INCIDE - Interdisciplinary Center for interactive Data Analysis, Modelling and Visual Exploration

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INCIDE Publications

2016

Automated Image Processing to Quantify Cell MigrationSingle-Image Insect Pose Estimation by Graph Based Geometric Models and Random Forests
  • Minmin Shen, Le Duan, Oliver Deussen
  • ECCV workshop on Bioimage Computing
  • 2016; pp. 217-230.
Automated Image Processing to Quantify Cell MigrationStem Cell Microscopic Image Segmentation Using Supervised Normalized Cuts
  • Xinyu Huang, Chen Li, Minmin Shen, Kimiaki Shirahama, Johanna Nyffeler, Marcel Leist, Marcin Grzegorzek, and Oliver Deussen
  • IEEE International Conference on Image Processing (ICIP)
  • 2016; pp. 4140-4144.

2015

Automated Image Processing to Quantify Cell MigrationInsects Interactive Tracking of Insect Posture
  • Minmin Shen, Chen Li, Wei Huang, Paul Szyszka, Kimiaki Shirahama, Marcin Grzegorzek, Dorit Merhof, Oliver Deussen
  • Patter Recognition, 48(11)
  • 2015; pp. 3560-3571.
Automated Image Processing to Quantify Cell MigrationAutomated Tracking and Analysis of Behavior in Restrained Insects
  • Minmin Shen, Paul Szyszka, Oliver Deussen, C. Giovanni Galizia, Dorit Merhof
  • Journal of Neuroscience Methods, 239(2015)
  • 2015; pp. 194-205.

2014

Automated Image Processing to Quantify Cell Migration Interactive Framework for Insect Tracking with Active Learning
  • Minmin Shen, Wei Huang, Paul Szyszka, C. Giovanni Galizia, Dorit Merhof
  • IEEE International Conference on Pattern Recognition (ICPR)
  • 2014; pp. 2733-2738; oral presentation

2013

Automated Image Processing to Quantify Cell Migration
Automated Image Processing to Quantify Cell Migration
  • Minmin Shen, Bastian Zimmer, Marcel Leist, Dorit Merhof
  • Bildverarbeitung für die Medizin (BVM)
  • 2013; pp. 152-157; oral presentation
INCIDE the Brain of a Bee: Visualising Honeybee Brain Activity in Real Time by Semantic Segmentation

The Looks of an Odor - Visualising Neural Odor Response Patterns in Real Time

  • Martin Strauch, Clemens Müthing, Marc P. Brög, Paul Szyska, Daniel Münch, Thomas Laudes, Oliver Deussen, C. Giovanni Galizia, Dorit Merhof
  • BMC Bioinformatics, 14(Suppl 19):S6
  • 2013;
Transition metal precipitates in mc Si: a new detection method using 3D-FIB

Transition metal precipitates in mc Si: a new detection method using 3D-FIB

  • Annika Zuschlag, Michail Schwab, Dorit Merhof, Giso Hahn
  • Gettering and Defect Engineering in Semiconductor Technology (GADEST); Solid State Phenomena 205-206
  • 2013; pp. 136-141
Automatic framework for tracking honeybee's antennae and mouthparts from low framerate video

Automatic framework for tracking honeybee's antennae and mouthparts from low framerate video

  • Minmin Shen, Paul Szyszka, C. Giovanni Galizia, Dorit Merhof
  • IEEE International Conference on Image Processing (ICIP)
  • 2013; pp.4112-4116;
Evaluation of a human neurite growth assay as specific screen for developmentally neurotoxic chemicals

Evaluation of a human neurite growth assay as specific screen for developmentally neurotoxic chemicals

  • Anne K. Krug, Nina V. Balmer, Florian Matt, Felix Schönenberger, Dorit Merhof, Marcel Leist
  • Archives of Toxicology 87(12)
  • 2013; pp. 2215-2231;

Intracellular tracking of single plasmid DNA-particles after delivery by electroporation

  • Christelle Rosazza, Annette Buntz, Thorsten Rieß, Dominik Wöll, Andreas Zumbusch, Marie-Pierre Rols
  • Molecular Therapy
  • 2013; (accepted)

2012

HiTSEE KNIME: A Visualization Tool for Hit Selection and Analysis in High-Throughput Screening Experiments for the KNIME Platform

HiTSEE KNIME: A Visualization Tool for Hit Selection and Analysis in High-Throughput Screening Experiments for the KNIME Platform

