Name: I2K 2024 Conference - From Images to Knowledge
Start: 2024-10-23T09:00:00+02:00
End: 2024-10-25T19:00:00+02:00
Location: Milan, Italy

I2K 2024 Conference - From Images to Knowledge

from Wednesday, 23 October 2024 (09:00) to Friday, 25 October 2024 (19:00)

Monday, 21 October 2024
Tuesday, 22 October 2024
Wednesday, 23 October 2024

09:00 ☕ Welcome Coffee & Registration
☕ Welcome Coffee & Registration
09:00 - 09:30

09:30 🎤 Opening Remarks
🎤 Opening Remarks
09:30 - 09:45
09:45 Fiji Progress and Priorities 2024 (Curtis Rueden, University of Wisconsin-Madison)
Fiji Progress and Priorities 2024 (Curtis Rueden, University of Wisconsin-Madison)
09:45 - 10:00
Contributions

09:45 Fiji Progress and Priorities 2024 - Curtis Rueden (University of Wisconsin-Madison)
10:00 Title to be announced (Ricardo Henriques, Instituto Gulbenkian de Ciência, IGC - University College London, UCL)
Title to be announced (Ricardo Henriques, Instituto Gulbenkian de Ciência, IGC - University College London, UCL)
10:00 - 10:30
Room: HT Auditorium

10:30 🚶‍♀️ Shuffle time
🚶‍♀️ Shuffle time
10:30 - 10:45
Room: Human Technopole
10:45
10:45 - 11:45
Contributions

10:45 Automating ImageJ without coding: A hands-on introduction to JIPipe - Ruman Gerst (Hans Knöll Institute)

10:45 Intermediate napari: from exploratory workflow to widgets - Peter Sobolewski (The Jackson Laboratory)

10:45 Leveraging the ImgLib2/BigDataViewer ecosystem for efficient batch inspection of large bioimage analysis datasets. - Christian Tischer (EMBL)

10:45 Object Tracking and track analysis using TrackMate and CellTracksColab - Joanna Pylvänäinen (Åbo Akademi University)

10:45 Omega – Harnessing the Power of Large Language Models for Bioimage Analysis - Loic A. Royer (CZ Biohub)

10:45 QuPath for Fiji Fans - Peter Bankhead (University of Edinbrugh)

10:45 Width Profile Tools - Volker Baecker (French Institute of Health and Medical Research)

10:45 clEsperanto: GPU-accelerated image processing library - Stéphane Rigaud (Institut Pasteur)
11:45 🚶‍♀️ Shuffle time
🚶‍♀️ Shuffle time
11:45 - 12:00
Room: Human Technopole
12:00
12:00 - 12:30
Contributions

12:00 Automated mapping of 3D smFISH gene expression data to electron microscopy - Elena Buglakova (EMBL)

12:02 Machine learning based Evaluation and Enhancement (EVEN) for optical microscopy - Elena Corbetta (Friedrich-Schiller-Universität Jena)

12:04 Exploring gene function and morphology using JUMP Cell Painting Consortium data - Alán Fernando Muñoz González (Broad Institute of Harvard and MIT)

12:06 A Bayesian solution to count the number of molecules within a diffraction limited spot - Alexander Hillsley (Howard Hughes Medical Institute)

12:08 pyCyto: A Pythonic Cytotoxicity Analysis Pipeline - Jacky Ka Long Ko (University of Oxford)

12:10 Fractal: An open-source framework for reproducible bioimage analysis at scale using OME-Zarrs - Joel Lüthi (University of Zurich)

12:12 Enhancing Synaptic-Resolution Connectomics with an Open-Source AI Ecosystem - Samia Mohinta (University of Cambridge, UK)

12:14 Continuous, interpretable, and transformation-invariant Morphometric for dynamic shape quantification - Roua Rouatbi (TU Dresden)

12:16 An Image Analysis Pipeline for Quantifying the Spatial Distribution of Fluorescently Labeled Cell Markers in Stroma-Rich Tumors - Antoine Ruzette (Harvard Medical School)

