Florian Jug

Research Interests

• (Semi-)automated Image and Data Analysis (BioImage Computing).
• Cellular organization in developing tissues.
• Inference and learning in discrete graphical models.
• Discrete optimization.

Active Projects

• Bacteria Tracking in the MotherMachine (joint with van Nimwegen Lab, Uni Basel)
• Interflagellar Intraflagellar Transport Transport (IIFTT, in collaboration with Wallace Marshall, UCSF, and Rob Phillips, Caltech)
• Life Long Learning for Interactive Tracking By Assignment (joint with Carsten Rother, CVLD, TU Dresden)
• Joint Cell Tracking and Cell Cycle Classification (joint with Jörg Mansfeld, BIOTEC Dresden)
• Distributed MAP Optimization (joint with Tobias Pietsch, MPI-CBG  and Jan Funke, Janelia Farms)
• IKNM during Retinal Development in Zebrafish – the holy grail of constraint 3D cell tracking! (joint with Norden Lab, MPI-CBG)
• Axolotl Brainbow Segmentation  (joint with Tanaka Lab, CRTD Dresden)

Student? Looking for an awesome thesis project?

• Contact me and lets find a project matching your interests!

News

• We have a poster at ASCB 2015 on IFT exchange between Chlamy flagella — Exciting!!!
• The slides of my keynote at the ImageJ Conference 2015 can be found here…
• Our workshop on BioImageComputing at this years CVPR was a success! Thanks to all the speakers giving a series of great talks. Slides can be found here…

Publications

2015

• Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos
  (joint with Carine Stapel (first author), Benoit Lombardot, Coleman Broaddus, Dagmar Kainmüller, Gene Myers, Nadine Vastenhouw)
  Development, December 2015, doi: 10.1242/dev.128918
• Moral Lineage Tracing
  (joint with Evgeny Levinkov, Corinna Blasse, Gene Myers, Björn Andres)
  arXiv, arXiv:1511.05512 [cs.CV], submitted
• ASCB poster: Equilibration and migration dynamics of intraflagellar transport (IFT) particles between the two flagella and the cytoplasm in Chlamydomonas reinhardtii
  (joint with Mathijs Vleugel, Manuel Razo-Mejia, Hiroaki Ishikawa, Wallace Marshall)
  ASCB Learning Center in Exhibit Halls D-H, Sunday, December 13
• ASCB poster: M1 and M2 polarized fused “hybrid” cells display distinct fusion mechanics and bioenergetics
  (joint with Tim Petrie, Jennifer Lippincott-Schwartz)
  ASCB Learning Center in Exhibit Halls D-H, Sunday, December 13
• ClearVolume: open-source live 3D visualization for light-sheet microscopy
  (joint with Royer Loïc (first author), Martin Weigert, Ulrik Günther, Nicola Maghelli, Ivo Sbalzarini, Gene Myers)
  Nature Methods, Vol 12, No. 6, June 2015, doi:10.1038/nmeth.3372

2014

• Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine (preprint)
  (joint with Tobias Pietzsch, Dagmar Kainmüller, Jan Funke, Matthias Kaiser, Erik van Nimwegen, Carsten Rother, Gene Myers)
  BAMBI@MICCAI 2014 – selected for oral presentation
• Tracking by Assignment Facilitates Data Curation (Best Paper Award)
  (joint with Tobias Pietzsch, Dagmar Kainmüller, Gene Myers)
  IMIC@MICCAI 2014 – selected for oral presentation
• Active Graph Matching for Automatic Joint Segmentation and Annotation of  C. elegans
  (joint with Dagmar Kainmüller (first author), Carsten Rother, and Gene Myers)
  MICCAI 2014
• Bioimage informatics in the context of Drosophila research 
  (joint with Tobias Pietzsch, Stephan Preibisch, and Pavel Tomancak)
  Methods, DOI:10.1016/j.ymeth.2014.04.004.

2013

• Reliable neuronal systems: the importance of heterogeneity
  (joint with Johannes Lengler (first author) and Angelika Steger)
  PLoS ONE, 8(12):e80694, DOI:10.1371/journal.pone.0080694.
• Poster: The Use of Microfluidic Devices to Understand How Transcriptional to External Stimuli Evolve in Natural Isolates of E. Coli
  (joint with Matthias Kaiser, Siddharth Desphande, Thomas Pfohl, F. J., Erik van Nimwegen, and Olin Silander)
  BAGECO 2013
  
• Poster: The Interactive MotherMachine — a CRF Approach to Simultaneous Cell Segmentation and Cell Tracking
  (joint with Gene Myers)
  ICVSS 2013

2012

• Recurrent Competitive Networks Can Learn Locally Excitatory Topologies [Preprint] (joint with Matthew Cook and Angelika Steger)
  International Joint Conference on Neural Networks (IJCNN 2012).
• Spiking networks and their rate-based equivalents: does it make sense to use Siegert neurons? [Abstract] [Poster] (joint with Johannes Lengler and Angelika Steger)
  Abstract and poster for the annual meeting of the Swiss Society for Neuroscience (SSN).
• On Competition and Learning in Cortical Networks [PDF-eBook] PhD Thesis

2011

• Interacting Maps for Fast Visual Interpretation [Preprint] (joint with Matthew Cook, Luca Gugelmann, Christoph Krautz, and Angelika Steger)
  International Joint Conference on Neural Networks (IJCNN 2011).
• Neuronal Projections Can Be Sharpened by a Biologically Plausible Learning Mechanism [Preprint] (joint with Matthew Cook, and Christoph Krautz)
  21st International Conference on Artificial Neural Networks (ICANN ’11).

2010

• Unsupervised Learning of Relations [Preprint] (joint with Matthew Cook, Christoph Krautz, and Angelika Steger)
  20th International Conference on Artificial Neural Networks (ICANN ’10).
  
• A model of functional recovery after significant loss of neural tissue: biofeedback based healing of vestibular dysfunction [Preprint] (joint with Christoph Krautz and Angelika Steger)
  BMC Neuroscience.
• Holistically convergent modular networks: a biological principle for recurrent network architecture [Preprint] (joint with Matthew Cook, Luca Gugelmann, and Christoph Krautz)
  BMC Neuroscience.

2009

• Sharpening Projections [Preprint] [Poster] (joint with Matthew Cook and Christoph Krautz)
  BMC Neuroscience

2005

• Automated quality assurance for UML models [Preprint] (joint with Tilman Seifert and Günther Rackl)
  Informatik LIVE, volume 2, pages 496-500. Jahrestagung Informatik 2005, Gesellschaft für Informatik, September 2005

Teaching Experience (@TU Dresden)

Course Assistance

Teaching (@ETH Zurich)

Courses

Course Assistance