  • Hendrik Strobelt, Enrico Bertini, Joachim Braun, Oliver Deussen, Ulrich Groth, Thomas U. Mayer, Dorit Merhof
  • BMC Bioinformatics, 13(Suppl 8):S4
  • 2012; pp. 1-13;
An Advanced Image Processing Approach based on Parallel Growth and Overlap Handling to Quantify Neurite Growth
An Advanced Image Processing Approach based on Parallel Growth and Overlap Handling to Quantify Neurite Growth
  • Felix Schönenberger, Anne Krug, Marcel Leist, Elisa Ferrando-May, Dorit Merhof
  • 9th International Workshop on Computational Systems Biology (WCSB)
  • 2012; pp. 92-95;
Image Analysis of Nuclear Envelope Breakdown Events using KNIME
Image Analysis of Nuclear Envelope Breakdown Events using KNIME
  • Thorsten Rieß, Joseph Marino, Cornelia Wandke, Dorit Merhof, Oliver Deussen, Gábor Csúcs, Ulrike Kutay, Péter Horváth
  • 9th International Workshop on Computational Systems Biology (WCSB)
  • 2012; pp. 72-75;
INCIDE the Brain of a Bee: Visualising Honeybee Brain Activity in Real Time by Semantic Segmentation

INCIDE the Brain of a Bee: Visualising Honeybee Brain Activity in Real Time by Semantic Segmentation
(--- Honorable Mention Award ---)
video1, video2

  • Martin Strauch, Marc P. Brög, Clemens Müthing, Paul Szyska, Oliver Deussen, C. Giovanni Galizia, Dorit Merhof
  • 2nd IEEE Symposium on Biological Data Visualization (IEEE BioVis)
  • 2012; pp. 17-24;

 2011

Automated Image Processing for the Analysis of DNA Repair Dynamics
Automated Image Processing for the Analysis of DNA Repair Dynamics
  • Thorsten Rieß, Christian Dietz, Martin Tomas, Elisa Ferrando-May, Dorit Merhof
  • 3rd International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies (BIOTECHNO)
  • 2011; pp. 31-36; ISBN: 978-1-61208-007-9
A Versatile Framework for the Analysis of High-Throughput Screening Data
A Versatile Framework for the Analysis of High-Throughput Screening Data
  • Johannes Hamecher, Thorsten Riess, Enrico Bertini, Karol Kozak, Johanna Kastl, Thomas U. Mayer, Dorit Merhof
  • 8th International Workshop on Computational Systems Biology (WCSB)
  • 2011; pp. 57-60;
A Versatile Framework for the Analysis of High-Throughput Screening Data
Automated Image Processing to Quantify Neurite Growth in LUHMES Human Neuronal Precursor Cells
  • Dorit Merhof, Felix Schönenberger, Nina Stiegler, Anne Krug, Thorsten Riess, Christiaan Karreman, Marcel Leist, Elisa Ferrando-May
  • 8th International Workshop on Computational Systems Biology (WCSB)
  • 2011; pp. 133-136;
A Versatile Framework for the Analysis of High-Throughput Screening Data

Automated quantification of histone relocation in cell nuclei

  • Thorsten Rieß, Christian Dietz, Martin Horn, Oliver Deussen, Tanja Waldmann, Marcel Leist, Dorit Merhof
  • VipIMAGE2011 - 3rd ECCOMAS Thematic Conference on Computational Vision and Medical Image Processing
  • 2011; pp. 423-428;
HiTSEE: A Visualization Tool for Hit Selection and Analysis in High-Throughput Screening Experiments

HiTSEE: A Visualization Tool for Hit Selection and Analysis in High-Throughput Screening Experiments
(--- Honorable Mention Award ---)

  • Enrico Bertini, Hendrik Strobelt, Joachim Braun, Oliver Deussen, Ulrich Groth, Thomas U. Mayer, Dorit Merhof
  • 1st IEEE Symposium on Biological Data Visualization (IEEE BioVis)
  • 2011; pp. 95-102;

2010

Automated Image Processing for the Analysis of DNA Repair Dynamics
Automated Image Processing for the Analysis of DNA Repair Dynamics
  • Thorsten Rieß, Christian Dietz, Martin Tomas, Elisa Ferrando-May, Dorit Merhof
  • Technical Report
  • 2010;

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Publications supported by INCIDE

2010

A dual function for chaperones SSB-RAC and the NAC nascent polypeptide-associated complex on ribosomes
A dual function for chaperones SSB-RAC and the NAC nascent polypeptide-associated complex on ribosomes
  • Ansgar Koplin, Steffen Preissler, Yulia Ilina, Miriam Koch, Annika Scior, Marc Erhardt, Elke Deuerling
  • The Journal of Cell Biology 189(1)
  • 2010; pp. 57-68;

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