User Tools

Site Tools


Downloads (-2016)
Downloads (2016-)
RSS aggregates

EMBL BioImage Data Analysis



—- Contact
CMCI Alumni
EMBL Heidelberg
EMBL Intranet

Popularity Ranking

Timeline of @cmci_

cmci_ avatar

RT @biomicugm: Topics: Biostatistics, computational evolutionary biology, computational genomics and proteomics, graph models, image analys…
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @JustinMCrocker: We are looking for an interdisciplinary EIPOD postdoc to join our group @EMBL! Potential projects with @Eileen_Furlong,…
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @BioImagingUK: This maybe of interest to the @NEUBIAS_COST @openmicroscopy communities #imageAnalysis #imagingScientist
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @BioImagingUK: Software developer position on large image data analysis - working closely with the lab of @bayraktar_lab @sangerinstitut…
About 1 week, 2 days ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @AssafZaritsky: Modeling the interplay of lamellipodial motion and the intercellular actomyosin cable during epithelial wound healing h…
About 1 week, 2 days ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @jytinevez: @florianjug says be careful when using #CARE for intensity based quantification; CARE restoration is like a non linear trans…
About 1 week, 4 days ago by: Kota Miura (@cmci_)

BIAS 2014 People

Keynote Speech

Takeo Kanade

Dr. Kanade's research interests span a wide range of areas: vision, sensors, control, multimedia, manipulators, and autonomous mobile robots. His contributions range from basic theories to devices and total systems. He has written more than 300 technical papers and holds more than 20 patents. His contributions in vision include: face recognition (one of the earliest computer face recognition programs, and later face detectors), shape recovery from line drawings (known as Origami World theory and skew symmetry), stereo (multi-baseline stereo and the world's first full-image video-rate stereo machine), motion image analysis (known as the Lucas-Kanade tracker) and a structure-from-motion theory (known as Tomasi-Kanade factorization), and VLSI computational sensors. He was the co-developer of the concept of direct-drive manipulators and the world's first prototype (CMU DD Arm I). He has initiated, led and collaborated on several major autonomous mobile robots and various application systems since the mid-1980s, including Carnegie Mellon's driverless cars (NavLab), the autonomous helicopter (Robocopter), the computer-assisted hip-replacement surgery system (HipNav), and video surveillance and monitoring system (VSAM). Since 1995, Kanade has been developing a new visual media, which he named “Virtualized Reality”. A time-varying event, such as sports, dancing or surgery, is captured by a large number of surrounding cameras, and transformed to a complete 4-D description (time, 3D, and appearance). As one of the applications of such multi-camera technology, he developed a Matrix-like replay system used for broadcasting portions of Super Bowl IIIV in 2001 called CBS “EyeVision”.

excrept from

Other links:


Invited Lectures

Ivo Sbalzarini

Ivo F. Sbalzarini is Senior Research Group Leader at the Max Planck Institute of Molecular Cell Biology and Genetics since June 2012. He is the founder and head of the MOSAIC Group.

Ivo is a Swiss citizen and was born in 1977 in Arbon, Switzerland. During 1997-2002 he studied Mechanical Engineering at ETH Zurich (Switzerland), with majors in Computational Science (Applied Mathematics) and Control. In 2002 he received his Diploma in Mechanical Engineering, which was awarded the Willi Studer Prize. Between 2002 and 2006, Ivo was a Ph.D. student with the Computational Science and Engineering Lab at ETH Zurich, where he pioneered the close collaboration between Biology and Computational Science at ETH Zurich. In January 2006, he received his PhD in Computer Science under the supervision of Professor Petros Koumoutsakos. His thesis work was awarded the prestigious Chorafas Prize for 2006.

Ivo intermediately stayed at the NASA Ames Research Center, USA (2000), at the Center for Turbulence Research at Stanford University, USA (2002), and at the California Institute of Technology in Pasadena, USA (2005). In addition, he was an invited Professor of Biology at Ecole Normale Supérieure (ENS), Paris, France (2007) and a research group leader in Bioinformatics at the Mediterranean Institute for Life Sciences in Split, Croatia (2007-2008).

