We are proud to share with you the publications of ImageInLife consortium:

Laurent Boucontet, Gabriella Passoni, Valéry Thiry, Ludovico Maggi, Philippe Herbomel, Jean-Pierre Levraud and Emma Colucci-Guyon: A Model of Superinfection of Virus-Infected Zebrafish Larvae: Increased Susceptibility to Bacteria Associated With Neutrophil Death. Front Immunol. 2018 May 24;9:1084.

Quang Tien Phan, Tamara Sipka, Catherine Gonzalez, Jean-Pierre Levraud, Georges Lutfalla, Mai Nguyen-Chi: « Neutrophils use superoxide to control bacterial infection at a distance ». PLoS Pathog. 2018 Jul 17;14(7):e1007157 Published: July 17, 2018,

Neophytos Christodoulou, Christos Kyprianou, Antonia Weberling, Ran Wang, Guizhong Cui, Guangdum Peng, Naihe Jing & Magdalena Zernicka-Goetz: “Sequential formation and resolution of multiple rosettes drive embryo remodelling after implantation”. Nature Cell Biology volume 20, pages 1278–1289 (2018).

3D + Time Imaging and Image Reconstruction of Pectoral Fin During Zebrafish Embryogenesis. Nguyen H, Boix-Fabrés J, Peyriéras N, Kardash E. Methods Mol Biol. 2019;2040:135-153. doi: 10.1007/978-1-4939-9686-5_8.

Sipka, T., Peroceschi, R., Hassan-Abdi, R., Groß, M., Ellett, F., Begon-Pescia, C., Gonzalez, C., Lutfalla, G., and Nguyen-Chi, M. (2021). « Damage-Induced Calcium Signaling and Reactive Oxygen Species Mediate Macrophage Activation in Zebrafish« . Front. Immunol. 12, 636585.

Moussouni, M., Berry, L., Sipka, T., Nguyen-Chi, M. & Blanc-Potard, A-B. (2021) « Pseudomonas aeruginosa OprF plays a role in resistance to macrophage clearance during acute infection. » Sci Rep 11, 359.

SA Park, T Sipka, Z Kriva, M Ambroz, M Kollar, B Kosa, M Nguyen-Chi, G Lutfalla, K Mikula. (2020) « Macrophage image segmentation by thresholding and subjective surface method », Tatra Mt. Math. Publ., 75(1), 103-120.

Nguyen‐Chi, M., Luz‐Crawford, P., Balas, L., Sipka, T., Contreras‐López, R., Barthelaix, A., Lutfalla, G., Durand, T., Jorgensen, C., and Djouad, F. (2020). « Pro‐resolving mediator protectin D1 promotes epimorphic regeneration by controlling immune cell function in vertebrates. » Br J Pharmacol 177, 4055–4073. DOI: 10.1111/bph.15156

Kardash E, Nguyen H, Behrndt M, Heisenberg CP, Peyriéras N, and Gonzalez-Gaitan M. « A contractile acto-myosin belt promotes growth anisotropy during the early stages of pectoral fin development in zebrafish. » BioRxiv, (2019)

Salomé Muñoz-Sánchez, Michiel van der Vaart, Annemarie H Meijer. « Autophagy and Lc3-Associated Phagocytosis in Zebrafish Models of Bacterial Infections. » Cells. 2020 Oct 29;9(11):2372. doi: 10.3390/cells9112372.

Christodoulou N*, Weberling A*, Strathdee D, Anderson KI, Timpson P & Zernicka-Goetz M:  « Morphogenesis of extra-embryonic tissues directs the remodelling of the mouse embryo at implantation. » Nature Communications. 2019 doi: 10.1038/s41467-019-11482-5. (* equal contribution)

Weberling A & Zernicka-Goetz M: « Trophectoderm mechanics direct epiblast shape upon embryo implantation. » Cell Reports. 2021 doi: 10.1016/j.celrep.2020.108655

Molè MA*, Weberling A*, Fässler R, Campbell A, Fishel S & Zernicka-Goetz M: « Integrin β1 coordinates embryo survival and morphogenesis upon implantation and pluripotency transition. » Cell Reports. 2021 doi: 10.1016/j.celrep.2021.108834 (*equal contribution)

Kósa B, Mikula K, Markjoe Uba M, Weberling A, Christodoulou N & Zernicka-Goetz M: « 3D Image Segmentation Supported By A Point Cloud. » Discrete and Continuous Dynamical Systems Series S. 2021 doi: 10.3934/dcdss.2020351

O. Uba, K. Mikula, Z. Kriva, H. Nguyen, T. Savy, E. Kardash and N. Peyrieras: « 3D Cell Image Segmentation by Modified Subjective Surface Method. » Tatra Mountains Mathematical Publications, (2020) 75, 147-162. doi: 10.2478/tmmp-2020-0010.

