IbSB 2020

from Thursday, 1 October 2020 (09:00) to Friday, 2 October 2020 (22:50)


        : Sessions
    /     : Talks
        : Breaks
1 Oct 2020
2 Oct 2020
AM
09:00
Opening (until 09:10) (Main Session)
09:00 Opening - Marc Thilo Figge (Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany)   (Main Session)
09:10
Session 1 (until 10:50) (Main Session)
09:10 Image Restoration and Downstream Processing - old problems and new solutions - Prof. Florian Jug (Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) Dresden, Germany Center for Systems Biology Dresden (CSBD), Germany)   (Main Session)
09:50 Computational augmentations of single molecule super-resolution microscopy - Prof. Christophe Zimmer (Institut Pasteur, Paris, France)   (Main Session)
10:30 3D segmentation of biofilms with convolutional neural networks - Takuya Ohmura (Max Planck Institute for Terrestrial Microbiology)   (Main Session)
10:50 --- Break ---
11:00
Poster session & Networking (until 11:30) (Poster rooms)
11:00 A role for Taok2 in Listeria monocytogenes vacuolar escape - Javier Pizarro-Cerda (Institut Pasteur)   (Poster room 1)
11:00 Automated and high-throughput quantification of microglia activation to map radiation-induced inflammation - Sindi Nexhipi   (Poster room 2)
11:00 Automatic recognition and counting of fossil pollen - how far are we? - Nia Siradze   (Poster room 3)
11:00 Bacterial shape changes for fast detection of antibiotic susceptibility - Astrid Tannert (Leibniz-IPHT)   (Poster room 4)
11:00 BiofilmQ, a quantiative image analysis tool - Hannah Jeckel (Max Planck Institute for Terrestrial Microbiology, Marburg, Germany)   (Poster room 5)
11:00 Enhanced segmentation of label-free cells for automated migration and interaction tracking - Ivan Belayaev (Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI))   (Poster room 6)
11:00 FitMultiCell: Simulating and parameterizating computational models of multi-cellular processes - Emad Alamoudi (University of Bonn)   (Poster room 7)
11:00 Image-based analysis of Candida albicans invasion in a gut-on-chip model - Stefan Hoffmann (Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)) Raquel Alonso-Roman (Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany)   (Poster room 8)
11:00 JIPipe: a graphical batch-Processing language for ImageJ - Ruman Gerst (HKI Jena)   (Poster room 9)
11:00 Morpheus: A user-friendly simulation framework for multi-cellular systems biology - Lutz Brusch (Center for Information Services and High Performance Computing (ZIH), Technische Universität Dresden, Germany)   (Poster room 10)
11:00 Quantification of the dynamics of fungal confrontation assays - Alexander Tille (Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI))   (Poster room 11)
11:00 Quantitative characterisation of Aspergillus fumigatus hyphal growth and branching behaviour in an “Invasive aspergillosis-on-a-chip” disease model of the Human lung - Dr Susann Hartung (Infections in Hematology and Oncology, Leibniz Insitute for Natural Product Research and Infection Biology) Mai T.N. Hoang (Infections in Hematology and Oncology, Leibniz Insitute for Natural Product Research and Infection Biology)   (Poster room 12)
11:00 Role of hepatic macrophage polarization in the acute phase of bacteraemia with Staphylococcus aureus - Fatina Siwczak (CSCC) Dr Zoltán Cseresnyés (Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany)   (Poster room 13)
11:00 Virtual phagocytosis assays reveal strain-specific differences in the microscopic parameters of the interaction between alveolar macrophages and two Aspergillus fumigatus strains - Sandra Timme (HKI Jena)   (Poster room 14)
11:30
Session 2 (until 12:30) (Main Session)
11:30 OME’s Bio-Formats, OME-TIFF, OMERO, & IDR: Making BioImage Data FAIR - Prof. Jason R. Swedlow (University of Dundee, UK)   ()
