المؤلفون: Nora, Elphège P, Caccianini, Laura, Fudenberg, Geoffrey, So, Kevin, Kameswaran, Vasumathi, Nagle, Abigail, Uebersohn, Alec, Hajj, Bassam, Saux, Agnès Le, Coulon, Antoine, Mirny, Leonid A, Pollard, Katherine S, Dahan, Maxime, Bruneau, Benoit G

المصدر: Nature communications. 11(1)

مصطلحات موضوعية: Cell Line, Chromosomes, Mammalian, Chromatin, Animals, Mice, Drosophila, Cell Cycle Proteins, Chromosomal Proteins, Non-Histone, Binding Sites, Amino Acid Motifs, Protein Binding, Structure-Activity Relationship, Mutation, Cricetinae, Nucleotide Motifs, CCCTC-Binding Factor

الوصف: Current models propose that boundaries of mammalian topologically associating domains (TADs) arise from the ability of the CTCF protein to stop extrusion of chromatin loops by cohesin. While the orientation of CTCF motifs determines which pairs of CTCF sites preferentially stabilize loops, the molecular basis of this polarity remains unclear. By combining ChIP-seq and single molecule live imaging we report that CTCF positions cohesin, but does not control its overall binding dynamics on chromatin. Using an inducible complementation system, we find that CTCF mutants lacking the N-terminus cannot insulate TADs properly. Cohesin remains at CTCF sites in this mutant, albeit with reduced enrichment. Given the orientation of CTCF motifs presents the N-terminus towards cohesin as it translocates from the interior of TADs, these observations explain how the orientation of CTCF binding sites translates into genome folding patterns.

الوصول الحر: https://escholarship.org/uc/item/4sf4c6mkTest

المؤلفون: Prigent, Sylvain, Nguyen, Hoai-Nam, Leconte, Ludovic, Valades-Cruz, Cesar, Augusto, Hajj, Bassam, Salamero, Jean, Kervrann, Charles

المساهمون: Biologie Cellulaire et Cancer, Institut Curie Paris -Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Imagerie Spatio-Temporelle, Intelligence Artificielle et Calcul Numérique pour la Biologie Cellulaire et Chemobiologie (SAIRPICO), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Chimie biologique des membranes et ciblage thérapeutique (CBMCT - UMR 3666 / U1143), Institut Curie Paris -Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie - CNRS Chimie (INC-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Curie Paris -Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie - CNRS Chimie (INC-CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Physico-Chimie Curie Institut Curie (PCC), Institut Curie Paris -Institut de Chimie - CNRS Chimie (INC-CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), This work was jointly supported by the French National Research Agency (France-BioImaging ANR-10-INBS-04-07 and ANR-10-INBS-04-01, DALLISH-ANR-16-CE23-0005, LabEx Cell(n)Scale (ANR-11-LABX-0038) as part of the Idex PSL ANR-10-IDEX-0001-02) and Innopsys company. This work was also supported by ITMO Cancer (18CQ091)., L'institution (Inria) a financé les frais de publication pour que cet article soit en libre accès, ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011)

المصدر: ISSN: 2045-2322.

مصطلحات موضوعية: optimization, sparsity, regularization, fluorescence microscopy, denoising, deconvolution, [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], [SDV.IB]Life Sciences [q-bio]/Bioengineering, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing

الوصف: International audience ; Modern fluorescent microscopy imaging is still limited by the optical aberrations and the photon budget available in the specimen. A direct consequence is the necessity to develop flexible and "off-road" algorithms in order to recover structural details and improve spatial resolution, which is critical when restraining the illumination to low levels in order to limit photo-damages. Here, we report SPITFIR(e) a flexible method designed to accurately and quickly restore 2D-3D fluorescence microscopy images and videos (4D images). We designed a generic sparse-promoting regularizer to subtract undesirable out-of-focus background and we developed a primal-dual algorithm for fast optimization. SPITFIR(e) is a "swiss-knife" method for practitioners as it adapts to any microscopy techniques, to various sources of signal degradation (noise, blur), to variable image contents, aswell as to low signal-to-noise ratios. Our method outperforms existing state-of-the-art algorithms, and is more flexible than supervised deep-learning methods requiring ground truth datasets. The performance, the flexibility, and the ability to push the spatiotemporal resolution limit of sub-diffracted fluorescence microscopy techniques are demonstrated on experimental datasets acquired with various microscopy techniques from 3D spinning-disk confocal up to lattice light sheet microscopy.

