Microscopic Image Analysis with Applications in Biology
Heidelberg, Germany, September 2, 2011

List of Papers:

Segmentation of Microscopy Images

Fluorescence Image Segmentation by using Digitally Reconstructed Fluorescence Images
Clemens Blumer, Cyprien Vivien, Thomas Oertner, Thomas Vetter, University of Basel
[Full Paper] [pdf] [bibtex]

Two-Step Watershed Segmentation of Epithelial Cells
Kevin Keraudren, Martin Spitaler, Vania M.M. Braga, Daniel Rueckert, Luis Pizarro, Imperial College London
[Full Paper] [pdf] [bibtex]

3D Model-Based Quantification of EGF Receptor Internalization from Three-Channel 3D Microscopy Images
Stefan Wörz, Eileen Reinz, Angel Alonso, Karl Rohr, University of Heidelberg, DKFZ Heidelberg
[Full Paper] [pdf] [bibtex]

TICAL - a web-tool for multivariate image clustering and data topology preserving visualization
Daniel Langenkämper, Jan Kölling, Sylvie Abouna, Michael Khan, Karsten Niehaus, Tim W. Nattkemper, University of Bielefeld, University of Warwick
[Full Paper] [pdf] [bibtex]

Three dimensional cell nuclei extraction from fluorescence microscopy images using locally adaptive threshold
M. Khayrul Bashar, Koji Komatsu, Toshihiko Fujimori, Tetsuya Kobayashi, University of Tokyo, National Institute for Basic Biology, Aichi, Japan
[Abstract] [pdf] [bibtex]

Evaluation of an interactive cell segmentation for fluorescence-microscopy based on the Graph Cut algorithm
Claudia Dach, Christian Held, Jens Wenzel, Sophia Gerlach, Roland Lang, Ralf Palmisano, Thomas Wittenberg, Fraunhofer IIS, University of Erlangen
[Full Paper] [pdf] [bibtex]

A Framework for Molecular Co-Expression Pattern Analysis in Multi-Channel Toponome Fluorescence Images
Ahmad Humayun, Shan-e-Ahmed Raza, Christine Waddington, Sylvie Abouna, Michael Khan, Nasir M. Rajpoot, University of Warwick
[Full Paper] [pdf] [bibtex]

Analysis of time-resolved images

Dynamic Time Warping for Automated Cell Cycle Labelling
Amr El-Labban, Andrew Zisserman, Yusuke Toyoda, Alex Bird, Anthony Hyman, University of Oxford, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden [Full Paper] [pdf] [bibtex]

Large-Scale Tracking for Cell Migration and Proliferation Analysis and Experimental Optimization of High-Throughput Screens
Nathalie Harder, Richa Batra, Sina Gogolin, Nicolle Diessl, Roland Eils, Frank Westermann, Rainer König, Karl Rohr, University of Heidelberg, DKFZ Heidelberg
[Full Paper] [pdf] [bibtex]

Efficient fluorescence image normalization for time lapse movies
Michael Schwarzfischer, Carsten Marr, Jan Krumsiek, Philipp S. Hoppe, Timm Schroeder, Fabian J. Theis, Helmholtz Zentrum München, Technische Universität München
[Full Paper] [pdf] [bibtex]

Learning to Count Cells: Applications to Lens-free Imaging of Large Fields
Giselle Flaccavento, Victor Lempitsky, Iestyn Pope, Paul Barber, Andrew Zisserman, J. Alison Noble, Boris Vojnovic, University of Oxford
[Full Paper] [pdf] [bibtex]

Evaluation of cell-tracking algorithms with respect to the characteristics of bioimages
Yusuke Azuma, Shuichi Onami, RIKEN, Japan
[Abstract] [pdf] [bibtex]

Probabilistic Multi-Target Tracking Approach to Motion Analysis of Stress Granules
Oliver Greß, Nadine Stöhr, Stefan Hüttelmaier, Stefan Posch, Martin Luther University Halle-Wittenberg
[Abstract] [pdf] [bibtex]

Non-Invasive Imaging-Based Monitoring for Characterisation and Optimisation of Embryonic Stem Cell Processes
Nicolas Jaccard, Rhys Macown, Farlan Veraitch, Nicolas Szita, Lewis Griffin, University College London
[Full Paper] [pdf] [bibtex]

Automated Image Analysis of the Interaction between Phagocytes and Aspergillus fumigatus during Infection
Franziska Mech, Andreas Thywißen, Reinhard Guthke, Axel Brakhage, Marc Thilo Figge, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Friedrich Schiller University, Jena
[Full Paper] [bibtex]

