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

Deliverables

Report on Congress presentations and Scientific Publications II

Report on Congress presentations and Scientific Publications

PhDs

Report on already awarded PhDs

Application of image processing and analysis methods to ImageInLife data

Application of image processing and analysis methods to ImageInLife data

New protocols to image the developing vertebrate embryos to the subcellular level

New protocols to image the developing vertebrate embryos to the subcellular level

Ultrastructural data correlated to fluorescence images

Ultrastructural data correlated to fluorescence images: Correlate confocal and electron microscopy data

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

Dissemination of knowledge

Draft (midterm) and final version (final report) of the plan for the use and dissemination of knowledge

Search & optimisation

Parameter search & optimisation: comparison between simulations & data

Design of image processing and analysis methods

Design of image processing and analysis methods

Final report

Final report to the commission

Virus propagation

Virus propagation model: immune status, cell response, pathways of virus dissemination

Report on Congress Presentations and Scientific Publications I

Report on Congress Presentations and Scientific Publications

in vivo tracers, reporters & actuators

in vivo tracers, reporters & actuators: validation of staining strategies for signalling pathways and gene expression patterns

Consortium agreement

Consortium agreement

Outreach activities

Record of all participants’ contributions to outreach activities targeted at schools and at the general public

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,

Computer implementation of image processing and analysis methods

Computer implementation of image processing and analysis methods

Infection protocols

Infection protocols for high throughput imaging of infected zebrafish embryo

Genetic/molecular control

Models of Genetic/molecular control : gene regulation network, chemical signalling, interface with BioTapestry, reverse engineering of circuits from atlases

Data Management Plan

Frist version of the Data Management Plan

Final version of the Data Management Plan

Final version of the Data Management Plan

Brochure, Website & Advertising

ImageInLife Brochure, website & vacancies advertising

MOOCs

Online dissemination using MOOCs

Wikipedia article

Wikipedia article

Video series

Video series for outreaches activities

Multimodal and multiscale LSFM workstation

Multimodal and multiscale LSFM workstation, software and image analysis

Incubation chambers

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

Image acquisition systems for infected embryos

Image acquisition systems for infected embryos using the VAST-BioImager

Super-resolution-LSFM for imaging of cellular processes within the embryo

Implementation of strategies for Super-resolution-LSFM for imaging of cellular processes within the embryo

Searching for OpenAIRE data...

Publications

Computational modelling unveils how epiblast remodelling and positioning rely on trophectoderm morphogenesis during mouse implantation

Author(s): Joel Dokmegang, Moi Hoon Yap, Liangxiu Han, Matteo Cavaliere, René Doursat
Published in: PLOS ONE, Issue 16/7, 2021, Page(s) e0254763, ISSN 1932-6203
DOI: 10.1371/journal.pone.0254763

Pro‐resolving mediator protectin D1 promotes epimorphic regeneration by controlling immune cell function in vertebrates

Author(s): Mai Nguyen‐Chi, Patricia Luz‐Crawford, Laurence Balas, Tamara Sipka, Rafael Contreras‐López, Audrey Barthelaix, Georges Lutfalla, Thierry Durand, Christian Jorgensen, Farida Djouad
Published in: British Journal of Pharmacology, Issue 177/17, 2020, Page(s) 4055-4073, ISSN 0007-1188
DOI: 10.1111/bph.15156

Quantification of cell behaviors and computational modeling show that cell directional behaviors drive zebrafish pectoral fin morphogenesis

Author(s): Joel Dokmegang, Hanh Nguyen, Elena Kardash, Thierry Savy, Matteo Cavaliere, Nadine Peyriéras, René Doursat
Published in: Bioinformatics, 2021, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btab201

Trophectoderm mechanics direct epiblast shape upon embryo implantation

Author(s): Antonia Weberling, Magdalena Zernicka-Goetz
Published in: Cell Reports, Issue 34/3, 2021, Page(s) 108655, ISSN 2211-1247
DOI: 10.1016/j.celrep.2020.108655

Integrin β1 coordinates survival and morphogenesis of the embryonic lineage upon implantation and pluripotency transition

Author(s): Matteo Amitaba Molè, Antonia Weberling, Reinhard Fässler, Alison Campbell, Simon Fishel, Magdalena Zernicka-Goetz
Published in: Cell Reports, Issue 34/10, 2021, Page(s) 108834, ISSN 2211-1247
DOI: 10.1016/j.celrep.2021.108834

Fiji plugins for qualitative image annotations: routine analysis and application to image classification

Author(s): Laurent S. V. Thomas, Franz Schaefer, Jochen Gehrig
Published in: F1000Research, Issue 9, 2020, Page(s) 1248, ISSN 2046-1402
DOI: 10.12688/f1000research.26872.2

Pseudomonas aeruginosa OprF plays a role in resistance to macrophage clearance during acute infection

Author(s): Malika Moussouni, Laurence Berry, Tamara Sipka, Mai Nguyen-Chi, Anne-Béatrice Blanc-Potard
Published in: Scientific Reports, Issue 11/1, 2021, ISSN 2045-2322
DOI: 10.1038/s41598-020-79678-0