العلاقة: hal-03518618; https://inria.hal.science/hal-03518618Test; https://inria.hal.science/hal-03518618v2/documentTest; https://inria.hal.science/hal-03518618v2/file/SPITFIRe-SciReports2023-HAL.pdfTest; BIORXIV: 2022.01.04.474883

الإتاحة: https://doi.org/10.1038/s41598-022-26178-yTest
https://inria.hal.science/hal-03518618Test
https://inria.hal.science/hal-03518618v2/documentTest
https://inria.hal.science/hal-03518618v2/file/SPITFIRe-SciReports2023-HAL.pdfTest

المؤلفون: Nakazawa, Koyomi, Kumar, Gaurav, Chauvin, Brieuc, Cicco, Aurélie Di, Pellegrino, Luca, Trichet, Michaël, Hajj, Bassam, Cabral, João, Sain, Anirban, Mangenot, Stéphanie, Bertin, Aurélie

المساهمون: Laboratoire Physico-Chimie Curie Institut Curie (PCC), Institut Curie Paris -Institut de Chimie - CNRS Chimie (INC-CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Indian Institute of Science Bangalore (IISc Bangalore), Department of Chemical Engineering London, Imperial College London, Microscopie Electronique IBPS (IBPS-ME), Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Indian Institute of Technology Bombay (IIT Bombay), Matière et Systèmes Complexes (MSC), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Fondation pour la Recherche MédicaleAAP Emergence (Sorbonne Université), ANR-13-JSV8-0002,SEPTIME,Assemblage et ultrastructure des septines, de la molécule à la cellule(2013), ANR-20-CE11-0014,SeptScort,Interaction spatiale et fonctionnelle entre septines et Escrt pendant la cytocinèse: une approche multi-échelle(2020)

المصدر: ISSN: 0021-9533.

مصطلحات موضوعية: [SDV]Life Sciences [q-bio]

الوصف: International audience ; Septins are cytoskeletal proteins interacting with the inner plasma membrane and other cytoskeletal partners. Being key in membrane remodeling processes, they often localize at specific micrometric curvatures. To analyze the behavior of human septins at the membrane and decouple their role from other partners, we used a combination of bottom-up in vitro methods. We assayed their ultrastructural organization, their curvature sensitivity, as well as their role in membrane reshaping. On membranes, human septins organize into a two-layered mesh of orthogonal filaments, instead of generating parallel sheets of filaments observed for budding yeast septins. This peculiar mesh organization is sensitive to micrometric curvature and drives membrane reshaping as well. The observed membrane deformations together with the filamentous organization are recapitulated in a coarse-grained computed simulation to understand their mechanisms. Our results highlight the specific organization and behavior of animal septins at the membrane as opposed to those of fungal proteins.

العلاقة: hal-04236725; https://cnrs.hal.science/hal-04236725Test; https://cnrs.hal.science/hal-04236725/documentTest; https://cnrs.hal.science/hal-04236725/file/Nakazawa_ms_jcs.pdfTest

الإتاحة: https://doi.org/10.1242/jcs.260813Test
https://cnrs.hal.science/hal-04236725Test
https://cnrs.hal.science/hal-04236725/documentTest
https://cnrs.hal.science/hal-04236725/file/Nakazawa_ms_jcs.pdfTest

المؤلفون: Laine, Romain, F, Heil, Hannah, S, Coelho, Simao, Nixon-Abell, Jonathon, Jimenez, Angélique, Wiesner, Theresa, Martínez, Damián, Galgani, Tommaso, Régnier, Louise, Stubb, Aki, Follain, Gautier, Webster, Samantha, Goyette, Jesse, Dauphin, Aurelien, Salles, Audrey, Culley, Siân, Jacquemet, Guillaume, Hajj, Bassam, Leterrier, Christophe, Henriques, Ricardo