12:10 BiofilmQ, a quantiative image analysis tool - Hannah Jeckel (Max Planck Institute for Terrestrial Microbiology, Marburg, Germany)   ()
09:00
Session 4 (until 10:40) (Main Session)
09:00 Deep Convolutional Neural Networks as a tool in image based Systems Biology - Prof. Carolina Wählby (Department of Information Technology and Science for Life Laboratory, Uppsala University, Sweden)   (Main Session)
09:40 Automatic Segmentation and Classification of Fungal-Infected Tissue using Deep Learning - Franziska Hoffmann (Department of Otolaryngology, University Hospital Jena, Jena, Germany) Jan-Philipp Praetorius (Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany)   (Main Session)
10:10 Action recognition in intravital microscopy: detecting cell death in vivo - Mr Alain Pulfer (IRB, USI) Diego Ulisse Pizzagalli (USI)   (Main Session)
10:40 --- Break ---
10:50
Poster session & Networking (until 11:20) (Poster rooms)
10:50 A Multimodality and Multiscale Imaging Pipeline for Image-Based Vascular Systems Biology - Akanksha Bhargava (Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States)   (Poster room 1)
10:50 Action recognition in intravital microscopy: detecting cell death in vivo - Mr Alain Pulfer (IRB, USI) Diego Ulisse Pizzagalli (USI)   (Poster room 2)
10:50 Automated detection of nascent myofibrils during myofibrillogenesis. - Ian Estabrook (TU Dresden)   (Poster room 3)
10:50 Automatic Segmentation and Classification of Fungal-Infected Tissue using Deep Learning - Franziska Hoffmann (Department of Otolaryngology, University Hospital Jena, Jena, Germany) Jan-Philipp Praetorius (Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany)   (Poster room 4)
10:50 Data-driven kinetic modeling of p53 signaling linked to cell Cycle progression - Muriel Heldring   (Poster room 5)
10:50 Dynamic Bayesian networks for the analysis of causal interactions in cell track data - Carl-Magnus Svensson (Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany)   (Poster room 6)
10:50 Intracellular Raman micro-spectroscopic detection of Coxiella burnetii and discrimination of their morphoforms in infected Buffalo Green Monkey cells - Nancy Unger (Leibniz-Institute of Photonic Technology, Jena)   (Poster room 7)
10:50 MISA++: a modular and high-performance framework for analysis of light sheet microscopy images - Ruman Gerst (HKI Jena)   (Poster room 8)
10:50 Objective and quantitative assessment of liver function by pixel-wise kinetic clustering of MSOT images - Bianca Hoffmann (HKI Jena)   (Poster room 9)
10:50 Reproducible 3D animations using natural language with 3Dscript - Benjamin Schmid (Optical Imaging Centre Erlangen, FAU Erlangen-Nuremberg)   (Poster room 10)
10:50 Semi-supervised machine learning facilitates tracking of fluorescent immune cells in intravital microscopy - Joy Bordini (Institute for Research in Biomedicine)   (Poster room 11)
10:50 Simulating morphogen gradients in zebrafish epiboly - Justina Stark (Max Planck Institute of Molecular Cell Biology and Genetics)   (Poster room 12)
10:50 Unravelling apoptotic signalling cascade by co-imaging extrinsic, intrinsic and effector caspase activity by fluorescence anisotropy microscopy - Mr Mauro Silberberg (IFIBA, CONICET % FCEN, UBA) Agustín Andrés Corbat (IFIBA, CONICET & FCEN, UBA)   (Poster room 13)
11:20
Session 5 (until 12:20) (Main Session)
11:20 Spatio-temporal patterns of cell differentation in mouse blastocysts - Prof. Sabine Fischer (Center for Computational and Theoretical Biology (CCTB), Biozentrum, Universität Würzburg)   (Main Session)
12:00 Simulating morphogen gradients in zebrafish epiboly - Justina Stark (Max Planck Institute of Molecular Cell Biology and Genetics)   (Main Session)
PM
12:30 --- Lunch Break ---
13:30
Session 2 (until 15:00) (Main Session )