Autophagy and Lc3-Associated Phagocytosis in Zebrafish Models of Bacterial Infections

Author(s): Salomé Muñoz-Sánchez, Michiel van der Vaart, Annemarie H. Meijer
Published in: Cells, Issue 9/11, 2020, Page(s) 2372, ISSN 2073-4409
DOI: 10.3390/cells9112372

3D Cell Image Segmentation by Modified Subjective Surface Method

Author(s): MarKjoe Olunna Uba, Karol Mikula, Zuzana Krivá, Hanh Nguyen, Thierry Savy, Eléna Kardash, Nadine Peyríeras
Published in: Tatra Mountains Mathematical Publications, Issue 75/1, 2020, Page(s) 147-162, ISSN 1338-9750
DOI: 10.2478/tmmp-2020-0010

Analysis of intracellular protein dynamics in living zebrafish embryos using light-sheet fluorescence single-molecule microscopy

Author(s): Matteo Bernardello, Radoslaw J. Gora, Patrick Van Hage, Gustavo Castro-Olvera, Emilio J. Gualda, Marcel J. M. Schaaf, Pablo Loza-Alvarez
Published in: Biomedical Optics Express, Issue 12/10, 2021, Page(s) 6205, ISSN 2156-7085
DOI: 10.1364/boe.435103

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

Macrophage Image Segmentation by Thresholding and Subjective Surface Method

Author(s): Seol Ah Park, Tamara Sipka, Zuzana Krivá, Martin Ambroz, Michal Kollár, Balázs Kósa, Mai Nguyen-Chi, Georges Lutfalla, Karol Mikula
Published in: Tatra Mountains Mathematical Publications, Issue 75/1, 2020, Page(s) 103-120, ISSN 1338-9750
DOI: 10.2478/tmmp-2020-0007

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

Light-sheet fluorescence microscopy for the in vivo study of microtubule dynamics in the zebrafish embryo

Author(s): Matteo Bernardello, Maria Marsal, Emilio J. Gualda, Pablo Loza-Alvarez
Published in: Biomedical Optics Express, Issue 12/10, 2021, Page(s) 6237, ISSN 2156-7085
DOI: 10.1364/boe.438402

Efficient 3D Shape Registration by Using Distance Maps and Stochastic Gradient Descent Method

Author(s): Polycarp Omondi Okock, Jozef Urbán, Karol Mikula
Published in: Tatra Mountains Mathematical Publications, Issue 75/1, 2020, Page(s) 81-102, ISSN 1338-9750
DOI: 10.2478/tmmp-2020-0006

In vivo High-Content Screening in Zebrafish for Developmental Nephrotoxicity of Approved Drugs

Author(s): Jens H. Westhoff, Petrus J. Steenbergen, Laurent S. V. Thomas, Jana Heigwer, Thomas Bruckner, Ledean Cooper, Burkhard Tönshoff, Georg F. Hoffmann, Jochen Gehrig
Published in: Frontiers in Cell and Developmental Biology, Issue 8, 2020, ISSN 2296-634X
DOI: 10.3389/fcell.2020.00583

Damage-Induced Calcium Signaling and Reactive Oxygen Species Mediate Macrophage Activation in Zebrafish

Author(s): Tamara Sipka, Romain Peroceschi, Rahma Hassan-Abdi, Martin Groß, Felix Ellett, Christina Begon-Pescia, Catherine Gonzalez, Georges Lutfalla, Mai Nguyen-Chi
Published in: Frontiers in Immunology, Issue 12, 2021, ISSN 1664-3224
DOI: 10.3389/fimmu.2021.636585

Characterization of a member of the CEACAM protein family as a novel marker of proton pump-rich ionocytes on the zebrafish epidermis

Author(s): Julien Kowalewski, Théo Paris, Catherine Gonzalez, Etienne Lelièvre, Lina Castaño Valencia, Morgan Boutrois, Camille Augier, Georges Lutfalla, Laure Yatime
Published in: PLOS ONE, Issue 16/7, 2021, Page(s) e0254533, ISSN 1932-6203
DOI: 10.1371/journal.pone.0254533

3D image segmentation supported by a point cloud

Author(s): Balázs Kósa, Karol Mikula, Markjoe Olunna Uba, Antonia Weberling, Neophytos Christodoulou, Magdalena Zernicka-Goetz
Published in: Discrete & Continuous Dynamical Systems - S, Issue 14/3, 2021, Page(s) 971-985, ISSN 1937-1179
DOI: 10.3934/dcdss.2020351

Application of Modified Subjective Surface Method to 3D Cell Membrane Image Segmentation

Author(s): M. O. Uba, K. Mikula, Z. Kriva, H. Nguyen, T. Savy, E. Kardash, N. Peyrieras
Published in: ALGORITMY 2020, 2020, Page(s) 51-60

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

3D + time imaging of normal and twin sea urchin embryos for the reconstruction of their cell lineage

Author(s): Antonio Ortiz, Elena Kardash, Nadine Peyriéras
Published in: Echinoderms, Part B, Issue 151, 2019, Page(s) 399-418
DOI: 10.1016/bs.mcb.2019.01.008