Past STSMs

Grantee, HOME Institution HOST, Lab & Institution Title Dates
Dr. Véronique Gebala ** Max Delbrueck Center for Molecular Medicine, Berlin (DE) Dr. Martin Jones The Francis Crick Institute, London (UK) Endothelial cell shape regulation by integrin beta 1 during sprouting angiogenesis in vivo 1 week, 09/2016
Mr Hamid Fehri ** University of Sheffield, Sheffield (UK) Dr. Erik Meijering Erasmus University Medical Center, Biomedical Imaging Group Rotterdam, Rotterdam (NL) Segmentation and Interpretation of Cells in Fluorescent Microscopy Images 2 months, 02-03/2017
Dr. Maria Smedh University of Gothenburg, Gothenburg (SE) Dr. Rainer Heintzmann Leibniz Institute of Photonic Technology (IPHT), Jena (DE) Processing and Analysis of SR-SIM and SMLM Super-Resolution Images 1 week, 11/2016
Dr Devrim Unay Izmir University of Economics, Izmir (TR) Dr. Stefan G. Stanciu University Politehnica of Bucharest, Bucharest (RO) Robust detection and description of local invariant features in Laser Scanning Microscopy Data Sets 1 week, 01/2017
Dr Laure Plantard University of Copenhagen, Copenhagen (DK) Dr. Simon Noerrelykke ScopeM-IDA , ETH-Zurich (CH) 2D and 3D analysis of fluorescent microscopy images using Imaris, MATLAB, Fiji, and CellProfiler with a focus on combining software packages and automating the analysis of batch of images 2 weeks, 10-11/2016
Mr Torsten Stoeter** Leibniz Institute for Neurobiology (DE) Lab 1: Dr. Chong Zhang 1) Universitat Pompeu Fabra, Barcelona (ES) “Exploration and Analysis of Large Microscopy Data Using ParaView” 5 weeks 02-03/2017
Lab 2: Julien Colombelli 2) Institute for Research in Biomedicine - IRB Barcelona (ES)
Dr Patricia Garcia-Cañadilla** Universitat Pompeu Fabra (ES) Dr. Marco Stampanoni Paul Scherrer Institute, Villigen-PSI (CH) “Detailed characterization of scar and fibrous tissue in hearts using high resolution phase-contrast X-ray imaging” 2 weeks 01-02/2017
Ms. Luiza Filipis** CNRS, Saint-Martin-d'Hères (FR) Dr. Panayiota Poirazi Institute of Molecular Biology and Biotechnology (IMBB), Heraklion (GR) "Developing NEURON models based on experimental Ca 2+ current optical measurements" 4 weeks, 05-06/2017
Dr Victor Caldas** Vrije Universiteit Amsterdam, Amsterdam (NL) Dr. Mark Fricker University of Oxford (UK) "Extracting graphs from symbiotic networks" 1 week, 06/2017
Dr Alex Hargreaves** University of Leeds (UK) Dr. Carolina Wählby Centre for Image Analysis, Uppsala University (SE) "Analysis Workflows to resolve Aniline Blue Assay for Sperm Chromatin Condensation" 2 weeks, 06-07/2017
Dr Irene Fondon** University of Seville (ES) Prof. Paula Sampaio* Instituto de Biologia Molecular e Celular / i3S - Porto (PT) "Development of image analysis workflows for the study of cellular aging" 2 weeks, 07/2017
Dr Tobias Rasse EMBL - Heidelberg (DE) Dr. Stephan Preibisch Max Delbrück Center for Molecular Medicine (MDC)- Berlin (DE) "Towards improved SPIM data analysis pipelines" 12 weeks, 07-09/2017
Dr Janka Nozkova* Faculty of Agrobiology and Food Resources, Nitra (SK) Dr. David ROUSSEAU Laboratoire CREATIS, Université Lyon 1 (FR) "Measuring of Agrobiodiversity from the View of Image Analysis" 1 week 07/2017
Mr Ross Laws** Newcastle University (UK) Dr. Eija Jokitalo University of Helsinki (FI) "Improving segmentation in challenging 3D-SEM data sets using MIB" 2 weeks 08/2017
Martin Maska*,** Masaryk University (Brno, CR) Dr. Carlos Ortiz de Solorzano Cancer Imaging Lab & Platform @ CIMA - Pamplona (ES) "Toward Robust Segmentation and Tracking of Cells with Filopodial Protrusions in 3D Fluorescence Microscopy" 4 weeks, 08/2017
Dr Marta Alabrudzinska** Karolinska Institutet, Stockholm (SE) Dr. Daniel Sage Ecole Polytechnique Fédérale de Lausanne, Biomedical Imaging Group (CH) "Segmentation of intravital images for quantification of tumor growth" 2 weeks, 09/2017
