This page is old: my lab can be found here!
Last edits on this page: February 2017
- Quantitative Bioimage Informatics.
- Inference and learning in discrete graphical models.
- Artificial embryos for deep network learning.
- Discrete optimization.
- Cellular organization in developing tissues.
- Transcriptional regulation and transcriptional stochasticity.
- Quantifying cellular dynamics, e.g. IFT dynamics in Chlamydomonas.
Student? Contact me and lets find a project matching both our interests!
- It's a done deal -- I'm going to start my lab in March 2017! Exciting!!!
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- Visiting the Hernan lab at UC Berkeley was so helpful! Tr2d's first real application, run and controlled from Matlab environment!
- The methods paper describing MoMA is finally on BioRxiv!
- Visiting the Goldstein lab at UNC was amazingly productive. (click to animate/enlarge)
- Tr2d is close to first productive rollout in the lab of my collaborators in UC Berkeley. (click to enlarge)
My work is, to a large degree, based on collaborations with groups conducting biological research as well as groups with which I develop image analysis and machine learning technology. I am a firm believer that collaborations benefit tremendously when all interacting parties have a shared understanding of the underlying biology, biophysics, and computational tools. The (alphabetic) list below does not contain short term collaborators.
- Group of Björn Andres, MPI for Informatics, Saarbrücken
- Group of Michael Berthold & KNIME, University of Konstanz
- Garcia Lab, UC Berkeley, San Francisco
- Goldstein Lab, UNC, Chapel Hill
- Lee Lab, Janelia Research Campus, Ashbury (Virginia)
- Marshall Lab, UCSF, San Francisco
- van Nimwegen Lab, University of Basel
- CVLD (Carsten Rother's group), TUD, Dresden
- Tomancak Lab, MPI-CBG, Dresden
- Efficient Algorithms for Moral Lineage Tracing
(Markus Rempfler, Jan-Hendrik Lange, FJ, Corinna Blasse, Eugene W. Myers, Bjoern H. Menze, Bjorn Andres)
arXiv 2017, arXiv:1702.04111 [cs.CV]
- Crowd Sourcing Image Segmentation with iaSTAPLE
(joint with Dmitrij Schlesinger, FJ (shared first), Gene Myers, Carsten Rother, and Dagmar Kainmüller)
- Tracking single-cell gene regulation in dynamically controlled environments using an integrated microfluidic and computational setup
(joint with Matthias Kaiser, FJ (shared first), Olin Silander, Siddharth Deshpande, Thomas Pfohl, Thomas Julou, Gene Myers, Erik van Nimwegen)
BioRxiv, doi: http://dx.doi.org/10.1101/076224
- Seamless HPC Integration of Data-intensive KNIME Workflows via UNICORE
(joint with Richard Grunzke, FJ (shared first), Bernd Schuller, René Jäkel, Gene Myers, and Wolfgang E. Nagel)
- Moral Lineage Tracing (version on arXiv)
(joint with FJ, Evgeny Levinkov (shared first), Corinna Blasse, Gene Myers, Björn Andres)
- 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, FJ, Gene Myers, Nadine Vastenhouw)
Development, December 2015, doi: 10.1242/dev.128918
- 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, FJ, Ivo Sbalzarini, Gene Myers)
Nature Methods, Vol 12, No. 6, June 2015, doi:10.1038/nmeth.3372
- Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine [get the 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)
- Bioimage informatics in the context of Drosophila research
(joint with Tobias Pietzsch, Stephan Preibisch, and Pavel Tomancak)
- 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)
- Poster: The Interactive MotherMachine -- a CRF Approach to Simultaneous Cell Segmentation and Cell Tracking
(joint with Gene Myers)
- Recurrent Competitive Networks Can Learn Locally Excitatory Topologies [get the 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]
- Interacting Maps for Fast Visual Interpretation [get the 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 [get the preprint]
(joint with Matthew Cook, and Christoph Krautz)
21st International Conference on Artificial Neural Networks (ICANN '11).
- Unsupervised Learning of Relations [get the 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 [get the preprint]
(joint with Christoph Krautz and Angelika Steger)
- Holistically convergent modular networks: a biological principle for recurrent network architecture [get the preprint]
(joint with Matthew Cook, Luca Gugelmann, and Christoph Krautz)
- Sharpening Projections [Preprint] [Poster]
(joint with Matthew Cook and Christoph Krautz)
- Automated quality assurance for UML models [get the 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)
Teaching (@ETH Zurich)
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