}}

Günther et al. (2011), Efficient computation of a hierarchy of discrete 3d gradient vector fields

July 21st, 2011

D. Günther, J. Reininghaus, S. Prohaska, T. Weinkauf, and H.-C. Hege. Efficient computation of a hierarchy of discrete 3d gradient vector fields. In Topological Methods in Data Analysis and Visualization II, pages 15–29. Springer, 2011.
[pdf]

@inproceedings{Gunther:2011,
	Author = {D. G{\"u}nther and J. Reininghaus and S. Prohaska
        and T. Weinkauf and H.-C. Hege},
	Booktitle = {Topological Methods in Data Analysis and Visualization II},
	Pages = {15--29},
	Publisher = {Springer},
	Title = {Efficient Computation of a Hierarchy of Discrete 3D
        Gradient Vector Fields},
	Year = {2011}}

Ritter et al. (2011), Osteocytes number and volume in osteoporotic and in healthy bone biopsies analysed using synchrotron CT: a pilot study

June 21st, 2011

Z. Ritter, A. Staude, S Prohaska, R. Brand, A. Friedmann, H.C. Hege, J. Goebbels, and D. Felsenberg. Osteocytes number and volume in osteoporotic and in healthy bone biopsies analysed using synchrotron CT: a pilot study. In Proc. ISB 2011, 2011.
[abstract]

@inproceedings{Ritter:2011,
	Author = {Ritter, Z. and Staude, A. and Prohaska, S and Brand, R. and
        Friedmann, A. and Hege, H.C. and Goebbels, J. and Felsenberg, D.},
	Booktitle = {Proc. ISB 2011},
	Title = {Osteocytes number and volume in osteoporotic and in healthy
        bone biopsies analysed using Synchrotron {CT}: a pilot study},
	Year = {2011}}

Why most published research findings are false

April 7th, 2011

In detail at PLoS Medicine, and in brief at xkcd.

Binner et al. (2010), Identification of descriptive parameters of the soil pore structure using experiments and CT data

December 12th, 2010

Richard Binner, Ulrike Homberg, Steffen Prohaska, Ute Kalbe, and Karl Josef Witt. Identification of descriptive parameters of the soil pore structure using experiments and CT data. In Proc. 5th Int. Conference on Scour and Erosion (ICSE-5), pages 397–407, 2010.

@inproceedings{Binner:2010,
	Author = {Richard Binner and Ulrike Homberg and Steffen Prohaska
        and Ute Kalbe and Karl Josef Witt},
	Booktitle = {Proc. 5th Int. Conference on Scour and Erosion
        ({ICSE-5})},
	Pages = {397--407},
	Title = {Identification of Descriptive Parameters of the Soil
        Pore Structure using Experiments and {CT} Data},
	Year = {2010}}

Clasen, M. and Prohaska, S. (2010), Image-Error-Based Level of Detail for Landscape Visualization

December 5th, 2010

Clasen, M. and Prohaska, S. (2010). Image-Error-Based Level of Detail for Landscape Visualization. In Proc. VMV 2010: Vision, Modeling and Visualization, pages 267–274.
[pdf, supplement]

@inproceedings{Clasen:VMV-2010--267-274,
	Author = {Malte Clasen and Steffen Prohaska},
	Booktitle = {Proc. VMV 2010: Vision, Modeling and Visualization},
	Pages = {267-274},
	Title = {{Image-Error-Based Level of Detail for Landscape Visualization}},
	Year = {2010}}

git-subtree

July 29th, 2010

There’s an interesting discussion about Avery Pennarun’s git-subtree and Git’s submodule concept on the git mailing list
[1, 2].

Ziegler et al. (2010), Opportunities and challenges for digital morphology

July 7th, 2010

Ziegler, A., Ogurreck, M., Steinke, T., Beckmann, F., Prohaska, S., and Ziegler, A. (2010). Opportunities and challenges for digital morphology. Biology Direct, 5(1):45. doi 10.1186/1745-6150-5-45.
[Open Access]

@article{Ziegler:BiologyDirect-2010-5-45,
	Author = {Ziegler, Alexander and Ogurreck, Malte
          and Steinke, Thomas and Beckmann, Felix
          and Prohaska, Steffen and Ziegler, Andreas},
	Journal = {Biology Direct},
	Number = {1},
	Pages = {45},
	Title = {Opportunities and challenges for digital morphology},
	Volume = {5},
	Year = {2010},
	Doi = {10.1186/1745-6150-5-45}}

Reininghaus et al. (2010), TADD: A computational framework for data analysis using discrete morse theory

July 7th, 2010

Reininghaus, J., Günther, D., Hotz, I., Prohaska, S., and Hege, H.-C. (2010). TADD: A computational framework for data analysis using discrete morse theory. In Fukuda, K., van der Hoeven, J., Joswig, M., and Takayama, N., editors, Mathematical Software – ICMS 2010, volume 6327 of Lecture Notes in Computer Science, pages 198–208. Springer.
[pdf]