12:18 Unsupervised Denoising for Signal-Dependent and Row-Correlated Imaging Noise - Benjamin Salmon (University of Birmingham)

12:20 How To Train Your Image Analyst: Perspectives from Upskilled Biologists - Maria Traver (NIH / NIAID)

12:22 TopoStats: taking AFM analysis to new heights - Laura Wiggins (University of Sheffield)
12:30 🚶‍♀️ Walking time to Triulza Academy
🚶‍♀️ Walking time to Triulza Academy
12:30 - 13:00

13:00 🍝 Lunch
🍝 Lunch
13:00 - 14:00
14:00
14:00 - 16:30
Contributions

14:00 MicroSplit: Semantic Unmixing of Fluorescent Microscopy Data - Ashesh Ashesh (Human Technopole)

14:00 pymmcore-plus: a pure python way to control your microscope with Micro-Manager - Federico Gasparoli (Harvard University)

14:00 Diffusion Models in Microscopy: Bleedthrough Removal, Image Splitting, and Dehazing - Anirban Ray (Human Technopole)

14:00 A contour-based alignment tool enabling to merge data from live acquisition & immunofluorescence - Anne-Sophie MACE (CNRS)

14:00 pyCyto: A Pythonic Cytotoxicity Analysis Pipeline - Jacky Ka Long Ko (University of Oxford)

14:00 Computational modeling of nanoscale synapse morphology and organization using correlative super-resolution microscopy - Antoine J.-F. Salomon (IINS)

14:00 A Comprehensive Image Analysis Pipeline for Investigating Autism Spectrum Disorder-like Behaviours in Drosophila melanogaster - Arianna Ravera (University of Lausanne)

14:00 BioImage.IO Chatbot: A Community-Driven AI Assistant for Integrative Computational Bioimaging - Caterina Fuster Barceló (Universidad Carlos III de Madrid)

14:00 Semi-automatic tracing and analysis of neurons in Brainbow images - Clément Caporal (Ecole Polytechnique/CNRS)

14:00 Automated mapping of 3D smFISH gene expression data to electron microscopy - Elena Buglakova (EMBL)

14:00 Untangling spaghetti: using BigTrace plugin to analyze 3D filaments in time and space - Eugene A. Katrukha (Utrecht University)

14:00 Deep learning-based classification for label-free microscopy - Franziska Schöb (University of Oslo)

14:00 Phenomic data exploration guides drug discovery in a human disease network - Alba Guembe Mülberger (Universitat Autònoma de Barcelona)

14:00 Deep learning enables cross-modality super-resolution for volumetric reconstruction - Hyoungjun Park (EMBL & ETH Zürich)

14:00 napari-signal-classifier: Leveraging Interactive Temporal Features Annotation to Classify Signals and Events - Marcelo Leomil Zoccoler (Physics of Life (PoL) - TU Dresden)

14:00 Morphodynamics of human brain organoid development - Akanksha Jain (ETH Zürich)

14:00 BrainGlobe: Accessible software for neuroanatomy of emerging model organisms - Alessandro Felder (University College London)

14:00 Quantification of microtubule-guided peroxisome migration using a hidden Markov chain model - Carl-Magnus Svensson (Leibniz-HKI)

14:00 Run-length based mathematical morphology for efficient processing of large 3D images - David Legland (INRAE)

14:00 A Cloud-Native Virtual Bioimage Analysis Research Desktop (BARD) for Deployment of Containerised Bioimage Tools on Kubernetes - Arif Khan (EMBL Heidelberg)

14:00 Shaping progress in biomedical image processing with project-based learning - Andreas Kist (Friedrich-Alexander-University Erlangen-Nürnberg)

14:00 Example of a FBIAS project: mutliple fish tracking - Arthur Meslin (FBIAS, Institut Curie)

14:00 High-throughput in-vivo single-molecule imaging of DNA repair in E. coli - Daniel Thedie (University of Edinburgh)