In April 2006, Ivo was named Assistant Professor of Computational Science in the Department of Computer Science of ETH Zurich (Switzerland), where he developed and implemented the concept of a creative trans-disciplinary research group, the MOSAIC Group. In June 2012, the MOSAIC Group moved from ETH Zurich to its present location at the MPI-CBG in Dresden, Germany, where it was one of the four founding groups of the Center of Systems Biology Dresden (CSBD).

Ivo's work focuses on developing, applying, and teaching particle methods for image-based systems biology. This includes particle methods for bio-image processing, hybrid particle-mesh methods for multi-scale simulations, parallel high-performance computing using particle methods, and bio-inspired optimization. Current applications revolve around the topic of Systems Biology of Development.

Ivo is a honorary member of the Technical Society of Zurich (TGZ) and was a member of the Project Group “Swiss National Strategic Plan for High Performance Computing and Networking”. Since 2013, Ivo is the Vice Dean for Systems Biology of the International Max Planck Research School (IMPRS) for Cell, Developmental and Systems Biology within the Dresden International PhD Program (DIPP). Also since 2013, Ivo serves on the Steering Committee of the Center of Systems Biology Dresden, and he is co-leader of the Biological Systems Path of the Center for Advancing Electronics Dresden (cfAED), the second Excellence Cluster in Dresden.

MOSAIC website

Ivo F. Sbalzarini, MPICBG page

Christophe Zimmer

Christophe Zimmer is a principal investigator at Institut Pasteur (Paris, France). He obtained a PhD in astrophysics from University Paris 7 and did a first postdoc at University of California Los Angeles on the physics of planetary magnetospheres and the subsurface oceans of Jupiter’s moons. He then did a second postdoc at Institut Pasteur on quantitative analysis of microscopy images.

He now heads the Imaging and Modeling Unit of Institut Pasteur, which develops computational and experimental approaches to quantitatively characterise selected processes in cell biology and microbiology. The lab currently focuses on the spatial architecture and function of the genome and on the early replication cycle of HIV.

Nadine Peyriéras

Nadine Peyriéras is a research director at the CNRS. She leads the "BioEmergences" laboratory in the Neurobiology Institute (Gif sur Yvette France). Trained as a biochemist (Ecole Normale Supérieure de Cachan, France), PhD on cell adhesion in preimplantation mouse embryo (1986 Pasteur Institute under the Supervision of François Jacob). Then explored various aspects of animal embryogenesis and launched in 2006 with Paul Bourgine, at the time director of the Ecole Polytechnique/CNRS laboratory “Research center in applied epistemology”, a transdisciplinary project for the reconstruction of multi level dynamics in animal morphogenesis, through two European projects of the FP6 program called “Embryomics” and “BioEmergences”. Born from a mathematician mother and a musician father in the countryside of Limousin (France), she can still talk about dancing, singing and keeping honey bees.

Nadine Peyriéras Lab

Fred A. Hamprecht

Fred Hamprecht is interested in image processing and machine learning, in particular active learning. With his group, he develops automated diagnostic systems with applications both in industrial quality control and the life sciences. Major applications include connectomics, tracking of all cells in a developing embryo and quantitative analysis of high-throughput experiments. The group puts particular emphasis on the the user-friendly training of such systems, and is actively developing open source libraries and program suites such as

Fred studied and earned his PhD at the Swiss Federal Institute of Technology (ETH). After a brief period at the Seminar for Statistics, he became a Professor for Multidimensional Image Processing at the University of Heidelberg in 2001. He is a co-founder of the Heidelberg Collaboratory for Image Processing (HCI), and was a fellow of the Marsilius Kolleg in 2010/11.


… and see his page in the University of Heidelberg website.. A great line up of lecture videos!


Kota Miura

Kota is an image processing and analysis specialist at the EMBL Heidelberg and is responsible for the Centre for Molecular and Cellular Imaging. One of the organizers of the BIAS 2014 course. He also plays ukulele.