@inproceedings{Reininghaus:ICMS-2010,
	Author = {Jan Reininghaus and David G{\"u}nther and Ingrid Hotz
        and Steffen Prohaska and Hans-Christian Hege},
	Booktitle = {Mathematical Software -- ICMS 2010},
	Crossref = {conf:icms:2010},
	Ee = {http://dx.doi.org/10.1007/978-3-642-15582-6_35},
	Pages = {198-208},
	Title = {{TADD}: A Computational Framework for Data Analysis
        Using Discrete Morse Theory},
	Year = {2010}}

@proceedings{conf:icms:2010,
	Booktitle = {Mathematical Software -- ICMS 2010},
	Editor = {Komei Fukuda and Joris van der Hoeven
        and Michael Joswig and Nobuki Takayama},
	Ee = {http://dx.doi.org/10.1007/978-3-642-15582-6},
	Isbn = {978-3-642-15581-9},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Third International Congress on Mathematical Software,
         Kobe, Japan, September 13-17, 2010. Proceedings},
	Volume = {6327},
	Year = {2010}}

Lindow et al. (2010), Accelerated visualization of dynamic molecular surfaces

July 7th, 2010

Lindow, N., Baum, D., Prohaska, S., and Hege, H.-C. (2010). Accelerated visualization of dynamic molecular surfaces. Comput. Graph. Forum, 29:943–952.
[pdf]

@article{Lindow:CGA-2010-29-943,
	Author = {Norbert Lindow and Daniel Baum
          and Steffen Prohaska and Hans-Christian Hege},
	Journal = {Comput. Graph. Forum},
	Pages = {943--952},
	Title = {Accelerated Visualization of Dynamic Molecular Surfaces},
	Volume = {29},
	Year = {2010}}

Kuß et al. (2010), Effective techniques to visualize filament-surface relationships

July 7th, 2010

Kuß, A., Gensel, M., Meyer, B., Dercksen, V. J., and Prohaska, S. (2010). Effective techniques to visualize filament-surface relationships. Comput. Graph. Forum, 29:1003–1012.
[pdf]

@article{Kuss:CGA-2010-29-1003,
	Author = {Anja Ku{\ss} and Maria Gensel
          and Bj{\"o}rn Meyer and Vincent J. Dercksen
          and Steffen Prohaska},
	Journal = {Comput. Graph. Forum},
	Pages = {1003-1012},
	Title = {Effective Techniques to Visualize Filament-Surface
          Relationships},
	Volume = {29},
	Year = {2010}}

Recommendations for Independent Scholarly Publication of Data Sets

June 27th, 2010
  • Jonathan Rees’s Recommendations for Independent Scholarly Publication of Data Sets are available from the Science Common’s reading room [1]

GeForce GTX 480 and 470

March 27th, 2010
  • Tom’s Hardware reports comprehensive benchmarks of the new NVIDIA cards. [1]

Processing.js

March 7th, 2010

Processing.js is a JavaScript port of Processing. See the article Comparing native Processing & Processing.js for a comparison to native Processing.

Whatever Happened To Programming?

March 7th, 2010
  • Whatever Happened To Programming? [1]

Lean programming (the fridge vs the radiator)

March 7th, 2010

Lean programming (the fridge vs the radiator) by Jason Yip [1]


The Ignite presentation method

March 7th, 2010
  • The Ignite presentation method [1]
  • Ignite@O’Reilly [1]

Multi-Voting

February 27th, 2010
  • Perpetual multivote for pull scheduling [1]
  • Multi-Voting described at the Continuous Improvement Resources at Arizona State University [1, 2]

Kuß et al. (2009), Using ontologies for the visualization of hierarchical neuroanatomical structures

December 31st, 2009

Kuß, A., Prohaska, S., and Rybak, J. (2009). Using ontologies for the visualization of hierarchical neuroanatomical structures. In Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics. doi 10.3389/conf.neuro.11.2009.08.017.
[pdf]

@inproceedings{Kuss:INCF-2009,
	Author = {Anja Ku{\ss} and Steffen Prohaska
          and J{\"u}rgen Rybak},
	Booktitle = {Frontiers in Neuroinformatics.
          Conference Abstract: 2nd INCF Congress
          of Neuroinformatics},
	Title = {Using Ontologies for the Visualization
          of Hierarchical Neuroanatomical Structures},
	Year = {2009},
        Doi = {10.3389/conf.neuro.11.2009.08.017}}

Kanban for Software Engineering

November 28th, 2009
  • The Limited WIP Society is intended to be the home of kanban for software development community. [1]

PySide

August 25th, 2009
  • PySide provides LGPL Qt Python bindings. [1]

LSB Infrastructure Project, ABI compliance checker

August 22nd, 2009
  • LSB Infrastructure Project [1]
  • ABI compliance checker [1]