14:00 Unsupervised Model Selection Through Test Time Perturbation Consistency - Joshua Talks (EMBL)

14:00 Light-Insight: Spatiotemporal profiling of human early brain organoid development. - Gilles Gut (ETH Zürich)

14:00 Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy - Austin E. Y. T. Lefebvre (Calico Life Sciences LLC)

14:00 FAIR Image Analysis Workflows - Beatriz Serrano-Solano (Euro-BioImaging)

14:00 Enhancing Image Resolution Through Averaged Autocorrelation Inversion - Daniele Ancora (EMBL)

14:00 Exploring gene function and morphology using JUMP Cell Painting Consortium data - Alán Fernando Muñoz González (Broad Institute of Harvard and MIT)

14:00 conv-paint: an easy to train interactive pixel classifier for napari - Lucien Hinderling (Institute of Cell Biology - Universität Bern)

14:00 Discovering explanatory factors of spatial localization with point process models - Dominik Sturm (TU Dresden / MPI-CBG)

14:00 TopoStats: taking AFM analysis to new heights - Laura Wiggins (University of Sheffield)

14:00 nlScript: A framework for creating natural-language-based user interfaces - Benjamin Schmid (OICE, Friedrich-Alexander-Universität Erlangen-Nürnberg) Ralph Palmisano (Optical Imaging Competence Centre Erlangen, FAU OICE)

14:00 Detecting immunological synapses in patient samples through analysis of Imaging Flow Cytometry data - Bram van den Broek (The Netherlands Cancer Institute)

14:00 Automating the Neuronal Differentiation of Ntera-2 Cells - Heather McCourty (University of Sheffield)

14:00 Using Nextflow for scalable and reproducible batch image analysis - Christian Tischer (EMBL)

14:00 Pollen to pixels: perception of heat stress by machine learning to predict fertility - Daan van den Brink (Radboud University)

14:00 Investigating the structural complexities of DNA using high resolution atomic force microscopy - Harriet Read (University of Sheffield)

14:00 Machine learning based Evaluation and Enhancement (EVEN) for optical microscopy - Elena Corbetta (Friedrich-Schiller-Universität Jena)

14:00 Pre-Processing Quality Control and Image Exploration for Bioimage Analysis: A Novel Python Application - Ranit Karmakar (Harvard Medical School)

14:00 User-oriented tools to characterize epithelia dynamics - Gaëlle Letort (CNRS/Institut Pasteur)

14:00 Cell lineage reconstruction and comparison from light-sheet microscopy image datasets - Ioannis Liaskas (Institute of Molecular Biology and Biotechnology of the Foundation for Research and Technology Hellas (IMBB-FORTH))

14:00 Mars, a molecule archive suite for analysis of single molecule properties from bioimages - Karl Duderstadt (Technical University of Munich (TUM))

14:00 Fiji Progress and Priorities 2024 - Curtis Rueden (University of Wisconsin-Madison)

14:00 From pixels to insights: Learning morphological descriptors from cellular ultrastructure - Jonas Hellgoth (EMBL Heidelberg)

14:00 Automated Tracking and Analysis of Plasma Membrane Dynamics in TIRF-SIM - Adam Harmanec (Masaryk University, Brno & Charles University, Prague)

14:00 Bilayers - an easy way to make your favorite deep learning tool more user-friendly - Beth Cimini (Broad Institute)

14:00 fsdb - an open-source bioimage analysis and (meta) data management framework - Arnim Jenett (CNRS, TEFOR Paris-Saclay)

14:00 Quantifying intra-tumoral molecular subtype heterogeneity in MIBC from histological slides using a deep learning approach - Alice Blondel (Centre for Computational Biology (CBIO), Mines Paris, PSL University)

14:00 High-throughput microscopy for deciphering the genetics of cell cycle diversity in wild yeasts - Benedikt Mairhörmann (Helmholtz Munich)

