7th International Symposium on Image-based Systems Biology
September 26 – 27, 2024
7th International Symposium on Image-based Systems Biology
The adage that “a picture is worth a thousand words” also holds true in the field of systems biology. Image-based Systems Biology is a modern approach that aims to extract spatio-temporal information contained in images in a format that can be used to describe and model morphological, functional, and dynamical aspects of biological processes. Image-based Systems Biology seeks to take full advantage of the information in images and establishes an essential connection between experimental and theoretical examination of biological processes at a quantitative level. This approach includes:
Researchers from all fields are invited to communicate their results centered on Image-based Systems Biology in order to exchange novel scientific methods and to share recent achievements from image-driven research in biology. Joint studies of experiment and theory will be highly welcomed. Furthermore, demonstrations of methods for accurate segmentation and classification of regions of interest or object-tracking that can be applied for high-content and high-throughput screening are of interest, as well as computational methods for translating images into mathematical models ranging from differential equations to agent-based methods.
The International Symposium on Image-based Systems Biology has taken place biannually since 2012 at the HKI-Center for Systems Biology of Infection in Jena, Germany.
Invited speakers
Gallery
Sponsoring
This IbSB Symposium is sponsored by the Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll Institute (HKI); as well as the Cluster of Excellence Balance of the Microverse with the Jena School for Microbial Communication (JSMC) and the Collaborative Research Centers “FungiNet” and “PolyTarget” that are funded by the German Research Funding Organisation DFG.
Schedule
Registration & Light Lunch
11:00-12:00 CEST
Opening of IbSB 2024
12:00-12:10 CEST
Session I:
12:10-13:40 CEST
Chair: Carl-Magnus Svensson
12:10-12:50 CEST
From variational modelling to deep learning for biomedical imaging
Carola-Bibiane Schönlieb, University of Cambridge, UK
presenting remotely
Abstract
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12:50-13:10 CEST
Nanotexture enabling computational multiplexing of super-resolved intracellular structures with high fidelity
Gregor Jörg Gentsch, University of Jena, Germany
Gentsch GJ, Franke C
Abstract
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13:10-13:30 CEST
Image- and physics-based modeling soft tissue mechanics using conventional and AI-based solving techniques
Evgeny Gladilin, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
Abstract
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Coffee break
13:30-14:10 CEST
Session II:
14:10-15:30 CEST
Chair: Arjun Sarkar
14:10-14:50 CEST
Harnessing AI towards the limits of live-cell microscopy
Estibaliz Gómez-de-Mariscal, Instituto Gulbenkian de Ciência, Oeiras, Portugal
presenting remotely
Abstract
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14:50-15:10 CEST
Ergosterol and sphingolipids act in concert to promote aggregation of natamycin in the yeast plasma membrane
Daniel Wüstner, University of Southern Denmark, Odense, Denmark
Szomek M, Akkerman V, Lauritsen L, Egebjerg JM, Thaysen K, Walther HL, Juhl AD, Reinholdt P, Kongsted J, Bashawad M, Müller P, Scheidt H, Covey DF, Lehmann M, Wessig P, Obermaier S, Foster AJ, Poolman B, Werner S, Schneider G, Wüstner D
Abstract
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15:10-15:30 CEST
Correlative microscopy for imaging bacterial secretion systems
Fereshta Hafizi, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
Abstract
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Coffee break
15:30-16:00 CEST
Session III:
16:00-18:00 CEST
Chair: Dhruv Khatri
16:00-16:40 CEST
Cell Painting to accelerate drug discovery: finding disease phenotypes and candidate therapeutics using images
Anne Carpenter, Broad Institute of Harvard & MIT, Cambridge, MA, USA
presenting remotely
Abstract
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16:40-17:10 CEST
Modeling of intravenous caspofungin administration using an intestine-on-chip reveals altered Candida albicans microcolonies and pathogenicity
Tim Kaden & Parastoo Akbarimoghaddam; Dynamic42 GmbH & Leibniz Institute for Natural Product Research and Infection Biology – HKI Jena, Germany
Kaden T, Alonso-Román R, Akbarimoghaddam P, Mosig AS, Graf K, Raasch M, Hoffmann B, Figge MT, Hube B, Gresnigt MS
Abstract
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17:10-17:30 CEST
Unravelling the impact of interferon-immunotherapy on epithelial resistance to Candida albicans translocation
Beatriz Cristovao, Leibniz Institute for Natural Product Research and Infection Biology – HKI Jena, Germany
Cristovao B, Kirav Ö, Pekmezović M, Austermeier S, Cseresnyés Z, Figge MT, Gresnigt MS
Abstract
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17:30-18:00 CEST
Insights into Vibrio cholerae Biofilm Formation on Microplastics
Kerstin Thriene & Zoltan Cseresnyés, Leibniz Institute for Natural Product Research and Infection Biology – HKI, Jena, Germany
Thriene K, Cseresnyés Z, Huang Y, Sathe RRM, Figge MT, Hellmich UA, Stallforth P, Papenfort K
Abstract
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Dinner
18:00-19:00 CEST
Poster Session
19:00-21:00 CEST
Most (tandem) talks will also be presented as posters.