Mehlhorn et al. (2008), Modelling and analysis of particle and pore structures in soils

August 21st, 2009

Mehlhorn, T., Prohaska, S., Homberg, U., and Slowik, V. (2008). Modelling and analysis of particle and pore structures in soils. In Proc. Work. Internal Erosion 2008, number 21 in Schriftenreihe Geotechnik, pages 53–60. Bauhaus-Universität Weimar.
[pdf]

@inproceedings{Mehlhorn:InternalErosion-2008,
	Author = {Thobias Mehlhorn and Steffen Prohaska
          and Ulrike Homberg and Volker Slowik},
	Booktitle = {Proc. Work. Internal Erosion 2008},
	Number = {21},
	Pages = {53--60},
	Publisher = {Bauhaus-Universit{\"a}t Weimar},
	Series = {Schriftenreihe Geotechnik},
	Title = {Modelling and Analysis of Particle and Pore Structures in Soils},
	Year = {2009}}

Homberg et al. (2008). Determining geometric grain structures from x-ray micro-tomograms of gradated soils

August 21st, 2009

Homberg, U., Binner, R., Prohaska, S., Dercksen, V. J., Kuß, A., and Kalbe, U. (2008). Determining geometric grain structures from x-ray micro-tomograms of gradated soils. In Proc. Work. Internal Erosion 2008, number 21 in Schriftenreihe Geotechnik, pages 37–52. Bauhaus-Universität Weimar.
[pdf]

@inproceedings{Homberg:InternalErosion-2008,
	Author = {Ulrike Homberg and Richard Binner
        and Steffen Prohaska and Vincent J. Dercksen and Anja Ku{\ss}
        and Ute Kalbe},
	Booktitle = {Proc. Work. Internal Erosion 2008},
	Number = {21},
	Pages = {37--52},
	Publisher = {Bauhaus-Universit{\"a}t Weimar},
	Series = {Schriftenreihe Geotechnik},
	Title = {Determining Geometric Grain Structures from
        X-Ray Micro-Tomograms of Gradated Soils},
	Year = {2009}}

Semar et al. (2008). Conditions for suffosive erosion phenomena in soils

August 21st, 2009

Semar, O., Binner, R., Homberg, U., Kalbe, U., Mehlhorn, T., Prohaska, S., Slowik, V., and Witt, J. (2008). Conditions for suffosive erosion phenomena in soils. In Proc. Work. Internal Erosion 2008, number 21 in Schriftenreihe Geotechnik, pages 29–35. Bauhaus-Universität Weimar.
[pdf]

@inproceedings{Semar:InternalErosion-2008,
	Author = {Olivier Semar and Richard Binner and Ulrike Homberg
        and Ute Kalbe and Thobias Mehlhorn and Steffen Prohaska
        and Volker Slowik and Josef Witt},
	Booktitle = {Proc. Work. Internal Erosion 2008},
	Number = {21},
	Pages = {29--35},
	Publisher = {Bauhaus-Universit{\"a}t Weimar},
	Series = {Schriftenreihe Geotechnik},
	Title = {Conditions for Suffosive Erosion Phenomena in Soils},
	Year = {2009}}

CUDA, Clean Code Developer

August 15th, 2009
  • Rob Farber explains CUDA in a multi-part article at Dr. Dobb’s [1].
  • Become a Clean Code Developer [1].

Safer Software, GFS II

August 14th, 2009
  • Researchers at NICTA proved correctness of a kernel [1].
  • Google is developing a successor of the Google File System [1, 2].

Git 1.6.3.2 on Windows

June 8th, 2009

Git 1.6.3.2 on Windows is available at http://code.google.com/p/msysgit/downloads.

Dercksen et al. (2009): Automatic alignment of stacks of filament data

May 22nd, 2009

Dercksen, V. J., Weber, B., Günther, D., Oberlaender, M., Prohaska, S., and Hege, H.-C. (2009). Automatic alignment of stacks of filament data. In Proc. 2009 IEEE Int. Symp. on Biomedical Imaging: From Nano to Macro (ISBI), pages 971–974.
[pdf]

@inproceedings{Dercksen:ISBI-2009,
	Author = {Vincent J. Dercksen and Britta Weber and David G{\"u}nther
        and Marcel Oberlaender and Steffen Prohaska and Hans-Christian Hege},
	Booktitle = {Proc. 2009 IEEE Int. Symp. on Biomedical Imaging:
        From Nano to Macro (ISBI)},
	Pages = {971--974},
	Title = {Automatic Alignment of Stacks of Filament Data},
	Year = {2009}}

Petz et al. (2009): Hierarchical vortex regions in swirling flow

April 24th, 2009

Petz, C., Kasten, J., Prohaska, S., and Hege, H.-C. (2009). Hierarchical vortex regions in swirling flow. Computer Graphics Forum, 28(3):863–870.
[pdf]