14:00 Using deep learning on single-cell images to unlock novel disease signatures and candidate therapeutics - Bianca Migliori (The New York Stem Cell Foundation)

14:00 Beyond spot detection with spotMAX - Francesco Padovani (Helmholtz Munich)

14:00 Segmentation of budding yeast organelles from bright field time-lapses - Diane Adjavon (HHMI Janelia/University of Edinburgh)

16:15 Interpreting Microscopy Images with Machine Learning - Inês Martins Cunha (SciLifeLab, University of Stockholm)

16:27 A Bayesian solution to count the number of molecules within a diffraction limited spot - Alexander Hillsley (Howard Hughes Medical Institute)

16:27 An Image Analysis Pipeline for Quantifying the Spatial Distribution of Fluorescently Labeled Cell Markers in Stroma-Rich Tumors - Antoine Ruzette (Harvard Medical School)
16:30 🚶‍♀️ Walking time to HT
🚶‍♀️ Walking time to HT
16:30 - 17:00
17:00
17:00 - 18:00
Contributions

17:00 Introduction to Piximi - Nodar Gogoberidze (Broad Institute)

17:00 Building Your Own Chatbot for BioImage Analysis - Caterina Fuster Barceló (Universidad Carlos III de Madrid)

17:00 Advancements in Cell Tracking: The Mastodon Solution for Large-Scale Datasets - Johannes Girstmair (MPI-CBG)

17:00 TopoStats: a tool for automated processing and quantification of AFM images - Laura Wiggins (University of Sheffield)

17:00 QuPath for Python Programmers - Alan O'Callaghan (University of Edinbrugh)

17:00 Segment Anything for Microscopy - Anwai Archit (University of Göttingen) Constantin Pape (University of Göttingen) Luca Freckmann (University of Göttingen) Sushmita Nair (University of Goettingen)

17:00 The Spatial Transcriptomics as Images Project (STIM) - Michael Innerberger (Janelia Research Campus) Stephan Preibisch (HHMI Janelia)

17:00 FAIR IPA - A Project Template - Jan Eglinger (Friedrich Miescher Institute for Biomedical Research, FMI) Tim-Oliver Buchholz (Friedrich Miescher Institute for Biomedical Research)
Thursday, 24 October 2024

09:00 Title to be announced (Sven Dorkenwald, Shanahan Foundation Fellow, Allen Institute)
Title to be announced (Sven Dorkenwald, Shanahan Foundation Fellow, Allen Institute)
09:00 - 09:30
Room: HT Auditorium

09:30 🚶‍♀️ Shuffle time
🚶‍♀️ Shuffle time
09:30 - 09:45
09:45
09:45 - 11:15
Contributions

09:45 PlantSeg 2.0: powerful and user-friendly tissue segmentation - Lorenzo Cerrone (University of Zurich) Qin Yu (EMBL Heidelberg)

09:45 Introduction to CellProfiler - Paula Llanos (Broad Institute)

09:45 Open-source bio-image analysis using surface meshes - Clément Benedetti (CNRS)

09:45 Versatile Deep Learning for 2D and 3D Bioimage Analysis with CytoDL - Benjamin Morris (Allen Institute for Cell Science)

09:45 Reproducible Scientific Figure Creation with Fiji/ImageJ and Inkscape - Jan Brocher (BioVoxxel) Jerome Mutterer (IBMP)

09:45 Deformable 2D and 3D big data image registration and transformation with BigWarp - John Bogovic (HHMI Janelia)

09:45 DaCapo: a modular deep learning framework for scalable 3D image segmentation - David Ackerman (Janelia Research Campus) Jeff Rhoades (HHMI Janelia)

09:45 Multiplexed tissue imaging: tools and approaches - Agustin Corbat (SciLifeLab) Anna Klemm (SciLifeLab) Frederic Ballllosera Navarro (Stanford University) Jonas Windhager (SciLifeLab) Kristína Lidayová (SciLifeLab)
11:15 ☕ Coffe break
☕ Coffe break
11:15 - 11:45