Advanced imaging tools and their application for data analysis
Aurélie Jost, Friedrich Schiller University Jena, Germany
Jost A, Then P, Neumann S, Eggeling C
Abstract
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Simulating elastic structures in image domains using deep learning approach
Anto Nivin Maria Antony, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
Maria Antony AN, Narisetti N, Gladilin E
Abstract
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Image Processing is not a Magic Wand – or is it? – Image Quality Control Measurements for Systems Biology
Sophie Neumann, Friedrich Schiller University Jena, Germany
Neumann S, Jost A, Then P, Eggeling C
Abstract
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Image analysis of the adhesion of the probiotic strain E. coli Nissle to the fungal pathogen C. albicans using JIPipe
Carl-Magnus Svensson, Leibniz Institute for Natural Product Research and Infection Biology – HKI, Jena, Germany
Svensson CM, Chamas A, Maneira C, Figge MT, Lackner G
Abstract
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An open source super-resolution microscopy extension with real time reconstruction capability
Haoran Wang, Leibniz Institute of Photonic Technology – IPHT, Jena, Germany
Wang H, Heintzmann R, Diederich B
Abstract
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Automated classification of treatment response in tumour spheroid control probability (SCP) assays
Jannik Schmied & Willy Ciecior, HTW Dresden – University of Applied Sciences, Dresden, Germany
Schmied J, Ciecior W, Michlíková S, Kunz-Schughart LA, Lange S, Voß-Böhme A
Abstract
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The Microverse of the Plastisphere
Kerstin Thriene, Friedrich Schiller University Jena, Germany
Huang Y, Sathe RRM, Thriene K, Hellmich UA, Papenfort K, Stallforth P
Abstract
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Analysis of Skin Patterning with Particle Image Velocimetry
Rutian Zhou, Frankfurt Institute for Advanced Studies, Frankfurt, Germany
Zhou R, Marí MP, Riddell J, Painter KJ, Headon DJ, Matthäus F
Abstract
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Session IV:
09:00-10:20 CEST
Chair: Parastoo Akbarimoghaddam
09:00-09:40 CEST
Exploring Biological Shape Analysis with Statistics, Geometry, and Topology
Jon Sporring, University of Copenhagen, Denmark
Abstract
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09:40-10:00 CEST
KnotResolver: Tracking self-intersecting filaments in microscopy using directed graphs
Dhruv Khatri, Leibniz Institute for Natural Product Research and Infection Biology – HKI Jena, Germany
Khatri D, Yadav S, Athale CC
Abstract
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10:00-10:20 CEST
Quantifying morphodynamics in continuous space and time
Roua Rouatbi, Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
Rouatbi R, Suarez JE, Sbalzarini IF
Abstract
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Coffee break
10:20-10:50 CEST
Session V:
10:50-12:35 CEST
Chair: Carl-Magnus Svensson
10:50-11:30 CEST
Large language models for Bio-image Analysis
Robert Haase, Data Science Center, Leipzig University, ScaDS.AI Dresden / Leipzig, Germany
Abstract
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11:30-12:00 CEST
High-Throughput Detection of Microbial Growth and Antibiotic Resistance at the Single-Cell Level Using Scattered Light Imaging and Convolutional Neural Networks
Arjun Sarkar & Martina Graf, Leibniz Institute for Natural Product Research and Infection Biology – HKI Jena, Germany
Sarkar A, Graf M, Svensson CM, Munser AS, Hengoju S, Figge MT, Rosenbaum MA
Abstract
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12:00-12:15 CEST
JIPipe: FAIR image analysis without programming
Ruman Gerst, Leibniz Institute for Natural Product Research and Infection Biology – HKI Jena, Germany
Gerst R, Cseresnyés Z, Figge MT
Abstract
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12:15-12:35 CEST
OptiCell3D: a pipeline for inferring the mechanical properties of cells from 3D microscopy images
Kevin A. Yamauchi, Department of Biosystems Science and Engineering (BSSE), ETH Zurich, Switzerland
Yamauchi KA
Abstract
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Lunch break
12:35-13:30 CEST
Session VI:
13:30-15:00 CEST
Chair: Anastasia Solomatina
13:30-14:00 CEST
Tracking the dynamics of interacting microbial populations
Joel Ching & Silvia Vareschi, Friedrich Schiller University, Jena, Germany
Ching J, Vareschi S, Mauri M, Zander A, Herbst R, Schuster S, Stallforth P, Allen R
Abstract
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14:00-14:20 CEST
Morpheus: A user-friendly simulation framework for multi-cellular systems biology
Lutz Brusch, TUD Dresden University of Technology, Germany
Starruß J, Jahn D, Müller R, Brusch L
Abstract
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14:20-14:40 CEST
Porous-media characteristics of the developing tissue shape morphogen gradients
Justina Stark, Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
Stark J, Harish RK, Sbalzarini IF, Brand M
Abstract
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14:40-15:00 CEST
Nonlinear PDE models of intracellular virus replication dynamics evaluated upon realistic reconstructed grid geometries
Markus M. Knodel, Simulation in Technology – TechSim, Ölbronn-Dürrn, Germany
Knodel MM, Nägel A, Herrmann E, Wittum G
Abstract
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