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Training European Experts in Multilevel Bioimaging, Analysis and Modelling of Vertebrate Development and Disease

Deliverables

Tissue geometry & physics

Tissue geometry & physics : cell-cell interactions, subcellular elements, extracellular matrix Generic models with simulation/visualisation software, customised to zebrafish or mammalian datasets

Design of image processing and analysis methods

Design of image processing and analysis methods

Report on Congress Presentations and Scientific Publications I

Report on Congress Presentations and Scientific Publications

Consortium agreement

Consortium agreement

Midterm report

Midterm report to the commission. The due date is indicative. This deliverable must be submitted at least one month before the Midterm review meeting.

Cell biomechanics

Models of Cell biomechanics : cell types, shapes & behaviours,

Infection protocols

Infection protocols for high throughput imaging of infected zebrafish embryo

Data Management Plan

Frist version of the Data Management Plan

Brochure, Website & Advertising

ImageInLife Brochure, website & vacancies advertising

Wikipedia article

Wikipedia article

Incubation chambers

Incubation chambers for multilevel imaging of embryos, mammals and zebrafish, normal and infected, at different imaging resolutions

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Publications

A Model of Superinfection of Virus-Infected Zebrafish Larvae: Increased Susceptibility to Bacteria Associated With Neutrophil Death

Author(s): Laurent Boucontet, Gabriella Passoni, Valéry Thiry, Ludovico Maggi, Philippe Herbomel, Jean-Pierre Levraud, Emma Colucci-Guyon
Published in: Frontiers in Immunology, Issue 9, 2018, ISSN 1664-3224
DOI: 10.3389/fimmu.2018.01084

Neutrophils use superoxide to control bacterial infection at a distance

Author(s): Quang Tien Phan, Tamara Sipka, Catherine Gonzalez, Jean-Pierre Levraud, Georges Lutfalla, Mai Nguyen-Chi
Published in: PLOS Pathogens, Issue 14/7, 2018, Page(s) e1007157, ISSN 1553-7374
DOI: 10.1371/journal.ppat.1007157

Sequential formation and resolution of multiple rosettes drive embryo remodelling after implantation

Author(s): Neophytos Christodoulou, Christos Kyprianou, Antonia Weberling, Ran Wang, Guizhong Cui, Guangdun Peng, Naihe Jing, Magdalena Zernicka-Goetz
Published in: Nature Cell Biology, Issue 20/11, 2018, Page(s) 1278-1289, ISSN 1465-7392
DOI: 10.1038/s41556-018-0211-3

Morphogenesis of extra-embryonic tissues directs the remodelling of the mouse embryo at implantation

Author(s): Neophytos Christodoulou, Antonia Weberling, Douglas Strathdee, Kurt I. Anderson, Paul Timpson, Magdalena Zernicka-Goetz
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-019-11482-5

TRIM8 is required for virus-induced IFN response in human plasmacytoid dendritic cells

Author(s): Ghizlane Maarifi, Nikaïa Smith, Sarah Maillet, Olivier Moncorgé, Célia Chamontin, Joanne Edouard, Frédéric Sohm, Fabien P. Blanchet, Jean-Philippe Herbeuval, Georges Lutfalla, Jean-Pierre Levraud, Nathalie J. Arhel, Sébastien Nisole
Published in: Science Advances, Issue 5/11, 2019, Page(s) eaax3511, ISSN 2375-2548
DOI: 10.1126/sciadv.aax3511

IFN-Stimulated Genes in Zebrafish and Humans Define an Ancient Arsenal of Antiviral Immunity

Author(s): Jean-Pierre Levraud, Luc Jouneau, Valérie Briolat, Valerio Laghi, Pierre Boudinot
Published in: The Journal of Immunology, Issue 203/12, 2019, Page(s) 3361-3373, ISSN 0022-1767
DOI: 10.4049/jimmunol.1900804

Multi-template matching: a versatile tool for object-localization in microscopy images

Author(s): Laurent S. V. Thomas, Jochen Gehrig
Published in: BMC Bioinformatics, Issue 21/1, 2020, ISSN 1471-2105
DOI: 10.1186/s12859-020-3363-7

ImageJ/Fiji ROI 1-click tools for rapid manual image annotations and measurements

Author(s): Laurent SV Thomas and Jochen Gehrig
Published in: microPublication Biology, 2020, ISSN 2578-9430
DOI: 10.17912/micropub.biology.000215

A contractile acto-myosin belt promotes growth anisotropy during the early stages of pectoral fin development in zebrafish.

Author(s): Elena Kardash, Hanh Nguyen, Martin Behrndt, Carl-Philipp Heisenberg, Nadine Peyrieras, Marcos Gonzalez-Gaitan
Published in: Biorxiv, 2019
DOI: 10.1101/512038

Multi-Template Matching: a versatile tool for object-localization in microscopy images

Author(s): Laurent S. V. Thomas, Jochen Gehrig
Published in: Biorxiv, 2019
DOI: 10.1101/619338

3D + Time Imaging and Image Reconstruction of Pectoral Fin During Zebrafish Embryogenesis

Author(s): Hanh Nguyen, Jaume Boix-Fabrés, Nadine Peyriéras, Elena Kardash
Published in: Computer Optimized Microscopy - Methods and Protocols, Issue 2040, 2019, Page(s) 135-153
DOI: 10.1007/978-1-4939-9686-5_8

MACROPHAGE IMAGE SEGMENTATION BY THRESHOLDING AND SUBJECTIVE SURFACE METHOD

Author(s): Seol Ah Park, Tamara Sipka, Zuzana Kriva, Martin Ambroz, Michal Kollar, Balazs Kosa, Mai Nguyen-Chi, Georges Lutfalla, Karol Mikula
Published in: Tatra Mountains Mathematical Publications, 2019, ISSN 1210-3195