11:45 Title to be announced (Tingying Peng, Helmholtz Zentrum München)
Title to be announced (Tingying Peng, Helmholtz Zentrum München)
11:45 - 12:15
Room: HT Auditorium
12:15 ZEISS Microscopy Software Ecosystem for Image Acquisition and Analysis
ZEISS Microscopy Software Ecosystem for Image Acquisition and Analysis
12:15 - 12:30
Contributions

12:15 ZEISS Microscopy Software Ecosystem for Image Acquisition and Analysis - Francesco Biancardi (ZEISS)
12:30 🚶‍♀️ Walking time to Triulza Academy
🚶‍♀️ Walking time to Triulza Academy
12:30 - 13:00

13:00 🍝 Lunch
🍝 Lunch
13:00 - 14:00
14:00
14:00 - 16:30
Contributions

14:00 Enhanced Bacterial Cytological Profiling with super resolution techniques and fluorescent D amino acids - Joseph Ratcliff (University of Warwick)

14:00 Leonardo: a toolset to remove sample-induced aberrations in light sheet microscopy images - Yu Liu (Technical University of Munich, TUM)

14:00 An AI-based pipeline to extract predictive mechano-features in Triple Negative Breast Cancers - Emanuele Martini Mattia Tonani (IFOM)

14:00 Quantifying the Heterogeneity of DNA Interactions in AFM Images - Max Gamill (University of Sheffield)

14:00 FLUTE: A Python GUI for interactive phasor analysis of FLIM data - Chiara Stringari (CNRS - Ecole Polytechnique)

14:00 Robust detection and quantification of beating cells in microscopic 2D videos of cardiomyocytes - Oleksiy Nosov (DNTOX GmbH)

14:00 Fractal: An open-source framework for reproducible bioimage analysis at scale using OME-Zarrs - Joel Lüthi (University of Zurich)

14:00 Building Foundations for AI-Driven Bioimage Analysis: Infrastructure and Annotation Platforms - Nils Mechtel (KTH Royal Institute of Technology)

14:00 Unsupervised Denoising for Signal-Dependent and Row-Correlated Imaging Noise - Benjamin Salmon (University of Birmingham)

14:00 How To Train Your Image Analyst: Perspectives from Upskilled Biologists - Maria Traver (NIH / NIAID)

14:00 Continuous, interpretable, and transformation-invariant Morphometric for dynamic shape quantification - Roua Rouatbi (TU Dresden)

14:00 An AI approach for timing analysis of cytokinesis from microscopy data - Thomas Bonte (Université PSL - Institut Curie)

14:00 RNA point cloud segmentation for image-based spatial transcriptomics - Thomas Defard (Institut Pasteur, Ecole des Mines)

14:00 Enhancing Synaptic-Resolution Connectomics with an Open-Source AI Ecosystem - Samia Mohinta (University of Cambridge, UK)

14:00 napari-phasors: Integrating Hyperspectral and FLIM Data Analysis into an Open-Source Bioimaging Framework - Marcelo Leomil Zoccoler (DFG Cluster of Excellence Physics of Life - TU Dresden)

14:00 METEOR: Enabling precise 3D correlative cryo-FIB milling for high throughput cryo-ET lamella production - Kevin Homberg (Delmic Cryo B.V)

14:00 Create web-based OME-Zarr galleries with Zarrcade - Konrad Rokicki (HHMI Janelia Research Campus)

14:00 Taggathon on BIII.eu: contributing to a unique database of image analysis tools and workflows - Perrine Paul-Gilloteaux (University of Nantes)

14:00 A QuPath extension for Data-driven Microscopy - Michael S. Nelson (University of Wisconsin, Madison)

14:00 Integrative Open-Source Analysis Pipeline of RNA In Situ Hybridization Immunofluorescence Images - Nur Muhammad Renollet (University of Michigan)

14:00 PIXIMI: A web-based deep learning tool for biomedical image analysis - Nodar Gogoberidze (Broad Institute)