المساهمون: Laboratory for Molecular Cell Biology, University College of London London (UCL), The Francis Crick Institute London, Instituto Gulbenkian de Ciência Oeiras (IGC), Fundação Calouste Gulbenkian, Janelia Research Campus Ashburn (HHMI Janelia), Howard Hughes Medical Institute (HHMI), Cambridge Institute for Medical Research (CIMR), University of Cambridge UK (CAM), Institut de neurophysiopathologie (INP), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Physico-Chimie Curie Institut Curie (PCC), Institut Curie Paris -Institut de Chimie - CNRS Chimie (INC-CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Turku Centre for Biotechnology, University of Turku-Åbo Academy University, School of Business and Economics Åbo Akademi University, Åbo Academy University-Åbo Academy University, Department of Physiology and EMBL Australia Node for Single Molecule Science, Génétique et Biologie du Développement, Institut Curie Paris -Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), BioImagerie Photonique – Photonic BioImaging (UTechS PBI), Institut Pasteur Paris (IP)-Université Paris Cité (UPCité), Turku PET Centre (Turku University Hospital), Åbo Akademi University Turku, Cell Imaging Core Turku, Finland (Turku Centre for Biotechnology), Åbo Akademi University Turku -University of Turku, A*MIDEX, a French ‘Investissements d’Avenir’ program AMX- 19-IET-002, ANR-20-CE13-0024,ASHA,L'échafaudage d'actine/spectrine façonne la physiologie de l'axone(2020), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), ANR-19-CE42-0003,VISION,Excitation et imagerie super-résolution volumétrique confinée à basse température : étude de l'architecture du chromosome durant l'expression des gènes(2019), ANR-11-LABX-0038,CelTisPhyBio,Des cellules aux tissus: au croisement de la Physique et de la Biologie(2011), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), European Project: 666003,H2020,H2020-MSCA-COFUND-2014,IC-3i-PhD(2016)

المصدر: ISSN: 1548-7091.

مصطلحات موضوعية: Image processing, Single-molecule biophysics, Super-resolution microscopy, [SDV]Life Sciences [q-bio]

الوصف: International audience ; Live-cell super-resolution microscopy enables the imaging of biological structure dynamics below the diffraction limit. Here we present enhanced super-resolution radial fluctuations (eSRRF), substantially improving image fidelity and resolution compared to the original SRRF method. eSRRF incorporates automated parameter optimization based on the data itself, giving insight into the trade-off between resolution and fidelity. We demonstrate eSRRF across a range of imaging modalities and biological systems. Notably, we extend eSRRF to three dimensions by combining it with multifocus microscopy. This realizes live-cell volumetric super-resolution imaging with an acquisition speed of ~1 volume per second. eSRRF provides an accessible super-resolution approach, maximizing information extraction across varied experimental conditions while minimizing artifacts. Its optimal parameter prediction strategy is generalizable, moving toward unbiased and optimized analyses in super-resolution microscopy.

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/37957430; info:eu-repo/grantAgreement//666003/EU/Institut Curie 3-i PhD Program/IC-3i-PhD; hal-04291504; https://amu.hal.science/hal-04291504Test; https://amu.hal.science/hal-04291504/documentTest; https://amu.hal.science/hal-04291504/file/s41592-023-02057-w.pdfTest; PUBMED: 37957430

الإتاحة: https://doi.org/10.1038/s41592-023-02057-wTest
https://amu.hal.science/hal-04291504Test
https://amu.hal.science/hal-04291504/documentTest
https://amu.hal.science/hal-04291504/file/s41592-023-02057-w.pdfTest

المؤلفون: Galgani, Tommaso, Fedala, Yasmina, Zapata, Romeo, Caccianini, Laura, Viasnoff, Virgile, Sibarita, Jean- Baptiste, Galland, Rémi, Dahan, Maxime, Hajj, Bassam

المساهمون: Laboratoire Physico-Chimie Curie Institut Curie (PCC), Institut Curie Paris -Institut de Chimie - CNRS Chimie (INC-CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Mechanobiology Institute Singapore (MBI), National University of Singapore (NUS), Interdisciplinary Institute for Neuroscience Bordeaux (IINS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)

المصدر: https://hal.science/hal-04048939Test ; 2023.