@article{Petz:EuroVis-2009,
	Author = {Christoph Petz and Jens Kasten and Steffen Prohaska
        and Hans-Christian Hege},
	Journal = {Computer Graphics Forum},
	Number = {3},
	Pages = {863--870},
	Title = {Hierarchical Vortex Regions in Swirling Flow},
	Volume = {28},
	Year = {2009}}

Rosanwo et al. (2009): Dual streamline seeding

April 9th, 2009

Rosanwo, O., Petz, C., Prohaska, S., Hotz, I., and Hege, H.-C. (2009). Dual streamline seeding. In Proc. Pacific Vis ’09, pages 9–16.
[pdf]

@inproceedings{Rosanwo:PacificVis-2009,
	Author = {Olufemi Rosanwo and Christoph Petz and Steffen Prohaska
        and Ingrid Hotz and Hans-Christian Hege},
	Booktitle = {Proc. Pacific Vis '09},
	Pages = {9--16},
	Title = {Dual Streamline Seeding},
	Year = {2009}}

Rosanwo et al. (2008): Dual streamline seeding – method and implementation

February 13th, 2009

Rosanwo, O., Petz, C., Prohaska, S., Hotz, I., and Hege, H.-C. (2008). Dual streamline seeding – method and implementation. ZIB Report ZR-08-49. [pdf]

@techreport{DualStreamlineSeeding-ZR-05-49,
	Author = {Olufemi Rosanwo and Christoph Petz and Steffen Prohaska
        and Ingrid Hotz and Hans-Christian Hege},
	Institution = {Zuse Institute Berlin},
	Month = {December},
	Number = {ZR-08-49},
	Title = {Dual Streamline Seeding - Method and Implementation},
	Year = {2008}}

eigenfactor.org

February 8th, 2009

eigenfactor.org is a free source to search for influential journals in a specific research field. It provides lists ranked by influence based on citation analysis, similar to but different in detail from ISI’s impact factor (see Impact Factor and Citation Index on Wikipedia).

Here are direct links to some specific areas:
COMPUTER IMAGING,
MEDICAL IMAGING,
COMPUTER SCIENCE,
FLUID MECHANICS,
MOLECULAR AND CELL BIOLOGY,
NEUROSCIENCE.

Amdahl’s Law in the Multicore Era

February 8th, 2009

This Google tech talk presentation by Mark D. Hill is very worthwhile to watch. Based on a few fundamental assumptions, Hill develops an extended version of Amdahl’s Laws and discusses whether processor designers should focus on improving the performance of single cores or on increasing the number of cores. He concludes that they should do both.

Kuß et al. (2008): Ontology-based visualization of hierarchical neuroanatomical structures

October 11th, 2008

Kuß, A., Prohaska, S., Meyer, B., Rybak, J., and Hege, H.-C. (2008). Ontology-based visualization of hierarchical neuroanatomical structures. In Proc. Work. Visual Computing for Biomedicine 2008, pages 177–184. [bib] [pdf]

Git 1.6.0.2 on Windows

September 21st, 2008

Git 1.6.0.2 on Windows is available at http://code.google.com/p/msysgit/downloads.

Git 1.5.6.1 on Windows

July 1st, 2008

Git 1.5.6.1 on Windows is available at http://code.google.com/p/msysgit/downloads. This release brings a fixed msys-1.0.dll that supports Vista. The 1.5.6 release was broken in this regards.

Git 1.5.6 on Windows

June 22nd, 2008

Git 1.5.6 on Windows is available at http://code.google.com/p/msysgit/downloads.

AMD’s Linux Support for their GPUs competitive?

June 20th, 2008

Michael Larabel reports on Phoronix that AMD has greatly improved Linux support for their GPUs. Michael writes that drivers are now competitive with NVIDIA’s drivers.

Medical Apps on the iPhone

June 10th, 2008

Here are two things I found particularly interesting while watching the WWDC 2008 Keynote:

At 45:30 S. Mark Williams from Modality introduces a medical learning application for anatomy running on the iPhone 2.0 API.

At 48:30 Mark Cain from MIMvista introduces a combined PET-CT viewer running on the iPhone 2.0 API.

goosh

June 3rd, 2008

Shell aficionados will immediately get hooked on goosh.org, the new (unofficial) interface to Google.

CT-Reconstruction With 8 GPUs

May 31st, 2008

Slashdot links to an article on DV Hardware that presents work by the Vision Lab of the University of Antwerp on GPU-based CT-reconstruction. The researchers gave their “desktop supercomputer” the name FASTRA. Watching their official movie on YouTube, I recognized around 3:30 that they might be using our software Amira for visualizing their “test patient” Bob.

