Jan Funke

Position:	Postdoc -- ended Jul 2015
Email:	funke@ini.uzh.ch
Work phone:
Home page:	http://www.ini.uzh.ch/~funke

I am a PhD student in Matthew Cook's group at the Institure ot Neuroinformatics in Zurich, Switzerland. I received a master degree in Computer Science from the Technische Universität Dresden in Germany, where I wrote my thesis about Object Detection in Visual SLAM and co-authored slamdunk, an evaluation framework for visual SLAM.

Since October 2010, I am working on the 3D reconstruction of neurons from serial section electron microscopy images in a collaboration with the Heidelberg Collaboratory for Image Processing and Albert Cardona from the Janelia Farm Research Campus. I am a member of the Research Training Group "Spatio/Temporal Graphical Models and Applications in Image Analysis" in Heidelberg.

Supervisor

Matthew Cook

Sub-Projects

Neuron Morphology Reconstruction from Electron Microscope Images

Publications

2018

Julia Buhmann*, Renate Krause*, Rodrigo Ceballos Lentini, Nils Eckstein, Matthew Cook, Srinivas Turaga, Jan Funke Synaptic Partner Prediction from Point Annotations in Insect Brains, Medical Image Computing and Computer Assisted Intervention – MICCAI 2018, 11071: 309-316, 2018

2016

Fabian Tschopp, Julien N. P. Martel, Srinivas C. Turaga, Matthew Cook, Jan Funke Efficient convolutional neural networks for pixelwise classification on heterogeneous hardware systems, IEEE ISBI, 2016

2015

Funke, Jan and Hamprecht, Fred A. and Zhang, Chong Learning to Segment: Training Hierarchical Segmentation under a Topological Loss, MICCAI, 2015
Funke, Jan and Klein, Jonas and Cardona, Albert and Cook, Matthew A Tolerant Edit Distance for Evaluation and Training of Electron Microscopy Reconstruction Algorithms, arXiv.org , 2015
Kreshuk, Anna and Funke, Jan and Cardona, Albert and Hamprecht, Fred A. Who Is Talking to Whom: Synaptic Partner Detection in Anisotropic Volumes of Insect Brain, Medical Image Computing and Computer-Assisted Intervention 661-668, 2015

2014

Funke, Jan and Martel, Julien and Gerhard, Stephan and Ciresan, Björn Andres Dan C. and Giusti, Alessandro and Gambardella, Luca and Pfister, Jürgen Schmidhuber Hanspeter and Cardona, Albert and Cook, Matthew Candidate Sampling for Neuron Reconstruction from Anisotropic Electron Microscopy Volumes, MICCAI 2014, Medical Image Computing and Computer Assisted Intervention, (proceedings are in Lecture Notes in Computer Science), 8673: 17-24, 2014

2013

Gerhard, Stephan and Funke, Jan and Martel, Julien and Cardona, Albert and Fetter, Richard Segmented anisotropic ssTEM dataset of neural tissue, figshare, 2013

2012

Funke, Jan and Andres, Bjoern and Hamprecht, Fred A. and Cardona, Albert and Cook, Matthew Efficient Automatic 3D-Reconstruction of Branching Neurons from EM Data , Proceedings of the IEEE International Conference on Computer Vision and Pattern Recognition 2012 1004 - 1011, 2012

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