O. Uba, K. Mikula, Z. Kriva, H. Nguyen, T. Savy, E. Kardash, N. Peyrieras: « Application of Modified Subjective Surface Method to 3D Cell Membrane Image Segmentation », ALGORITMY 2020, Conference on Scientific Computing, Podbanske, Slovakia, 2020, Proceedings of contributed papers, 51 – 60.

Dokmegang J, Nguyen H, Kardash E, Savy T, Cavaliere M, Peyriéras N, Doursat R: « Quantification of cell behaviors and computational modelling show that cell directional behaviors drive zebrafish pectoral fin morphogenesis », Bioinformatics. 2021 Mar 24:btab201. doi: 10.1093/bioinformatics/btab201.

Levraud J.-P., Jouneau L., Briolat V., Laghi V. & P. Boudinot. « IFN-stimulated genes in zebrafish and humans define an ancient arsenal of antiviral immunity. » J. Immunol. 203:3361-3373 (2019)

Laghi V., Rezelj V., Boucontet L., Boudinot P., Salinas I., Lutfalla G., Vignuzzi M. & J.-P. Levraud. « Exploring zebrafish larvae as a COVID-19 model: probable SARS-COV-2 replication in the swim bladder. » Preprint.

J Dokmegang, MH Yap, L Han, M Cavaliere, R Doursat: « Computational modelling unveils how epiblast remodelling and positioning rely on trophectoderm morphogenesis during mouse implantation » PLOS One: (2021)

Laurent S.V. Thomas and Jochen Gehrig: « ImageJ/Fiji ROI 1-click tools for rapid manual image annotations and measurements », microPublication Biology, 28/01/2020, DOI: 10.17912/MICROPUB.BIOLOGY.000215

Laurent S.V. Thomas and Jochen Gehrig: « Multi-template matching: a versatile tool for object-localization in microscopy images », BMC Bioinformatics, 05/02/2020, DOI: 10.1186/s12859-020-3363-7

Jens H. Westhoff, Petrus J. Steenbergen, Laurent S. V. Thomas, Jana Heigwer, Thomas Bruckner, Ledean Cooper, Burkhard Tönshoff, Georg F. Hoffmann and Jochen Gehrig: « In vivo High-Content Screening in Zebrafish for Developmental Nephrotoxicity of Approved Drugs », Frontiers in cell and developmental biology – 10/07/2020, DOI: 10.3389/fcell.2020.00583

Laurent S.V. Thomas, Franz Schaefer, Jochen Gehrig: « Fiji plugins for qualitative image annotations: routine analysis and application to image classification », F1000 research – 12/02/2021, DOI: 10.12688/f1000research.26872.2

Polycarp Okock, Jozef Urbán and Karol Mikula, « Efficient 3D shape registration by using distance maps and stochastic gradient descent method », Tatra Mountains Mathematical Publications, vol.75, no.1, 2020, pp.81-102.

Antonio Ortiz, Elena Kardash, Nadine Peyriéras, 3D+time imaging of normal and twin sea urchin embryos for the reconstruction of their cell lineage, PMID: 30948021 DOI: 10.1016/bs.mcb.2019.01.008

Julien Kowalewski, Théo Paris, Catherine Gonzalez, Etienne Lelièvre, Lina Castaño Valencia, Morgan Boutrois, Camille Augier, Georges Lutfalla, Laure Yatime, Characterization of a member of the CEACAM protein family as a novel marker of proton pump-rich ionocytes on the zebrafish epidermis, Published: July 12, 2021, https://doi.org/10.1371/journal.pone.0254533

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 and Sébastien Nisole, TRIM8 is required for virus-induced IFN response in human plasmacytoid dendritic cells, Science Advances, 20 Nov 2019: Vol. 5, no. 11, eaax3511, DOI: 10.1126/sciadv.aax3511

Accepted publications:

Polycarp Okock, Jozef Urbán and Karol Mikula, « Improvement, and handling of segmentation model with an inflation term », Tatra Mountains Mathematical Publications, Accepted

Matteo Bernardello, Radoslaw J. Gora, Patrick Van Hage, Gustavo Castro-Olvera, Emilio J. Gualda, Marcel J. M. Schaaf, Pablo Loza-Alvarez « Analysis of Intracellular Protein Dynamics in Living Zebrafish Embryos Using Light-Sheet Fluorescence Single-Molecule Microscopy », Biomedical Optics Express, Accepted

Matteo Bernardello, Maria Marsal, Emilio J. Gualda, Pablo Loza-Alvarez: « Light-Sheet Fluorescence Microscopy for the in vivo study of microtubule dynamics in the zebrafish embryo », Biomedical Optics Express, Accepted