Sahner et al. (2008): Extraction Of Feature Lines On Surface Meshes Based On Discrete Morse Theory

April 22nd, 2008

Sahner, J., Weber, B., Prohaska, S., and Lamecker, H. (2008). Extraction of feature lines on surface meshes based on discrete morse theory. Comput. Graph. Forum, 27(3):735–742.
[bib] [pdf]

Git 1.5.5 on Windows

April 13th, 2008

Git 1.5.5 is out and the Windows setup is available from http://code.google.com/p/msysgit/downloads. This release handles Windows line endings well. The release is, however, still tagged with preview because full support for case insensitive filesystems is not yet included.

ssh-agent on Mac OS X

April 12th, 2008

I recently installed Mac OS X 10.5 alias Leopard and since then I was wondering how the behavior of ssh-agent changed. The GUI application SSH Agent no longer works as it did on 10.4, instead a requester opens whenever I start an ssh connection.

The reason is that ssh-agent is now managed by launchd. David Dribin nicely describes the details in his blog and also gives advice how you can increase security even more.

MacVim

April 3rd, 2008

Today, I discovered MacVim, which is a port of the text editor Vim that seamlessly integrates with OS X. The integration includes an input manager that supports using Vim as an external editor in any Cocoa application, including Mail.app. I was always looking for such an integration, which allows me to write the body of my mails in Vim but use Mail.app for adding attachments and selecting addresses from my address book.

Although MacVim is only available as a snapshot release it works out of the box. Just download the snapshot, unpack it, move it to your Application, start MacVim, and select ‘Preferences > Integration > Install’ to activate MacVim as an external editor.

Great work. Thanks Björn. I am wondering if Steve sent him a new Mac. Björn would deserve it.

Slashdot: Physics Journal May Reconsider Wikipedia Ban

March 15th, 2008

A Slashdot post reports that Physical Review Letters (PRL) will reconsider its copyright policy, which currently does not allow authors to submit material to Wikipedia that is based on their published work. This happens after Jonathan Oppenheim and co-authors asked for a modified right agreement that would allow them to contribute to Wikipedia. Instead of agreeing, PRL withdrew acceptance of two articles. After protests against this decision, PRL plans to review its copyright policy at a meeting in May.

Git 1.5.4 on Windows

February 3rd, 2008

Git 1.5.4 is out and the Windows setup is available from http://code.google.com/p/msysgit/downloads. The Windows release is tagged as preview because support for line endings and case insensitive filesystems is still not satisfactory.

Petz et al. (2008): Near-Wall Flow Visualization in Flattened Surface Neighborhoods

January 25th, 2008

Our submission to SimVis 2008 was accepted:

Petz, C., Prohaska, S., Goubergrits, L., Kertzscher, U., and Hege, H.-C. (2008). Near-wall flow visualization in flattened surface neighborhoods. In Proc. SimVis 2008. [bib] [pdf]

Storing Scientific Data at Google?

January 20th, 2008

A post on Slashdot reports that Google will soon offer free storage for massive scientific data on http://research.google.com/. Alexis Madrigal mentions more details in a post on Wired. Pimm’s post on the same topic displays the device to send data on slide 10/16. Google seems to plan to collect data by shipping hard drives.

Maybe I’ll try with the 8 GByte micro-CT data set of a human vertebral body, which we published in 2005. Or is is too small for Google?

New Homepage

January 19th, 2008

I decided to replace my old XML/XLST-based homepage by a WordPress blog. The old homepage was an interesting exercise about XML technologies. But lately I became too lazy to maintain the XML source and started thinking about a new way of publishing. I browsed a bit and found out that Malte Clasen’s page is based on WordPress, which seems to be a useful tool. So I decided to follow his choice.

I completed only the very basic setup for which I migrated some parts of my old homepage to the new blog style. Up to now, only publications and talks are available as blog categories. Everything else remains at the old location. I also did not yet work on the design of my new page. It is still based on WordPress’s default Kubrick theme.

Skeleton-Based Visualization of Massive Voxel Objects with Network-Like Architecture

August 17th, 2007

I published my PhD thesis at the University of Potsdam:

Prohaska, S. (2007). Skeleton-Based Visualization of Massive Voxel Objects with Network-Like Architecture. PhD thesis, University of Potsdam. [bib]

The abstract and full text is available at the university’s publication server:

http://opus.kobv.de/ubp/volltexte/2007/1488/

Talks up to mid 2007

June 30th, 2007

I restructured my homepage and copied the old list of my talks below to make the information available on this new homepage.

April 25, 2007

Visuelle Datenanalyse mit Amira

HLRN-Workshop “Graphisches Postprocessing”.
Hannover, Germany.
April 25, 2007.

February 27, 2007

Analysis of 3D Data in Geo-Sciences: Visualization and Feature Extraction

Workshop on Rock Mechanics and Logistics in Mining.
Santiago de Chile.
February 26 – March 2, 2007.