Kota Miura works at the Centre for Molecular and Cellular Imaging, EMBL Heidelberg as Scientist and IT engineer. B.L.A. (Liberal Arts, ICU, Tokyo), M.Sc (Physiology, Osaka), Ph.D. (Cell and Developmental Biology, Munich). A biologist now very much specialized in image analysis. One of the organizers of the BIAS 2014 course. He likes Karate and Ukulele.

URL: Tel: +49 6221 387 404

Sebastien Tosi

Sébastien Tosi is a signal engineer working at the advanced digital microscopy core facility (ADMCF) of Institute for Research in Biomedicine (IRB Barcelona, Spain) since 2010. École préparatoire (Nancy, France, 1998), physics engineer (ENSPM Centrale Marseille, France and Tampere university of technology, Finland, 2001), Electrical engineering Ph.D. (High-density multitrack data storage, Limerick, Ireland 2006), system engineer in a telecommunication company (SIDSA, Madrid, 2007-2010). One of the organizers of the BIAS 2014 course.

Perrine Paul-Gilloteaux

Perrine Paul-Gilloteaux is CNRS research engineer in bio-image informatics on the PICT-IBISA microscopy facility, at Institut Curie Paris France. Electronic and computer sciences engineer, M.Sc (Signal and Image Processing), Ph.D. (Computer Vision for Image guided Neurosurgery), post doc in live cell imaging. One of the organizers of the BIAS 2014 course. She’s in an amateur dance company, and mother of one - her biggest (and only) fan.

Cornelia Monzel

Cornelia Monzel does her Postdoc at the Insitute for Physical Chemistry of Biosystems, University of Heidelberg. M.Sc (BioPhysics, Cambridge University, UK), Diploma in Physics (Bonn University, Germany), Ph.D. (Physical Chemistry, Bonn University and University Aix-Marseille, Germany and France). For her work she constantly analyzes microscopy images of cells using Matlab. She likes jogging, tennis and playing the piano.

Institute page:


Christian Tischer

Christian Tischer is a staff scientist at the Advanced Light Microscopy Facility at the EMBL in Heidelberg. Diploma in Physics (University of Heidelberg, Germany), Ph.D. in Biophysics (EMBL Heidelberg and Humboldt University Berlin, Germany). A physicist now very much specialized in microscopy and image analysis. In terms of hobbies he likes all sort of sports (climbing, ski-touring, …).

Contact: Christian.Tischer@EMBL.DE

Simon Flyvbjerg Nørrelykke

Simon is a physicist turned image-and-data analyst. He works in Zurich at ETH where he heads the IDA (Image and Data Analysis) unit as part of ScopeM (Scientific Center for Optical and Electron Microscopy). He no longer plays the ukulele, having chosen instead to express himself via the épée.

Chong Zhang

Chong's current research project focuses on cell detection and segmentation for high-throughput imaging, using machine learnig based methods. She studied as a medical imaging engineer in Barcelona, and works at CellNetworks Core Facility Math-Clinic in University of Heidelberg, as image analyst and postdoc for microscopy image processing and analysis. Contact:

Thomas Pengo

Thomas Pengo is a postdoc and image analysis specialist for the Advanced Light Microscopy Unit at the CRG (Center for Genomic Regulation) in Barcelona. His research interests cover computational aspects in microscopy, including image processing, analysis, and automation. Since 2011 he has also been active in the thriving field of single-molecule localization microscopy.

He studied Computer Engineering at Politecnico di Milano, got his doctoral degree at University of Navarra with Carlos Ortiz-de-Solórzano and Arrate Muñoz-Barrutía, before spending two years as a postdoc in the lab of Suliana Manley at EPFL.

He learned that great wonders can come from proper bridging of technology to biologists, and that's what makes him tick.

Szymon Stoma

Szymon Stoma holds a PhD in Computer Science and ​previously worked in Computational, Developmental and Systems Biology ​to finally join the Image and Data Analysis Unit of the Scientific Center for Optical and Electron Microscopy (SCOPEM) at ETH Zürich.​ Although he never played the ukulele, he has fed E. coli with his own pipet, written a compiler, run his own company and competed in a few sailing championships. More:​ ​

shared/bias2014/people.txt · Last modified: 2016/05/24 05:46 (external edit)