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at - Automatisierungstechnik

Methoden und Anwendungen der Steuerungs-, Regelungs- und Informationstechnik

[AT - Automation Technology: Methods and Applications of Control, Regulation, and Information Technology
]

Editor-in-Chief: Bretthauer, Georg

12 Issues per year


IMPACT FACTOR 2016: 0.675

CiteScore 2016: 0.55

SCImago Journal Rank (SJR) 2016: 0.262
Source Normalized Impact per Paper (SNIP) 2016: 0.645

Online
ISSN
2196-677X
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Volume 64, Issue 7 (Jul 2016)

Issues

Automation strategies for large-scale 3D image analysis

Automatisierungsstrategien zur Analyse von großen Datensätzen mit 3D-Bildern

Johannes Stegmaier
  • Corresponding author
  • Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
  • HeiKa – Heidelberg Karlsruhe Research Partnership, Heidelberg University, Karlsruhe Institute of Technology (KIT), Germany
  • Email:
/ Benjamin Schott
  • Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
/ Eduard Hübner
  • Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
/ Manuel Traub
  • Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
/ Maryam Shahid
  • Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
/ Masanari Takamiya
  • Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
/ Andrei Kobitski
  • Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany
/ Volker Hartmann
  • Institute for Data Processing and Electronics, Karlsruhe Institute of Technology, Karlsruhe, Germany
/ Rainer Stotzka
  • Institute for Data Processing and Electronics, Karlsruhe Institute of Technology, Karlsruhe, Germany
/ Jos van Wezel
  • Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Karlsruhe, Germany
/ Achim Streit
  • Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Karlsruhe, Germany
/ G. Ulrich Nienhaus
  • Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany
  • Institute of Nanotechnology, Karlsruhe Institute of Technology, Karlsruhe, Germany
  • Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
/ Uwe Strähle
  • Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
/ Markus Reischl
  • Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
  • HeiKa – Heidelberg Karlsruhe Research Partnership, Heidelberg University, Karlsruhe Institute of Technology (KIT), Germany
/ Ralf Mikut
  • Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
Published Online: 2016-07-02 | DOI: https://doi.org/10.1515/auto-2016-0019

Abstract

New imaging techniques enable visualizing and analyzing a multitude of unknown phenomena in many areas of science at high spatio-temporal resolution. The rapidly growing amount of image data, however, can hardly be analyzed manually and, thus, future research has to focus on automated image analysis methods that allow one to reliably extract the desired information from large-scale multidimensional image data. Starting with infrastructural challenges, we present new software tools, validation benchmarks and processing strategies that help coping with large-scale image data. The presented methods are illustrated on typical problems observed in developmental biology that can be answered, e.g., by using time-resolved 3D microscopy images.

Zusammenfassung

Neue bildgebende Verfahren ermöglichen eine detaillierte Analyse und Visualisierung verschiedenster unbekannter Phänomene in vielen wissenschaftlichen Bereichen mit hoher räumlicher und zeitlicher Auflösung. Die stetig wachsende Bilddatenmenge kann hierbei nur unzureichend manuell untersucht werden, weswegen künftig vermehrt automatische Auswertungsroutinen benötigt werden, um relevante Informationen zuverlässig aus großen, mehrdimensionalen Bilddaten zu extrahieren. Beginnend mit den infrastrukturellen Herausforderungen werden im Rahmen dieser Veröffentlichung neue Softwaretools, ein Validierungsbenchmark sowie verschiedene Verarbeitungsstrategien vorgestellt, um die Analyse großer Bilddaten zu ermöglichen und zu vereinfachen. Die präsentierten Methoden werden anhand von typischen Problemen aus der Entwicklungsbiologie veranschaulicht, die mittels zeitaufgelöster 3D Mikroskopie untersucht werden.

Keywords: Image analysis; Big Data; microscopy; developmental biology; parallel computing

Schlagwörter: Bildanalyse; Big Data; Mikroskopie; Entwicklungsbiologie; Paralleles Rechnen

About the article

Johannes Stegmaier

Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany; and HeiKa – Heidelberg Karlsruhe Research Partnership, Heidelberg University, Karlsruhe Institute of Technology (KIT), Germany

Benjamin Schott

Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany

Eduard Hübner

Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany

Manuel Traub

Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany

Maryam Shahid

Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany

Masanari Takamiya

Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany

Andrei Kobitski

Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany

Volker Hartmann

Institute for Data Processing and Electronics, Karlsruhe Institute of Technology, Karlsruhe, Germany

Rainer Stotzka

Institute for Data Processing and Electronics, Karlsruhe Institute of Technology, Karlsruhe, Germany

Jos van Wezel

Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Karlsruhe, Germany

Achim Streit

Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Karlsruhe, Germany

G. Ulrich Nienhaus

Institute of Nanotechnology, Karlsruhe Institute of Technology, Karlsruhe, Germany; and Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany; and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA

Uwe Strähle

Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany

Markus Reischl

Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany; and HeiKa – Heidelberg Karlsruhe Research Partnership, Heidelberg University, Karlsruhe Institute of Technology (KIT), Germany

Ralf Mikut

Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany


Accepted: 2016-05-19

Received: 2016-02-02

Published Online: 2016-07-02

Published in Print: 2016-07-28


Citation Information: at - Automatisierungstechnik, ISSN (Online) 2196-677X, ISSN (Print) 0178-2312, DOI: https://doi.org/10.1515/auto-2016-0019.

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