April 6, 2006

Interaktive Visualisierung und Datenanalyse: Herausforderungen durch wachsende Datenmengen

GeoVis 2006.
GFZ Potsdam.
April 5 – 6, 2006.

paper
October 17, 2005, 10:40

Rekonstruktion von Blutgefäßnetzwerken

Neuro Workshop.
Zuse Institut Berlin.
October 17, 2005.

slides
April 27, 2005, 11:00

Highly Interactive Data Analysis and Visualization with Amira

SGI VizDays.
Rüsselsheim.
April 26 – 27, 2005.

sgi
April 21, 2005, 20:30

Interactive Visualization of Large Remote AMR Data

Visualization Workshop.
Innsbruck University Center Obergurgl.
April 20 – 24, 2005.

talk
workshop
February 3, 2005, 10:30

Remote Data Access for Interactive Visualization

13th Annual Mardi Gras Conference: Frontiers of Grid Applications and Technologies.
Baton Rouge, Louisiana, USA.

paper
talk
conference
October 26, 2004, 14:00

Interactive Visual Data Analysis of Terascale Data: An Achieveable Goal?

CCT Seminar.
Baton Rouge, Louisiana, USA.

talk
CCT@LSU
October 14, 2004, 13:45, Large Data Session

Interactive Exploration of Large Remote Micro-CT Scans

IEEE Visualization.
Austin, Texas, USA.
October 10 – 15, 2004.

paper
talk
movie
conference
May 25, 2004

Exploring High-Resolution Medical Image Data

BIRS Workshop on Mathematical Foundations of Scientific Visualization, Computer Graphics, and Massive Data Exploration.
Banff, Alberta, Canada.
May 22 – 27, 2004.

talk.pdf
workshop
May 21, 2003, 10:00, Medical Care Session

A Virtual Laboratory for Assessment of Bone Biopsies

14th IAA Humans in Space Symposium.
Banff, Alberta, Canada.
May 18 – 22, 2003.

talk.pdf
conference
abstract.pdf
March 28, 2003, 10:30

Interactive Visualization to Support Quantification of Bone Biopsies

2nd European Congress “Achievements in Space Medicine into Health Care Practice and Industry”.
Berlin-Adlershof.
March 27 – 29, 2003.

talk.pdf
abstract@conference
abstract.pdf
November 18, 2002

Display and Handling of Large 3D Images for Analysis of Micro-Vascular Networks

Towards a Research Network on Imaging and Biomechanics of the Brain Microcirculation. Workshop.
Toulouse.
November 18 – 19, 2002.

talk.pdf
abstract.pdf
October 30, 2002

Fast Visualization of Plane-Like Structures in Voxel Data

IEEE Visualization 2002.
Boston.
October 27 – November 1, 2002.

talk.pdf (5.5 MB)
paper.pdf
July 27 – August 2, 2002

Advanced Visualization with amira and amiraVR

Training class.
BP Center for Visualization, University of Colorado, Boulder, Colorado.

webpage
June 27, 2002, 17:30

Analysis of Microvascular Networks

Summer School on Massive Data Sets.
BRICS, University of Aarhus, Denmark.
June 27 – July 1, 2002.

webpage
talk.pdf
June 3, 2002, 13:30

Visual Analysis of Trabecular Bone Structure

European Symposium on “Life in Space for Life on Earth”.
Karolinska Institutet, Stockholm, Sweden.
June 2 – 7, 2002.

talk.pdf
conference
abstract.pdf

Publications up to 2006

December 31st, 2006

I restructured my homepage. To maintain all information I copied the content of my old list of publications here:

teaser

Andrei Hutanu, Gabrielle Allen, Stephen D. Beck, Petr Holub, Hartmut Kaiser, Archit Kulshrestha, Milos Liska, Jon MacLaren, Ludek Matyska, Ravi Paruchuri, Steffen Prohaska, Edward Seidel, Brygg Ullmer, Shalini Venkataraman
Distributed and collaborative visualization of large data sets using high-speed networks

Future Generation Comp. Syst, 22(8):1004–1010, 2006 paper
teaser

Céline Fouard, Grégoire Malandain, Steffen Prohaska, Malte Westerhoff
Blockwise processing applied to brain micro-vascular network study

IEEE Trans. Medical Imaging, 25(10):1319, 2006 paper
teaser

Steffen Prohaska
Interaktive Visualisierung und Datenanalyse: Herausforderungen durch wachsende Datenmengen

Kartographische Schriften: Aktuelle Entwicklungen in Geoinformation und Visualisierung (GEOVIS 2006), volume 10, p. 103–110, 2006 paper
teaser

Francis Cassot, Frederic Lauwers, Céline Fouard, Steffen Prohaska, Valerie Lauwer-Cances
A novel three-dimensional computer assisted method for a quantitative study of microvascular networks of the human cerebral cortex

Microcirculation, 13:15–32, 2006 paper
teaser

ESA MAP Team AO-99-030
Assessment of Bone Structure and its Changes in Microgravity

SP-1290: Microgravity Applications Programme: Successful Teaming of Science and Industry, Ed.: A. Wilson, European Space Agency, p. 282–305, 2005 paper
teaser

