Loïc A. Royer

P1010416

Loic joined the Myers Lab as a post-doc first at HHMI's Janelia Farms Research Campus and then at the Max Planck Institute of Molecular Cell Biology and Genetics. He fell in love with microscopes and specialized in 'smart microscopy'. In particular, he designed the first smart adaptive light-sheet microscope for long-term, high-resolution imaging of living organisms. This work done in collaboration with the Keller lab (Janelia) was published in December 2016 in Nature Biotechnology and featured on the cover. In the 'news and views' section of the journal issue this work is described as an 'engineering tour-de-force'.

Loic builds robots for fun and hacks electronics in his free time, loves to code real-time image processing and analysis software, design software for instrument control, and in general loves to develop technology to look at the unseen with the ultimate goal of answering challenging biological questions.

 

 

Spatiotemporally adaptive imaging of Drosophila embryonic development. from Loic Royer.

Research Interests

  • Computational Microscopy
  • Adaptive lightsheet Microscopy
  • Smart Microscopy,
  • Artificial Intelligence and Deep Learning,
  • Simulation,
  • Real-time Control, Image Processing, Image Analysis, and Visualisation

Research experience

  • 2013—2017
    PostDoc in Gene Myers' Lab at the Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.

    Specialised in Smart Microscopy. Design of microscopes with tight integration of software, electron- ics and mechano-optical hardware - allowing instant image processing, 3D visualisation, and robotic control. Our work on instant 3D visualisation was published in Nature Methods and used in a col- laboration published in Cell. I am currently leading several projects on: instant virtual reality mi- croscopy in collaboration with the Sbalzarini lab (MPI-CBG and CSBD); deep neural networks applied to microscopy; next-generation smart microscopy via real-time simulation of the sample dynamics, hardware mechano-optics, and light propagation; automated optogenetic painting, phase-diversity based adaptive optics, and more...

  • 2012
    Research associate in Gene Myers' Lab at HHMI's Janelia Farms Research Campus, Ashburn, USA.

    Started designing together with Philipp Keller the first smart and adaptive light-sheet microscope for long-term, high-resolution imaging of living organisms. This work was published in December 2016 in Nature Biotechnology and featured on the cover. In the 'news and views' section of the journal issue our work is described as an 'engineering tour-de-force'.

  • 2011
    PostDoc in Stephan Grill's Lab at MPI CBG/PKS Dresden, Germany.

    Project: Full automation of a dual trap optical tweezer for single molecule transcription elongation experiments. For the first time, tedious single molecule RNA Polymerase experiments could be per- formed by a robotic system.

Education:

  • Ph.D in Michael Schroeder's group, BIOTEC, Dresden University of Technology, Germany
    “Unraveling the Structure and Assessing the Quality of Protein Networks with Power Graph Analysis” Conceived a novel formalism for complex network representation and analysis and and applied it to three bio-medical applications as well as for the first information theoretic estimation of protein inter- action quality.
    Obtained the highest distinction: suma cum laude and was nominated for the Ph.D Dissertation Award of the German Computer Science Society.
  • Master's degree in Computational Logic, Dresden University of Technology, Germany.
    “Subsumption Fluent Calculus : Towards a unification of representationalism and behaviourism through an abstraction action theory”
    Artificial intelligence, image analysis and robotics project. Obtained a grade of 1.3 (Excellent).
  • Engineering Degree from the elite Computer Science University EISTI, Paris, France.
    Speciality: Artificial Intelligence and Robotics. Obtained a grade of 15.5 (top 5%).
  • Classe Preparatoires MP Janson de Sailly, Paris, France.
    Preparatory school to the competitive exams of France’s elite engineering universities,
    Intensive training in Mathematics, Physics and Computer Science. 

Papers

2016

2015

2012

2010

  • “Tantalum coating induces earlier differentiation of mesenchymal stem cells compared with titanium surface.”
    Claudia Stiehler, Cody Bünger, Rupert Overall, Loic Royer, Michael Schroeder, Morten Foss, Flemming Besenbacher, Mogens Kruhoffer, Moustapha Kassem, Klaus-Peter Gunther, Maik Stiehler.
    Cellular and Molecular Bioengineering, 2012
  • “Expression profiling and network analysis reveal MELAS master regulators.”
    Susanne Mende, Loic Royer, Alexander Herr, Janet Schmiedel, Marcus Deschauer, Thomas Klopstock, Vladimir S. Kostic, Michael Schroeder, Heinz Reichmann, Alexander Storch.
    Neurological Research.
  • “Genome-wide expression profiling and functional network analysis upon neuroectodermal conversion of Human mesenchymal stem cells suggest HIF-1 and miR-124a as important regulators.”
    Martina Maisel, Hans-Jorg Habisch, Loic Royer, Alexander Herr, Javorina Milosevic, Stefan Liebau, Rolf Brenner, Johannes Schwarz, Michael Schroeder, and Alexander Storch.
    Experimental Cell Research.

2009

  • “GoGene: gene annotation in the fast lane”
    Conrad Plake, Loic Royer, Rainer Winnenburg, Jorg Hakenberg, and Michael Schroeder.
    Nucleic Acid Research. 
  • “Identification of cancer and cell cycle genes with protein interactions and literature mining.”
    Loic Royer, Conrad Plake and Michael Schroeder. In Stephen A. Krawetz, editor,
    Bioinformatics for Systems Biology. Humana Press.
    Presented at the German Bioinformatics Conference 2009.

2008

  • “Unraveling protein networks with power graph analysis”
    Loic Royer, Matthias Reimann, Bill An- dreopoulos, and Michael Schroeder.
    PLoS Computational Biology.
    According to the ISCB summer newsletter 2009 it was among the journal's top 3 most downloaded papers of 2009.
  • “Gene mention normalization and interaction extraction with context models and sentence motifs”
    Jorg Hakenberg, Conrad Plake, Loic Royer, Hendrik Strobelt, Ulf Leser, and Michael Schroeder. Genome Biology. 

2007

  • “Querying the semantic web: A case study.”
    Loic Royer, Benedikt Linse, Thomas Wachter, Francois Bry, and Michael Schroeder. In Christopher Baker and Kei-Hoi Cheung, editors,
    “Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences.” Springer.
  • “GoPubMed: Exploring PubMed with Ontological Background Knowledge.”
    Heiko Dietze, Dimitra Alexopoulou, Michael R. Alvers, Liliana Barrio-Alvers, Bill Andreopoulos, Andreas Doms, Jorg Hakenberg, Jan Monnich, Conrad Plake, Andreas Reischuck, Loic Royer, Thomas Wachter, Matthias Zschunke, and Michael Schroeder. In Stephen A. Krawetz, editor, Bioinformatics for Systems Biology. Humana Press.
  • “Me and my friends: gene mention normalization with background knowledge”
    Jörg Hakenberg, Loic Royer, Conrad Plake, Hendrik Strobelt, and Michael Schroeder.
    Proceedings of the 2nd BioCreative Challenge Evaluation Workshop. 
     

2006

  • “Improving Text Mining with Controlled Natural Language: A Case Study for Protein Interactions.”
    Tobias Kuhn, Loic Royer, Norbert E. Fuchs and Michael Schroeder.Proceedings of the 3rd International Workshop on Data Integration in the Life Sciences (DILS'06).
  • “Prova: Rule-based Java Scripting for Distributed Web Applications: A Case Study in Bioinformatics.”
    Alex Kozlenkov, Rafael Penaloza, Vivek, Nigam, Loic Royer, Gihan Dawelbait, and Michael Schroeder. In Christopher Baker and Kei-Hoi Cheung, editors, Springer.