Erin Cocks** Newcastle University (UK) Dr. Gerd Leitinger Research Unit Electron Microscopy Techniques, Med. Univ. Graz (AT) "Segmentation of SBF-SEM Data of the Locust Lobula Giant Movement Detector 2 Neuron" 2 weeks, 10/2017
Dr. Eldar Zehorai Weizmann Inst. Sci., Rehovot (IL) Prof. Karl Kadler University of Manchester (UK) 3D-morphometric analysis of SBF-SEM data of uterine ECM fibrils 1 week, 12/2017
Laura Murphy ** MRC-IGMM, Edinburgh (UK) Dr. Anne Carpenter Broad Institute, Boston (USA) Developing an image analysis service for high content microscopy data using CellProfiler and CellProfiler Analyst 4 weeks, 02/2018
Dr. Alessandra Procopio ** Univ. Bologna (IT) Dr. Andrea Sorrentino ALBA Synchroton, Barcelona (ES) Integration of post-processing analysis software of x-ray nanotomography and X-ray Absorption Near-Edge spectro-microscopy to study the early stages of bone mineralization mechanisms in differentiated bone marrow stem cells 3 weeks, 02/2018
Dr. Miguel Aroso i3S, Porto (PT) Dr. Marco Canepari Univ. Grenoble (FR) Development of a user-friendly, GUI-based toolbox for the analysis of voltage sensitive dye imaging data 3 weeks, 03/2018
Buda Bajic *, ** Univ. Novi Sad (RS) Dr. Moritz Kirschmann Univ. Zuerich (CH) Denoising of low signal-to-noise scanning electron micrographs by energy minimization and deep learning 2 weeks, 03/2018
Dr. Michael Barbier** Univ. Antwerp (BE) Prof. Peter Horvath BRC, Szeged (HU) Automated brain region recognition in fluorescently labelled brain tissue slices 3 weeks, 04/2018
Dr. Filippo Piccinini ISRT Cancer Res Hosp (IT) Prof. Peter Horvath BRC, Szeged (HU) 3D high-content screening: single-cell segmentation and classification from 3D cancer spheroids 6 weeks, 06-07/2018
Dr. Magalie Feyeux** SFR Santé François Bonamy (FR) Dr. Simon Noerrelykke ScopeM-IDA , ETH-Zurich (CH) Machine learning for Embryo selection for in-vitro fecundation, and organization of a bio image analysis facility. 2 weeks 08/2018
Maxime Lafarge** Eindhoven University of Technology (NL) Dr Anne Carpenter Broad Institute, Boston (MA, USA) Disentangled Generative Modeling of Cell Images 2 months 11-12/2018
Raimo Salo** A.I.Virtanen Institute for Molecular Sciences, Kuopio (FI) Dr Michela Fratini IRCCS Fondazione Santa Lucia, Rome (IT) Multimodal approach for the 3D investigation of the spinal cord and brain vascular and neuronal networks 2 weeks 11/2018
Marko Sostar** Institute Ruđer Bošković (HR) Prof. Till Bretschneider University of Warwick (UK) QuimP-assisted image analysis and modelling 2 weeks 12/2018
Arianne Bercowsky Rama** EPFL, Lausanne (CH) Dr. Jean-Yves Tinevez Institut Pasteur, Paris (FR) Analysis of Light Sheet Microscopy Data using Mastodon 1 week 12/2018
Dr. Chong Zhang Universitat Pompeu Fabra (ES) Dr. Perrine Paul-Gilloteaux SFR Santé François Bonamy, Nantes (FR) Biomedical image analysis workflow definition through a web interface and example queries 1 week 01/2019
Harold Gomez** ETH Zurich, Basel (CH) Dr. Florian Jug MPI-CBG Dresden (DE) Tailoring content-aware restoration networks framework (CARE) to denoise and isotropize 4D light-sheet datasets of murine embryonic lung development. 3 weeks 02/2018
Nikita Moshkov*,** BRC, Szeged (HU) Dr. Anne Carpenter Broad Institute, Boston (MA, USA) Deep learning based cytoplasm segmentation for cancer tissue slices 2months 03-04/2019
Carla Pereira*,** IPATIMUP, Porto (PT) Dr. Carolina Wählby Uppsala University (SE) Mapping intra-tumour heterogeneity of therapeutic targets in gastric cancer 1 month 03/2019