Ralf Kähler, Steffen Prohaska, Andrei Hutanu, Hans-Christian Hege
Visualization of Time-Dependent Remote Adaptive Mesh Refinement Data

Proc. IEEE Visualization ’05, p. 175–182, 2005 paper
teaser

Céline Fouard, Grégoire Malandain, Steffen Prohaska, Malte Westerhoff
Blockwise processing applied to brain micro-vascular network study

INRIA, Research Report, 5581, 2005 paper
teaser

Hans-Christian Hege, Tino Weinkauf, Steffen Prohaska, Andrei Hutanu
Towards Distributed Visualization and Analysis of Large Flow Data

JSME Int. J., Series B, 48(2):241, 2005
teaser

Vincent Jasper Dercksen, Steffen Prohaska, Hans-Christian Hege
Fast Cross-Sectional Display of Large Data Sets

IAPR Conference on Machine Vision Applications, Tsukuba, Japan, 2005 paper
teaser

J. S. Thomsen, A. Laib, B. Koller, S. Prohaska, Li. Mosekilde, W. Gowin
Stereological measures of trabecular bone structure: comparison of 3D micro computed tomography with 2D histological sections in human proximal tibial bone biopsies

J. Microscopy, 218:171, 2005 paper
teaser

Steffen Prohaska, Andrei Hutanu
Remote Data Access for Interactive Visualization

Proc. 13th Annual Mardi Gras Conf.: Frontiers of Grid Applications and Technologies, p. 17–22, 2005 paper
talk
teaser

Alexei Zaikin, Peter Saparin, Jürgen Kurths, Steffen Prohaska, Wolfgang Gowin
Modeling resorption in 2D CT and 3D µ-CT bone images

Int. J. Bifurcation and Chaos, 15(9):2995–3009, 2005 paper
teaser

Steffen Prohaska, Matthew Dreher, Mark W. Dewhirst, Ashutosh Chilkoti, Axel R. Pries, Malte Westerhoff, Annemiek J. M. Cornelissen
3-D Reconstruction of Tumor Vascular Networks

J. Vascular Research, 41:463, 2004 abstract
poster
teaser

Hans-Christian Hege, Tino Weinkauf, Steffen Prohaska, Andrei Hutanu
Distributed Visualization and Analysis of Fluid Dynamics Data

Proc. Fourth International Symposium on Advanced Fluid Information and Transdisciplinary Fluid Integration, Sendai, Japan, 2004 extended abstract
teaser

Steffen Prohaska, Andrei Hutanu, Ralf Kähler, Hans-Christian Hege
Interactive Exploration of Large Remote Micro-CT Scans

Proc. IEEE Visualization ’04, p. 345–352, Austin, Texas, 2004 paper
talk
movie
data set

Peter Saparin, Jesper S. Thomsen, Steffen Prohaska, Alexei Zaikin, Jürgen Kurths, Hans-Christian Hege, Wolfgang Gowin
Quantification of Spatial Structure of Human Proximal Tibial Bone Biopsies Using 3D Measures of Complexity

Acta Astronautica, 56(8):820–830, 2005 paper
teaser

Céline Fouard, Grégoire Malandain, Steffen Prohaska, Malte Westerhoff, Francis Cassot, Christophe Mazel, Didier Asselot, Jean-Pierre Marc-Vergnes
Skeletonization by Blocks for Large 3D Datasets: Application to Brain Microcirculation

IEEE Int. Symp. Biomedical Imaging: From Nano to Macro (ISBI ’04), Arlington, Virginia, 2004 conference
paper

Céline Fouard, Grégoire Malandain, Steffen Prohaska, Malte Westerhoff, Francis Cassot, Christophe Mazel, Didier Asselot, Jean-Pierre Marc-Vergnes
Squelettisation par blocs pour des grands volumes de données 3D: application à la microcirculation cérébrale

Reconnaissance des Formes et Intelligence Artificielle (RFIA 2004), Toulouse, France, 2004 conference
paper
teaser

Steffen Prohaska, Hans-Christian Hege, Michael Giehl, Wolfgang Gowin
A Virtual Laboratory for Assessment of Bone Biopsies

14th IAA Humans in Space Symposium, Banff, Alberta, Canada, 2003 conference
abstract

Peter Saparin, Wolfgang Gowin, Alexei Zaikin, Jesper S. Thomsen, Steffen Prohaska, Hans-Christian Hege, Jürgen Kurths
Quantification of Changes in Spatial Structure of Human Bone Biopsies Using 3D Measures of Complexity

14th IAA Humans in Space Symposium, Banff, Alberta, Canada, 2003 conference
abstract
teaser

Steffen Prohaska, Hans-Christian Hege, Michael Giehl, Wolfgang Gowin
Interactive Visualization to Support Quantitative Analysis of Bone Biopsies