14:00 Too good to be true: the perils of applying image quality metrics in fluorescence microscopy - Siân Culley (King's College London)

14:00 FISBe: A real-world benchmark dataset for instance segmentation of long-range thin filamentous structures - Lisa Mais (Max Delbrück Center for Molecular Medicine in the Helmholtz Association (Max Delbrück Center))

14:00 Integrating Shape and Function: Identifying growth drivers and their morphological expression in Gastric Tumor Organoids. - Maleeha Hassan (Technical University of Dresden)

14:00 BIOP-desktop , a versioned computer for image analysis in life sciences - Romain Guiet (EMBL)

14:00 Digital pathology and artificial intelligence-based approaches to characterize the complex interactions between cellular components of the tumor microenvironment and their spatial distribution - Marika Viatore (Università degli Studi di Milano)

14:00 3D quantitative image analysis of cell fate acquisition during lateral inhibition - Minh-Son Phan (Institut Pasteur Paris)

14:00 Self-supervised learning for sample localization on cryoem grids for tomogram acquisition - Ricardo M. Sánchez L. (EMBL)

14:00 Data-driven Unsupervised and Sparsely-Supervised Segmentation - Sheida Kordasiabi (Human Technopole)

14:00 DaCapo: a modular deep learning framework for scalable 3D image segmentation - Marwan Zouinkhi (HHMI - Janelia)

14:00 **multiview-stitcher: a modular and extensible toolbox for scalable image registration and fusion in python - Marvin Albert (Institut Pasteur)

14:00 A nextflow-based end to end workflow for decoding of in situ sequencing data - Nima Vakili (EMBL/GSK)

14:00 Virtual Embryo Zoo: A Web-Based Tool for Embryogenesis Cell Tracking Visualization - Teun Huijben (Chan Zuckerberg Biohub San Francisco)

14:00 Investigating DNA damage with Atomic Force Microscopy and TopoStats - Thomas Catley (University of Sheffield)

14:00 Two ways of quantifying inflammation in histopathology slices of the mouse pancreas - Maria Theiss (Harvard Medical School)

14:00 Joined segmentation of nuclei and cells - Thierry Pécot (Rennes University)

14:00 Enabling Access to Bioimage Analysis Tools on University Cluster - Ranit Karmakar (Harvard Medical School)

14:00 Foreground-aware virtual staining for 3D nuclear morphometry - Paula Llanos (Broad Institute)

14:00 The Human Protein Atlas in OMERO: an accessible dataset for teaching purposes - Rémy Dornier (EPFL - SV - PTECH - PTBIOP)

14:00 TOMOMAN•PY - A Python-Based Suite for Handling Large cryo-ET Datasets - Philipp S. Erdmann (Human Technopole)

14:00 Client-Server Approach for Bioimage Analysis in the Deep Learning Era: Enhancing Extensibility and Accessibility - Ko Sugawara (RIKEN BDR)

14:00 micronuclAI: Automated quantification of micronuclei for assessment of chromosomal instability - Miguel A. Ibarra-Arellano (Institute for Computational Biomedicine, University Hospital Heidelberg)

14:00 AI-powered analysis of histopathological tissues to study of the tumor immune microenvironment - Rebecca Polidori (University of Milan)

14:00 Probabilistic Framework for Calibrated Cell Tracking - Richard D. Paul (Forschungszentrum Jülich GmbH)

14:00 InstanSeg: a fast, flexible and user-friendly cell segmentation method for brightfield and multichannel images - Thibaut Goldsborough (University of Edinburgh)

14:00 Simplified processing for image-based cell profiling with pollen - Tom Ouellette (University of Toronto/Ontario Institute for Cancer Research)

14:00 Contextual Segmentation of Large, High-dimensional Medical Images - Victoria Porter (Queen's University Belfast)

14:00 MMV_H4Cells - a cell evaluation napari plugin - Lennart Kowitz (Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V.)