Classification and Machine Learning

Optimal Parameter Selection for an Image Processing Algorithm Through Active Learning
David Sheehan, James Muir, Josef Kittler, Lewis Griffin, University College London
[Full Paper] [pdf] [bibtex]

Phenotype Classification of Zebrafish Embryos by Supervised Learning
Nathalie Jeanray, Raphaël Marèe, Benoist Pruvot, Olivier Stern, Pierre Geurts, Louis Wehenkel, Marc Muller, University of Liège
[Full Paper] [pdf] [bibtex]

A circle-based method for detection of neural fibre cross-sections in classically stained 2D electron micrographs
Martin O'Reilly, Arnd Roth, Michael Häusser, Lewis D. Griffin, University College London
[Full Paper] [pdf] [bibtex]

Detection and Classification of Nano-Objects in Biosensor Data
Dominic Siedhoff, Frank Weichert, Pascal Libuschewski, Constantin Timm, TU Dortmund
[Abstract] [pdf] [bibtex]

Automatic Detection of Proliferative Cells in Immunohistochemically Images of Meningioma Using Fuzzy C-Means Clustering and HSV Color Space
Vahid Anari, Rasoul Amirfattahi, Islamic Azad University, Isfehan University of Technology
[Full Paper] [pdf] [bibtex]

Hierarchical Recognition System for Microscopic Images Using Histogram Measure and Feature Selection
Pei-Fang Guo, Prabir Bhattacharya, University of Cincinnati, OH, USA
[Full Paper] [pdf] [bibtex]

A framework for autophagy study based on machine learning
Xiaoyun Huang, Anne Hamacher-Brady, Nathan Brady, DKFZ Heidelberg, University of Heidelberg
[Abstract] [pdf] [bibtex]

Automatic particle picking using diffusion filtering and random forest classification
Paul Joubert, Stephan Nickell, Florian Beck, Michael Habeck, Michael Hirsch, Bernhard Schölkopf, Max Planck Institute for Intelligent Systems, Tübingen, Max Planck Institute of Biochemistry, Martinsried
[Full Paper] [pdf] [bibtex]

MiCA - Easy Cell Image Analysis with Normalized Snakes
Birgit Möller, Stefan Posch, Martin Luther University Halle-Wittenberg
[Full Paper] [pdf] [bibtex]

Imaging Methods and Biological Applications

Analysis of nociceptive neurons by quantitative automated microscopy (QuAM) - a tool for investigation inflammatory and chronic pain states
Christine Andres, René Buschow, Tim Hucho, Max Planck Institute for Molecular Genetics, Berlin, Freie Universität Berlin
[Full Paper] [pdf] [bibtex]

Unbiased digital image based quantification of IGF pathway signalling responses in Ewing sarcoma of bone
Claudia Buehnemann, Haiyue Yu, Simon Li, Harriet White, Alison Noble, Bass Hassan, University of Oxford
[Abstract] [pdf] [bibtex]

Super-resolution Fluorescence Imaging of Biological Nanostructures
Christoph Cremer, University of Heidelberg, Institute of Molecular Biology, Mainz
[Abstract] [pdf] [bibtex]

A stereoscopic approach for three dimensional tracking of marine biofouling microorganisms
Stojan Maleschlijski, Laura Leal-Taixé, Sebastian Weiße, Alessio Di-Fino, Nicholas Aldred, Anthony Clare, Hernán Sendra, Bodo Rosenhahn, Axel Rosenhahn, Karlsruhe Institute of Technology, Leibniz University Hannover, Ruprecht-Karls-University Heidelberg, Newcastle University
[Full Paper] [pdf] [bibtex]

A web-based framework for visualization, annotation, and automatic exploitation of high-resolution bioimages
Raphaël Marée, Benjamin Stévens, Loëc Rollus, Natacha Rocks, Didier Cataldo, Louis Wehenkel, University of Liège
[Abstract] [pdf] [bibtex]

Quantification of Golgi Complex Assembly and Disassembly in Live Cell Fluorescence Microscopy Images
Petr Matula, Tautvydas Lisauskas, Vytaute Starkuviene, Karl Rohr, University of Heidelberg, DKFZ Heidelberg, Masaryk University, Brno
[Full Paper] [pdf] [bibtex]

Denoising and detection of Her2/neu gene amplification in fluorescence microscopic data
Jenny Wagner, Eberhard Schmitt, Florian Riede, Michael Hausmann, Jürgen Hesser, University of Heidelberg, Kantonsspital Basel
[Full Paper] [pdf] [bibtex]