2nd European Congress on Achievements in Space Medicine into Health Care Practice and Industry, Berlin-Adlershof, 2003 conference
abstract
talk

Peter Saparin, Wolfgang Gowin, Alexei Zaikin, Steffen Prohaska
Quantification of changes in human bone structure at different skeletal locations using measures of complexity

2nd European Congress on Achievements in Space Medicine into Health Care Practice and Industry, Berlin-Adlershof, 2003 conference
abstract

Wolfgang Gowin, Peter Saparin, Steffen Prohaska, Hans-Christian Hege, Stefan Beller, Dieter Felsenberg
Architectural Reasons for the Femoral Neck Fracture Location

2nd European Congress on Achievements in Space Medicine into Health Care Practice and Industry, Berlin-Adlershof, 2003 conference
abstract

Alexei Zaikin, Peter Saparin, Steffen Prohaska, Jürgen Kurths, Wolfgang Gowin
2D and 3D bone modelling for analysis of changes in the bone architecture and for evaluation of structural measures

2nd European Congress on Achievements in Space Medicine into Health Care Practice and Industry, Berlin-Adlershof, 2003 conference
abstract
paper

J. S. Thomsen, B. Koller, A. Laib, S. Prohaska, M. Giehl, W. Gowin
Comparison between Static Histomorphometric Measures Conducted by Traditional 2D Histomorphometry and 3D µ-CT Human Tibial Biopsies

2nd European Congress on Achievements in Space Medicine into Health Care Practice and Industry, Berlin-Adlershof, 2003 conference
abstract
teaser

Hans-Christian Hege, Hartmut Schirmacher, Malte Westerhoff, Hans Lamecker, Steffen Prohaska, Stefan Zachow
From Image Data to Three-Dimensional Models – Case Studies on the Impact of 3D Patient Models

Proceedings of MMVR ’03, Newport Beach, California, 2003 conference
abstract
teaser

Steffen Prohaska
Display and Handling of Large 3D Images for Analysis of Micro-Vascular Networks

to be published in Proceedings of the Workshop Towards a Research Network on Imaging and Biomechanics of the Brain Circulation, 2003 abstract
talk
teaser

Steffen Prohaska, Hans-Christian Hege
Fast Visualization of Plane-Like Structures in Voxel Data

Proc. IEEE Visualization ’02, p. 29–36, Boston, Massachusetts, 2002 paper
talk (5MB)

W. Gowin, P. Saparin, S. Prohaska, H.-C. Hege, D. Felsenberg
Femoral Neck Fractures: Reasons for the Most Common Location of Fractures

Acta Orthop Scand (Suppl 304), 73:26, 2002
teaser

Hans-Christian Hege, Hartmut Schirmacher, Malte Westerhoff, Hans Lamecker, Steffen Prohaska, Stefan Zachow
From Image Data to Three-Dimensional Models – Case Studies on the Impact of 3D Patient Models

Proc. of the Japan Korea Computer Graphics Conference 2002, CDROM, Kanazawa University, Kanazawa City, Ishikawa, Japan, 2002 conference

A. Zaikin, P. Saparin, S. Prohaska, J. Kurths, W. Gowin
Bone Modeling and Structural Measures of Complexity

Poster at Dynamic Days Europe, Heidelberg, Germany, 2002
teaser

Steffen Prohaska, Hans-Christian Hege, Michael Giehl, Wolfgang Gowin
Visual Analysis of Trabecular Bone Structure

J. Grav. Physiol., 9(1):171–172, 2002 abstract
talk

Steffen Prohaska, Hans-Christian Hege, Michael Giehl, Wolfgang Gowin
Visual Analysis of Trabecular Bone Structure

Proceedings of Life in Space for Life on Earth, 2-7 June 2002, Karolinska Institutet, Stockholm, Sweden, p. 75–76, 2002 abstract
talk

A. Zaikin, P. Saparin, S. Prohaska, J. Kurths, W. Gowin
Bone Modeling and Structural Measures of Complexity

Proceedings of Life in Space for Life on Earth, 2-7 June 2002, Karolinska Institutet, Stockholm, Sweden, p. 79–80, 2002 abstract

A. Zaikin, P. Saparin, S. Prohaska, J. Kurths, W. Gowin
Bone Modeling and Structural Measures of Complexity

J. Grav. Physiol., 9(1):175–176, 2002 abstract

W. Gowin, P. Saparin, D. Felsenberg, J. Kurths, A. Zaikin, S. Prohaska
Regional Structural Skeletal Discordance Assessed by Measures of Complexity

Poster at the IOF World Congress on Osteoporosis, Lisbon, 2002

Cornelia Kober, Robert Sader, Hans-Florian Zeilhofer, Steffen Prohaska, Stefan Zachow, Peter Deuflhard
Anisotrope Materialmodellierung für den menschlichen Unterkiefer

Zuse Institute Berlin, Preprint, ZR-01-31, 2001 abstract
pdf