14:00 Mastodon – a Large-Scale Tracking and Track-Editing Framework for Large, Multi-View Images and Extensions for 3D Visualization and Lineage Comparison - Matthias Arzt (MPI-CBG) Stefan Hahmann (TU Dresden)

14:00 Quantifying bacterial dynamics over a wide range of species with TrackMate-Omnipose - Marie Anselmet (Institut Pasteur)

14:00 Potentials and limitations in the application of Convolutional Neural Networks for mosquito species identification using wing images - Kristopher Nolte (Bernhard-Nocht-Institute for Tropical Medicine)

14:00 Robust segmentation and measurement of single bacterial cells within a chain - Octavio Reyes-Matte (Max Planck Institute for Evolutionary Biology)

14:00 Single protein pinpointing in light microscopy using DNA-PAINT - Rafal Kowalewski (Max Planck Institute of Biochemistry, Ludwig-Maximilians University of Munich)

14:00 Combining Incremental Deep Learning, Eye Tracking and Virtual Reality for Human-in-the-Loop Cell Tracking: a Progress Report - Samuel Pantze (CASUS - Center for Advanced Systems Understanding)

16:15 OptiCell3D: inference of the mechanical properties of cells from 3D microscopy images - Kevin Yamauchi (ETH Zurich)
16:30 🚶‍♀️ Walking time to HT
🚶‍♀️ Walking time to HT
16:30 - 17:00
17:00
17:00 - 18:00
Contributions

17:00 Annotation and Visualization of Large 3D Datasets with Paintera - Caleb Hulbert (HHMI Janelia)

17:00 ScaleFEx℠,: Single cell feature extraction from large scale datasets - Bianca Migliori (The New York Stem Cell Foundation)

17:00 DL4MicEverywhere: Making your deep learning pipelines flexible, shareable, and reproducible - Estibaliz Gómez-de-Mariscal (Instituto Gulbenkian de Ciência) Iván Hidalgo-Cenalmor (Instituto Gulbenkian de Ciência)

17:00 motile: Multi-Object Tracking with Integer Linear Equations - Anniek Stokkermans (Hubrecht Institute) Carolin Mailin-Mayor (HHMI Janelia)

17:00 Accelerating Microscopy Image Annotation with SAMJ Annotator - Caterina Fuster Barceló (Universidad Carlos III de Madrid)

17:00 QuPath for Beginners - Fiona Inglis (University of Edinbrugh)

17:00 BigStitcher-Spark - Michael Innerberger (Janelia Research Campus) Stephan Preibisch (HHMI Janelia) Tobias Pietzsch (Janelia Research Campus)

17:00 An end-to-end image-based spatial transcriptomic pipeline in Nextflow - Stanislaw Makarchuk (Sanger Institute) Tong Li (Sanger Institute)
18:00 🍹 Social Happy Hour
🍹 Social Happy Hour
18:00 - 19:30
Friday, 25 October 2024

09:00 Explorations in embryogenesis (Hari Shroff, HHMI Janelia)
Explorations in embryogenesis (Hari Shroff, HHMI Janelia)
09:00 - 09:30
Room: HT Auditorium

09:30 🚶‍♀️ Shuffle time
🚶‍♀️ Shuffle time
09:30 - 09:45
09:45
09:45 - 11:15
Contributions

09:45 BiaPy: deep learning based Bioimage Analysis for all audiences - Ignacio Arganda-Carreras (Universidad del Pais Vasco)

09:45 Recent Advances in ilastik - Benedikt Best (EMBL) Dominik Kutra (EMBL)

09:45 Lazy parallel processing and visualization of large data with ImgLib2, BigDataViewer, the N5-API, and Spark - Stephan Saalfeld (HHMI Janelia) Tobias Pietzsch (HHMI Janelia)

09:45 Tif2Blender: 3D image visualization in Blender - Oane Gros (EMBL)

09:45 Non linear registration of whole slide images with Fiji and QuPath - Olivier Burri (EPFL)

09:45 ZEISS arivis: the unique platform for your image analysis - Riccardo Tognato (ZEISS)