13:30 Slice2Volume - The next dimension of multi-modal image data fusion - Mr Johannes Müller (1,2) Theresa Suckert (OncoRay/ DKTK Dresden)   (Main Session )
14:00 JIPipe: a graphical batch-Processing language for ImageJ - Ruman Gerst (HKI Jena)   (Main Session )
14:20 Morpheus: A user-friendly simulation framework for multi-cellular systems biology - Lutz Brusch (Center for Information Services and High Performance Computing (ZIH), Technische Universität Dresden, Germany)   (Main Session )
14:40 FitMultiCell: Simulating and parameterizating computational models of multi-cellular processes - Emad Alamoudi (University of Bonn)   (Main Session )
15:00 --- Break ---
15:10
Poster session & Networking (until 15:40) (Poster rooms)
15:10 A role for Taok2 in Listeria monocytogenes vacuolar escape - Javier Pizarro-Cerda (Institut Pasteur)   (Poster room 1)
15:10 Automated and high-throughput quantification of microglia activation to map radiation-induced inflammation - Sindi Nexhipi   (Poster room 2)
15:10 Automatic recognition and counting of fossil pollen - how far are we? - Nia Siradze   (Poster room 3)
15:10 Bacterial shape changes for fast detection of antibiotic susceptibility - Astrid Tannert (Leibniz-IPHT)   (Poster room 4)
15:10 BiofilmQ, a quantiative image analysis tool - Hannah Jeckel (Max Planck Institute for Terrestrial Microbiology, Marburg, Germany)   (Poster room 5)
15:10 Enhanced segmentation of label-free cells for automated migration and interaction tracking - Ivan Belayaev (Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI))   (Poster room 6)
15:10 FitMultiCell: Simulating and parameterizating computational models of multi-cellular processes - Emad Alamoudi (University of Bonn)   (Poster room 7)
15:10 Image-based analysis of Candida albicans invasion in a gut-on-chip model - Raquel Alonso-Roman (Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany) Stefan Hoffmann (Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI))   (Poster room 8)
15:10 JIPipe: a graphical batch-Processing language for ImageJ - Ruman Gerst (HKI Jena)   (Poster room 9)
15:10 Morpheus: A user-friendly simulation framework for multi-cellular systems biology - Lutz Brusch (Center for Information Services and High Performance Computing (ZIH), Technische Universität Dresden, Germany)   (Poster room 10)
15:10 Quantification of the dynamics of fungal confrontation assays - Alexander Tille (Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI))   (Poster room 11)
15:10 Quantitative characterisation of Aspergillus fumigatus hyphal growth and branching behaviour in an “Invasive aspergillosis-on-a-chip” disease model of the Human lung - Dr Susann Hartung (Infections in Hematology and Oncology, Leibniz Insitute for Natural Product Research and Infection Biology) Mai T.N. Hoang (Infections in Hematology and Oncology, Leibniz Insitute for Natural Product Research and Infection Biology)   (Poster room 12)
15:10 Role of hepatic macrophage polarization in the acute phase of bacteraemia with Staphylococcus Aureus - Fatina Siwczak (CSCC) Dr Zoltán Cseresnyés (Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany)   (Poster room 13)
15:10 Virtual phagocytosis assays reveal strain-specific differences in the microscopic parameters of the interaction between alveolar macrophages and two A. fumigatus strains - Sandra Timme (HKI Jena)   (Poster room 14)
15:40
Session 3 (until 17:20) (Main Session)
15:40 Faster and better: taking localisation microscopy into live cells - Prof. Susan Cox (King’s College London, UK)   (Main Session)
16:20 Quantitative characterisation of Aspergillus fumigatus hyphal growth and branching behaviour in an “Invasive aspergillosis-on-a-chip” disease model of the Human lung - Dr Susann Hartung (Infections in Hematology and Oncology, Leibniz Insitute for Natural Product Research and Infection Biology) Mai T.N. Hoang (Infections in Hematology and Oncology, Leibniz Insitute for Natural Product Research and Infection Biology)   (Main Session)