Dr. Jonas Ogaard Oslo University Hospital (NO) Dr John Cupitt Imperial College London (UK) Implementation and usage of low memory feature extraction on whole slide images for use with machine learning 2 weeks 03/2019
Dr. Ana Stojiljkovic Universität Bern (CH) Dr Davide Danovi King's College London (UK) High-content characterisation of canine induced pluripotent stem cells 2 weeks 03/2019
Dr. Claire Barnes Swansea University (UK) Dr. Anne Carpenter Broad Institute, Boston (MA, USA) Deep Learning for BioImage Analytics 1 month 03/2019
Martin Weigert** MPI-CBG Dresden (DE) Dr Juan Nunez-iglesias Monash University (AU) Accelerating image analysis in Python with GPUs 2 weeks 03/2019
Uwe Schmidt** MPI-CBG Dresden (DE) Dr Volker Hilsenstein Monash University (AU) A fully open source lattice light sheet workflow 2 weeks 03/2019
Mr Debayan Saha ** Max Planck Institute of Molecular Cell Biology and Genetics (DE) Prof Martin Booth University of Oxford (UK) Machine-learned phase-retrieval for image-based sensorless adaptive optics 3 weeks 03/2019
Mr Assaf Nahum ** Ben-Gurion University of the Negev (IL) Dr Jean-yves Tinevez Institut Pasteur (FR) Quantifying 3D cell-ECM interactions 2 weeks 03/2019
Marco Tarasco*,** Center of Marine Sciences (CCMAR), Algarve (PT) Dr Fabrice Cordelières Bordeaux Imaging Center (FR) Assessment of bone regeneration in zebrafish caudal fin through morphometric analysis of bone formation and patterning. 2 weeks 04/2019
Carlos Javier García** Universidad Carlos III de Madrid (ES) Dr. Daniel Sage Ecole Polytechnique Fédérale de Lausanne, Biomedical Imaging Group (CH) Bridging Deep Neuronal Network to ImageJ 4 weeks 04/2019
Dr Tomas Majtner ** Maersk Mc-Kinney Moller Institute (DK) Pr. Natasa Sladoje University of Novi Sad (RS) Development and evaluation of αLBP-maps for improved texture-based image classification via deep learning in biomedical domain 2 weeks, 04/2109
Ms Estibaliz Gómez de Mariscal ** Universidad Carlos III de Madrid (ES) Dr. Daniel Sage Ecole Polytechnique Fédérale de Lausanne, Biomedical Imaging Group (CH) Bridging Deep Neuronal Network to ImageJ 2 weeks 07/2019
Mr Pau Carrillo Barberà ** Universitat de València (ES) Dr André Maia IBMC-Instituto de Biologia Molecular e Celular (PT) Deployment of bioimage analysis pipelines for high content screening assays 2 weeks 08/2019
Dr Sian Culley ** MRC Laboratory for Molecular Cell Biology (UK) Dr. Uwe Schmidt MPI-CBG Dresden (DE) Developing Machine Learning Approaches for Automated Detection of Dividing Thermophilic Archaea 2 weeks 10/2019
Dr Devrim Unay * Izmir Democracy University (TR) Prof Gabriella Cincotti University Rome Tre (IT) Automated detection and segmentation of bacteria from multimodal microscopy images 2 weeks, 01/2020
Nikita Moshkov*,** BRC, Szeged (HU) Dr. Anne Carpenter Broad Institute, Boston (MA, USA) Image-based profiling using deep learning 7 weeks 01-03/2020
Dr Debora Olivier ** CBI / LBCMCP UMR 5088 CNRS/Université Toulouse III (FR) Dr. Anne Carpenter Broad Institute, Boston (MA, USA) Generating an automated pipeline to track cells & foci and align them within the cell cycle using CellProfiler and CellProfiler Tracer. 2 weeks, 02/2020
Dr Jiri Tyc *,** Biology Centre CAS (CR) Dr Laurent Gelman Friedrich Miescher Institute for Biomedical Research, Facility for advanced imaging and microscopy (CH) Finding the perfect parameters for large SBEM data analysis 2 weeks 08/2020
Marco Tarasco*,** Center of Marine Sciences (CCMAR), Algarve (PT) Dr Fabrice Cordelières Bordeaux Imaging Center (FR) Development of a Java plug-in for the analysis of therapeutic-relevant molecules affecting bone mineralization and regeneration 2 weeks 09/2020
F M * Inclusiveness Target Country ** Early Career Investigator Imaging Facility or Center/Image Analysis Center or Facility Research Lab