Bioimage Analysis
Connected Community Activities
- Upcoming Activities
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Coming soon
- Past Activities
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Methods for Learning with Few Data by Marcus Liwicki
Machine Learning with neural networks by Prof. Bernhard Mehlig
How to get involved?
Contact
CC lead: Oriol Gallego (UPF). Email: oriol.gallego@upf.edu
Local Facilitator: Laia Cotet (laia.cotet@upf.edu)
Connected Community Members
- Lead: Oriol Gallego (UPF). Email: oriol.gallego@upf.edu
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Photo
Dr Oriol Gallego is a tenure-track group leader at the MELIS department of UPF, leading the Live-cell structural biology Group in the interface between cell and structural biology. His research focuses on the development of new imaging and image analysis approaches that allow a quantitative understanding of the spatial and temporal organization of the protein machinery that controls cell growth. Oriol did a postdoc at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, under the supervision of Anne-Claude Gavin and Marko Kaksonen. In his postdoc Oriol established a lipid-binding assay for high-throughput screening of protein-lipid interactions and a light microscopy technique to investigate the structure of protein complexes directly in living cells. Already as a Ramón y Cajal researcher at the Institute for Research in Biomedicine at Barcelona (IRB), Spain, he solved the architecture of the exocyst complex bound to a secretory vesicle in yeast, a work that provided unprecedented understanding of the mechanism that controls vesicle tethering in exocytosis. Currently the group of Oriol Gallego has a particular interest for the molecular mechanisms that control exocytosis as a paradigm of a complex and dynamic cellular process that controls the growth of eukaryotic cells. His group combines advanced microscopy (SMLM, particle tracking, PICT and cryo-ET), biochemistry, proteomics and integrative modelling to generate quantitative models of the molecular mechanism that regulates exocytosis. The implementation of unconventional model organisms allowed them to embark on the field of evolutionary cell biology with the aim of understanding the molecular principles that underlie eukaryotes adaptation to different ecological niches - Partner: Caroline Adiels (GU). Email: caroline.adiels@physics.gu.se
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Originally trained as a biologist, I am now an associate professor in the Department of Physics at the University of Gothenburg, specializing in optics, microfluidics, and active (biological) matter. My research focuses on single-cell analysis and communication, which expands into the development and use of organ-on-a-chip technology. I incorporate image analysis with AI-based software customized for life science research, fostering an interdisciplinary research portfolio bridging physics and biology. - Partner: Daniel Midtvedt (GU). Email: daniel.midvedt@physics.gu.se
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I am an assistant professor at the department of physics at University of Gothenburg. My research focuses on studying biological systems using quantitative microscopy enhanced with deep learning. Of particular interest is understanding how weak intermolecular interactions govern intracellular organization. - Partner: Giovanni Volpe (GU). Email: giovanni.volpe@physics.gu.se
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Giovanni Volpe is Full Professor at the Physics Department of the University of Gothenburg University, where he leads the Soft Matter Lab (http://softmatterlab.org). His research interests include soft matter, optical trapping and manipulation, statistical mechanics, brain connectivity, and machine learning. He has authored more than 100 articles and reviews on soft matter, statistical physics, optics, physics of complex systems, brain network analysis, and machine learning. He co-authored the books "Optical Tweezers: Principles and Applications" (Cambridge University Press, 2015) and “Simulation of Complex Systems” (IOP Press, 2021). He has developed several software packages for optical tweezers (OTS — Optical Tweezers Software), brain connectivity (BRAPH—Brain Analysis Using Graph Theory), and microscopy enhanced by deep learning (DeepTrack). He's also co-author of the upcoming book "Deep Learning Crash Course" (No Starch Press, 2024) and co-founder of the stat-ups Lucero Bio AB, IFLAI AB, and Identinano AB. - Partner: Ivo Sbalzarini (GU). Email: ivos@mpi-cbg.de
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Ivo F. Sbalzarini is a Professor in the Institute of Artificial Intelligence on the Faculty of Computer Science of TU Dresden, and he is a director of the Center for Systems Biology Dresden (CSBD). Since 2021, Ivo is the Dean of the Faculty of Computer Science at TU Dresden. He also is a tenured Senior Research Group Leader with the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, Germany. He serves as Area Lead for Biomedical Data Science and AI in the Federal Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) and a Research Avenue Leader for Scientific Computing and Smart Microscopy in the DFG Cluster of Excellence "Physics of Life". Ivo's research focuses on computer algorithms for machine learning, data-driven modeling, and high-performance computing in image-based computational biology - Partner: Mattias Goksör (GU). Email: mattias.goksor@physics.gu.se
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Mattias Goksör is a Professor in Physics and interested in Complex Systems, especially experimental single cell analysis using optical imaging, optical manipulation, microfluidics, and AI. He also has a master’s degree in economics and business administration and is cofounder and CEO of the spinoff company IFLAI (Innovation for Life Sciences through Artificial Intelligence. Mattias Goksör was Vice President of the University of Gothenburg (2017-2021) and Head of Department of Physics (2012-2017). - Partner: Till Bretschneider (UoW). Email: till.bretschneider@warwick.ac.uk
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Till Bretschneider is a Professor for Systems Biology who employs machine learning and image-based modelling to investigate actin-based cellular dynamics. He obtained his PhD on computational models for morphogenesis from Ludwig-Maximilians-University, Munich (1998). He joined Warwick University in 2007, after spending time as postdoc in Applied Mathematics at Bonn University (1998-2001) and being a fellow and researcher at the Max-Planck-Institute of Biochemistry in Martinsried (2001-2007). - Partner: Javier Sanjuan (UPF). Email: xavier.sanjuan@upf.edu
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I got a Biology degree in 1998 at University of Barcelona. Later I got a master's degree in Cell Biology in 2001 also at the same site, during which I discovered, became an extensive user and got in love with confocal microscopy. Since 2004 I work as a microscopy technician at Universitat Pompeu Fabra (UPF), where I have gotten expertise in a variety of optical microscopy methods ranging from confocal microscopy, multiphoton microscopy, in vivo epifluoescence and super-resolution microscopy. Since 2005 I have been teaching optical microscopy at UPF both in the Human Biology degree and in PhD courses. - Partner: Carlo Manzo (UVic -external partner). Email: carlo.manzo@uvic.cat
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Carlo Manzo is an Associate Professor at the University of Vic, Spain where he leads the Quantitative Bioimaging lab (https://mon.uvic.cat/qubilab/). His research focuses on the quantitative study of biophysical processes. Combining deep-learning algorithms and single-molecule imaging tools, he explores the spatiotemporal organization and dynamics of cell membrane components in health and disease. After graduating in Physics in 2001 and completing his Ph.D. in 2005 at the University of Naples 'Federico II', he has held postdoctoral roles at the University of Emory in Atlanta, the IBEC in Barcelona, and the ICFO in Barcelona. In 2017, he was awarded the "Ramón y Cajal” Fellowship and earned the “E. Pérez Payá” prize from the Sociedad de Biofisica de España. He leads the organization of the Anomalous Diffusion (AnDi) challenge, a community-driven effort to enhance methods for analyzing single-molecule motion.