09:45 Connecting software tools into reproducible workflows with CellProfiler plugins - Beth Cimini (Broad Institute)

09:45 Segment Anything using Python for Microscopy Data - Ranit Karmakar (Harvard Medical School)
11:15 ☕ Coffee break
☕ Coffee break
11:15 - 11:45

11:45 Title to be announced (Josh Moore, German Bioimaging)
Title to be announced (Josh Moore, German Bioimaging)
11:45 - 12:15
Room: HT Auditorium

12:15 🚶‍♀️ Shuffle time
🚶‍♀️ Shuffle time
12:15 - 12:30
12:30
12:30 - 13:30
Contributions

12:30 Introduction to AI4Life and BioImage Model Zoo - Anna Kreshuk (EMBL) Theodoros Katzalis (EMBL)

12:30 Introducing ultrack: cell tracking in python under segmentation uncertainty - Jordão Bragantini (CZ Biohub) Teun Huijben (Chan Zuckerberg Biohub San Francisco)

12:30 coLoↄ: A Collaborative Board Game for Teaching Co-Localization Analysis - Romain Guiet (EMBL)

12:30 Annotating and sharing large images with OME-Zarr and WEBKNOSSOS - Norman Rzepka (Scalable Minds)

12:30 AI4Life: Empowering BioImaging through the BioEngine - Estibaliz Gómez-de-Mariscal (Instituto Gulbenkian de Ciência) Nils Mechtel (KTH Royal Institute of Technology)

12:30 Using BigTrace for the analysis of curvilinear biological structures - Eugene A. Katrukha (Utrecht University)

12:30 pymmcore-plus: a pure python way to control your microscope with Micro-Manager. - Federico Gasparoli (Harvard University)

12:30 Phasor analysis of Fluorescence Lifetime Microscopy data with FLUTE - Chiara Stringari (École polytechnique - Laboratory for Optics & Biosciences)
13:30 🍝 Lunch
🍝 Lunch
13:30 - 14:30
14:30
14:30 - 15:00
Contributions

14:30 Exploiting NanoPyx’s Liquid Engine to accelerate image analysis pipelines - Bruno Manuel Santos Saraiva (Instituto Gulbenkian de Ciência)

14:30 Denoising microscopy images with CAREamics - Joran Deschamps (Human Technopole)

14:30 QuPath for Groovy Scripters - Léo Plat (University of Edinbrugh)

14:30 Taggathon on BIII.eu: contributing to a unique database of image analysis tools and workflows - Perrine Paul-Gilloteaux (University of Nantes)

14:30 Intro to MemBrain v2: Membrane Analysis in Cryo-ET - Joel Valdivia Ortega (Helmholtz Zentrum München) Lorenz Lamm (Helmholtz Zentrum München)

14:30 conv-paint: an easy to train interactive pixel classifier for napari - Lucien Hinderling (Institute of Cell Biology - Universität Bern)

14:30 FeatureForest: leveraging foundational models for user guided semantic segmentation - Mehdi Seifi (Human Technopole, HT)
15:00 🚶‍♀️ Shuffle time
🚶‍♀️ Shuffle time
15:00 - 15:15
15:15
15:15 - 16:00
Room: HT Auditorium
Contributions

15:15 Too good to be true: the perils of applying image quality metrics in fluorescence microscopy - Siân Culley (King's College London)

15:30 Interpreting Microscopy Images with Machine Learning - Inês Martins Cunha (SciLifeLab, University of Stockholm)

15:45 OptiCell3D: inference of the mechanical properties of cells from 3D microscopy images - Kevin Yamauchi (ETH Zurich)
16:00 Title to be announced (Aubrey Weigel, HHMI Janelia)
Title to be announced (Aubrey Weigel, HHMI Janelia)
16:00 - 16:30
Room: HT Auditorium

16:30 ☕ Coffee break
☕ Coffee break
16:30 - 17:00

17:00

17:00 - 18:00

18:00

18:00 - 18:30