Deliverables
Report on Congress presentations and Scientific Publications
PhDsReport on already awarded PhDs
Application of image processing and analysis methods to ImageInLife dataNew 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 & physicsTissue geometry & physics : cell-cell interactions, subcellular elements, extracellular matrix Generic models with simulation/visualisation software, customised to zebrafish or mammalian datasets
Dissemination of knowledgeDraft (midterm) and final version (final report) of the plan for the use and dissemination of knowledge
Search & optimisationParameter search & optimisation: comparison between simulations & data
Design of image processing and analysis methodsFinal report
Final report to the commission
Virus propagationVirus propagation model: immune status, cell response, pathways of virus dissemination
Report on Congress Presentations and Scientific Publications IReport on Congress Presentations and Scientific Publications
in vivo tracers, reporters & actuatorsin vivo tracers, reporters & actuators: validation of staining strategies for signalling pathways and gene expression patterns
Consortium agreementOutreach activities
Record of all participants’ contributions to outreach activities targeted at schools and at the general public
Midterm reportMidterm report to the commission. The due date is indicative. This deliverable must be submitted at least one month before the Midterm review meeting.
Cell biomechanicsModels of Cell biomechanics : cell types, shapes & behaviours,
Computer implementation of image processing and analysis methodsInfection protocols
Infection protocols for high throughput imaging of infected zebrafish embryo
Genetic/molecular controlModels of Genetic/molecular control : gene regulation network, chemical signalling, interface with BioTapestry, reverse engineering of circuits from atlases
Frist version of the Data Management Plan
Final version of the Data Management PlanImageInLife Brochure, website & vacancies advertising
MOOCsOnline dissemination using MOOCs
Wikipedia articleVideo series
Video series for outreaches activities
Multimodal and multiscale LSFM workstation, software and image analysis
Incubation chambersIncubation chambers for multilevel imaging of embryos, mammals and zebrafish, normal and infected, at different imaging resolutions
Image acquisition systems for infected embryosImage acquisition systems for infected embryos using the VAST-BioImager
Super-resolution-LSFM for imaging of cellular processes within the embryoImplementation of strategies for Super-resolution-LSFM for imaging of cellular processes within the embryo
Publications
Author(s):
Valerio Laghi, Veronica Rezelj, Laurent Boucontet, Pierre Boudinot, Irene Salinas, Georges Lutfalla, Marco Vignuzzi, Jean-Pierre Levraud
Published in:
BioRxiv, 2021
Publisher:
bioRxiv
DOI:
10.1101/2021.04.08.439059
Author(s):
Elena Kardash, Hanh Nguyen, Martin Behrndt, Carl-Philipp Heisenberg, Nadine Peyrieras, Marcos Gonzalez-Gaitan
Published in:
Biorxiv, 2019
Publisher:
Cold Spring Harbor Laboratory
DOI:
10.1101/512038
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
Publisher:
Public Library of Science
DOI:
10.1371/journal.pone.0254763
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
Publisher:
Wiley-Blackwell
DOI:
10.1111/bph.15156
Author(s):
Joel Dokmegang, Hanh Nguyen, Elena Kardash, Thierry Savy, Matteo Cavaliere, Nadine Peyriéras, René Doursat
Published in:
Bioinformatics, 2021, ISSN 1367-4803
Publisher:
Oxford University Press
DOI:
10.1093/bioinformatics/btab201
Author(s):
Antonia Weberling, Magdalena Zernicka-Goetz
Published in:
Cell Reports, Issue 34/3, 2021, Page(s) 108655, ISSN 2211-1247
Publisher:
Cell Press
DOI:
10.1016/j.celrep.2020.108655
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
Publisher:
Cell Press
DOI:
10.1016/j.celrep.2021.108834
Author(s):
Laurent S. V. Thomas, Franz Schaefer, Jochen Gehrig
Published in:
F1000Research, Issue 9, 2020, Page(s) 1248, ISSN 2046-1402
Publisher:
F1000 Research Ltd.
DOI:
10.12688/f1000research.26872.2
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
Publisher:
Nature Publishing Group
DOI:
10.1038/s41598-020-79678-0
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
Publisher:
Cells
DOI:
10.3390/cells9112372
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
Publisher:
Tatra Mountains Mathematical Publications
DOI:
10.2478/tmmp-2020-0010
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
Publisher:
The Optical Society
DOI:
10.1364/boe.435103
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
Publisher:
Frontiers Media SA
DOI:
10.3389/fimmu.2018.01084
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
Publisher:
PLOS Pathogens
DOI:
10.1371/journal.ppat.1007157
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
Publisher:
Nature Publishing Group
DOI:
10.1038/s41556-018-0211-3
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
Publisher:
Nature Publishing Group
DOI:
10.1038/s41467-019-11482-5
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
Publisher:
Tatra Mountains Mathematical Publications
DOI:
10.2478/tmmp-2020-0007
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
Publisher:
American Association for the Advancement of Science
DOI:
10.1126/sciadv.aax3511
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
Publisher:
American Association of Immunologists
DOI:
10.4049/jimmunol.1900804
Author(s):
Laurent S. V. Thomas, Jochen Gehrig
Published in:
BMC Bioinformatics, Issue 21/1, 2020, ISSN 1471-2105
Publisher:
BioMed Central
DOI:
10.1186/s12859-020-3363-7
Author(s):
Laurent SV Thomas and Jochen Gehrig
Published in:
microPublication Biology, 2020, ISSN 2578-9430
Publisher:
microPublication
DOI:
10.17912/micropub.biology.000215
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
Publisher:
The Optical Society
DOI:
10.1364/boe.438402
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
Publisher:
Tatra Mountains Mathematical Publications
DOI:
10.2478/tmmp-2020-0006
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
Publisher:
Frontiers in Cell and Developmental Biology
DOI:
10.3389/fcell.2020.00583
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
Publisher:
Frontiers in Immunology
DOI:
10.3389/fimmu.2021.636585
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
Publisher:
Public Library of Science
DOI:
10.1371/journal.pone.0254533
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
Publisher:
AIMS
DOI:
10.3934/dcdss.2020351
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
Publisher:
Proceedings of the Conference Algoritmy 2020
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, ISBN 978-1-4939-9685-8
Publisher:
Springer New York
DOI:
10.1007/978-1-4939-9686-5_8
Author(s):
Antonio Ortiz, Elena Kardash, Nadine Peyriéras
Published in:
Echinoderms, Part B, Issue 151, 2019, Page(s) 399-418, ISBN 9780128170724
Publisher:
Elsevier
DOI:
10.1016/bs.mcb.2019.01.008
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