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EMBL BioImage Data Analysis



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RT @jytinevez: LimeSeg on bioRXiv: LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation
About 8 hours, 58 mins ago by: Kota Miura (@cmci_)

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Impressive and swift moderation @helenajambor !
About 2 days, 13 hours ago by: Kota Miura (@cmci_)

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RT @LuisDVerde: Now available as a #ggplot2 geom thanks to @naupakaz
About 2 days, 13 hours ago by: Kota Miura (@cmci_)

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RT @helenajambor: awesome, within 2 days .@naupakaz made a code publicly available for anyone wanting to make the half-and-half-plot FYI @…
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @dgaboriau: Thread on data visualisation: ggplots, boxplots and violin plots
About 2 days, 19 hours ago by: Kota Miura (@cmci_)

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RT @christlet: SUSHI from Valentin Nāgerl lab allows super-resolution microscopy of neuronal morphology by STED imaging of extracellular sp…
About 2 days, 22 hours ago by: Kota Miura (@cmci_)

BIAS 2016 People

Keynote Speech

Rainer Heintzmann

Invited Lectures

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!

Anne-Lise Routier-Kierzkowska

Anne Danckaert

Gregory Paul

Jean Salamero


Kota Miura

Kota is a freelance bioimage analyst working with

  • EMBL Heidelberg, Germany
  • National Institute of Basic Biology, Okazaki, Japan
  • Nikon Imaging Center, University of Heidelberg, Germany

and one of the organizers of the BIAS course since 2013. 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.

Tel: +49 6221 387 8404
Twitter: @cmci_

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 2016 course.

Perrine Paul-Gilloteaux

Perrine Paul-Gilloteaux is CNRS research engineer working as a bio image analyst on the SFR F.Bonamy facilities, at Nantes, France and for France-BioImaging. 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 2016 course.


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 is a computer science engineer specialized in medical and bioimage analysis. She works as PostDoc research fellow within the Maria de Maeztu Programme at the SIMBioSys (Simulation, Imaging and Modeling for Biomedical Systems) Group in the Department of Information and Communication Technologies at Universitat Pompeu Fabra (Barcelona, Spain).


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:​ ​

Fabrice Cordelières

Fabrice Cordelières is a CNRS research engineer who was trained as a cell biologist/microscopist (PhD) and self-trained to programming and images processing and analysis. His main interest consist in welcoming lost biologists into the bio-image analysis world. His free welcome pack includes a bunch of ImageJ/Icy plugins (Manual Tracking, 3D Object Counter, JACOP (colocalization), MetroloJ, Metamorph ROIs importer etc), designed with extra care about ergonomy in mind.

His favorite saying: “I owe the little I know to my ignorance” (Sacha Guitry)

Jean-Yves Tinevez

Jean-Yves background lies in experimental physics and biophysics. Having embraced the career path of facility engineer, he joined the imaging platform of the Institut Pasteur, led by Spencer Shorte, where he does microscopy and image analysis. His activities here involve service, facility management, user projects and development projects, for which he uses his skills in imaging, image analysis and computing.

Otherwise he plays video games with his kids, to the dismay of their mother. While Simon uses the sword, he favors the Vietnamese saber.

Qi Gao

Qi Gao is an image analyst within the CellNetworks Math-Clinic core facility at Universität Heidelberg. MSc in Computer Science at Universität des Saarlandes (Saarbrücken, Germany) and PhD candidate (computer vision and machine learning) in Computer Science at TU Darmstadt (Darmstadt, Germany). He also likes photography, hiking and DIY.


Giovanni Cardone

Giovanni Cardone is an electronic engineer with a longstanding interest in imaging applications, which led him around to do research on medical ultrasound, seismic exploration and electron microscopy. Currently he is an image analyst at the Light Imaging Facility of the MPI Biochemistry in Martinsried, Germany, providing support to users on quantitative and automated analysis.

Laurent Guerard

Laurent Guerard is a Bioinformatician coming from Nantes, France, who decided to focus on image data instead of genomics and proteomics data. He's now working as an image analyst at the Centre for Cellular Imaging facility at the University of Gothenburg, Sweden.

shared/bias2016/people.txt · Last modified: 2017/06/06 20:14 by kota