Stephan Gerhard

PhD Graduate -- ended Jan 2016
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I received my Bachelor's Degree in Computer Science in 2008, and my Master's Degree in Neural Systems and Computation in 2010 both from ETH Zurich. As a continuation of my Master Thesis, I worked as a research assistant at EPF Lausanne developing software to map, analyze and visualize structural connectivity of the human brain derived from Diffusion MRI ( In September 2011, I started my PhD in the lab of Albert Cardona, then group leader at INI, now at Janelia Farm Research Campus in Ashburn, USA. My research project investigates the synaptic variability of the nociceptive neural circuit across animal and development time in Drosophila melanogaster larva. We deal with large serial section electron microscopy datasets on a daily basis. I made major contributions to the open-source software tool CATMAID ( for collaborative, online neural circuit reconstruction in large volumetric image datasets. In collaboration with Matthew Cook's group at INI, I work on integrating recent state-of-the-art machine vision algorithms into CATMAID to enable faster, volumetric, semi-automatic circuit reconstruction. In my spare time, you can find me enjoying the West Coast Swing dance.


Matthew Cook



  • Schneider-Mizell, Casey and Gerhard, Stephan and Longair, Mark and Kazimiers, Tom and Li, Feng and Zwaart, Maarten and Champion, Andrew and Midgley, Frank and Fetter, Richard and Saalfeld, Stephan and Cardona, Albert Quantitative neuroanatomy for connectomics in Drosophila, eLife, 2016


  • 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



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