16:50 Role of hepatic macrophage polarization in the acute phase of bacteraemia with Staphylococcus Aureus - Dr Zoltán Cseresnyés (Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany) Fatina Siwczak (CSCC)   (Main Session)
17:20
Networking opportunities (until 18:00) (Zoom)
12:20 --- Lunch Break ---
13:20
Session 6 (until 15:10) (Main Session)
13:20 Image based modelling of plant-soil interaction - Prof. Tiina Roose (Faculty of Engineering and Physical Sciences, University of Southampton, UK)   (Main Session)
14:00 Unravelling apoptotic signalling cascade by co-imaging extrinsic, intrinsic and effector caspase activity by fluorescence anisotropy microscopy - Agustín Andrés Corbat (IFIBA, CONICET & FCEN, UBA) Mr Mauro Silberberg (IFIBA, CONICET % FCEN, UBA)   (Main Session)
14:30 Quantitative imaging of membrane contact sites for sterol transfer between endo-lysosomes and mitochondria - Dr Daniel Wüstner (Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark)   (Main Session)
14:50 Data-driven kinetic modeling of p53 signaling linked to cell Cycle progression - Muriel Heldring   (Main Session)
15:10
Closing words (until 15:20) (Main Session)
15:10 Closing words - Marc Thilo Figge (Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany)   (Main Session)
15:20
Poster session & Networking (until 16:20) (Poster Rooms)
15:20 A Multimodality and Multiscale Imaging Pipeline for Image-Based Vascular Systems Biology - Akanksha Bhargava (Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States)   (Poster room 1)
15:20 Action recognition in intravital microscopy: detecting cell death in vivo - Mr Alain Pulfer (IRB, USI) Diego Ulisse Pizzagalli (USI)   (Poster room 2)
15:20 Automated detection of nascent myofibrils during myofibrillogenesis. - Ian Estabrook (TU Dresden)   (Poster room 3)
15:20 Automatic Segmentation and Classification of Fungal-Infected Tissue using Deep Learning - Franziska Hoffmann (Department of Otolaryngology, University Hospital Jena, Jena, Germany) Jan-Philipp Praetorius (Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany)   (Poster room 4)
15:20 Data-driven kinetic modeling of p53 signaling linked to cell Cycle progression - Muriel Heldring   (Poster room 5)
15:20 Dynamic Bayesian networks for the analysis of causal interactions in cell track data - Carl-Magnus Svensson (Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany)   (Poster room 6)
15:20 Intracellular Raman micro-spectroscopic detection of *Coxiella burnetii* and discrimination of their morphoforms in infected Buffalo Green Monkey cells - Nancy Unger (Leibniz-Institute of Photonic Technology, Jena)   (Poster room 7)
15:20 MISA++: a modular and high-performance framework for analysis of light sheet microscopy images - Ruman Gerst (HKI Jena)   (Poster room 8)
15:20 Objective and quantitative assessment of liver function by pixel-wise kinetic clustering of MSOT images - Bianca Hoffmann (HKI Jena)   (Poster room 9)
15:20 Reproducible 3D animations using natural language with 3Dscript - Benjamin Schmid (Optical Imaging Centre Erlangen, FAU Erlangen-Nuremberg)   (Poster room 10)
15:20 Semi-supervised machine learning facilitates tracking of fluorescent immune cells in intravital microscopy - Joy Bordini (Institute for Research in Biomedicine)   (Poster room 11)
15:20 Simulating morphogen gradients in zebrafish epiboly - Justina Stark (Max Planck Institute of Molecular Cell Biology and Genetics)   (Poster room 12)
15:20 Unravelling apoptotic signalling cascade by co-imaging extrinsic, intrinsic and effector caspase activity by fluorescence anisotropy microscopy - Mr Mauro Silberberg (IFIBA, CONICET % FCEN, UBA) Agustín Andrés Corbat (IFIBA, CONICET & FCEN, UBA)   (Poster room 13)
15:50 Networking opportunities   (Networking rooms)