مصطلحات موضوعية: [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph]

الوصف: Light sheet fluorescence microscopy (LSFM) has become a leading standard in high-resolution imaging of living samples in 2-and 3-dimensions. Biological samples are however not restricted to a single observation plane and several molecular processes evolve rapidly in 3D. The conventional mechanical scanning required in LSFM limits the range of observable dynamics and are usually restricted in resolution. Here we introduce a new strategy for instantaneous volumetric excitation and volumetric imaging of singlemolecules in cell aggregates. The technique combines, for the first time, the use of light sheet microscopy and multifocus microscopy (MFM) and enables a volumetric 4D imaging of biological samples with singlemolecule resolution. We engineered the excitation beam to yield a modular and uniform excitation matching the observable detection range of MFM. The strength of the method is highlighted with examples of singlemolecule 3D tracking and 3D super-resolution imaging in multicellular samples.

العلاقة: hal-04048939; https://hal.science/hal-04048939Test; https://hal.science/hal-04048939/documentTest; https://hal.science/hal-04048939/file/V-LSFM_main%20text.pdfTest; BIORXIV: 2022.12.02.518828

الإتاحة: https://doi.org/10.1101/2022.12.02.518828Test
https://hal.science/hal-04048939Test
https://hal.science/hal-04048939/documentTest
https://hal.science/hal-04048939/file/V-LSFM_main%20text.pdfTest

المؤلفون: Hajj, Bassam

مرشدي الرسالة: Cachan, Ecole normale supérieure, Chauvat, Dominique, Zyss, Joseph

مصطلحات موضوعية: Effet Pockels, Microscopie, Interférométrie, Cartographie de champs électriques, Films minces organiques, Nano-cristaux, Bicouche artificielle, Cellule type PC12, Patch-clamp, Refraction, Double, Microscopy, Interferometry, ANanophotonics

الوصف: Le but de ce mémoire est de valider la microscopie électro-optique Pockels comme méthode de mesure et de cartographie de champ électrique aux échelles micro et nanométriques. Une première partie est dédiée à la description de l’instrumentation d’imagerie mise en jeu. Nous développons ensuite son application en physique et biophysique. Une étude de couches minces monocristallines de 2-methyl-4-nitroaniline (MNA) a permis de sonder localement la variation de champ électrique appliqué, mais aussi d’étudier l’orientation des axes optiques de ce cristal dans l’espace. A l’échelle sub-longueur d’onde nous avons pu isoler la modulation électro-optique de la diffusion de lumière associée à une nanoparticule isolée de KTiOPO4 (KTP) d’une taille de 150nm. La dépendance polaire du signal Pockels sur la polarisation lumineuse incidente a permis de prédire l’orientation de la maille cristalline du KTP dans l’espace. De telles sondes de champs électriques nanométriques peuvent avoir de nombreuses applications en nano-photonique. Dans le cas d’entité biologiques comme des neurones, la propagation de l’information est assurée par celle d’un champ électrique dans les membranes plasmiques. Dans une première étape, nous nous sommes intéressés à l’étude de bicouches artificielles dopées par un colorant non-linéaire, le DI-8-ANEPPS. Un signal électro-optique Pockels y a été mesuré pour la première fois. La caractérisation de l’insertion du colorant dans la membrane a été aussi discutée. La grande sensibilité à la mesure d’un champ électrique assurée par l’interféromètre permet d’envisager des possibilités d’applications dans des cellules vivantes. Des expériences menées sur des cellules de type PC12 ont montré l’existence d’un signal optique qui est associé à la distribution spatiale du champ électrique. L’ensemble de ces travaux montrent que la microscopie électro-optique s’avère constituer un outil important pour la physique et biophysique.
The aim of this thesis is to validate the electro-optical Pockels microscopy as a powerful technique for electric field imaging at nano and micrometer scales. A first part of this manuscript is dedicated to the instrumental aspects of this new microscope modality. Then we discuss its application in physical and biophysical domains. We have investiguqted 2-methyl-4-nitroaniline(MNA) monocrystalline molecular thin films where the electric field distribution could be imaged, and crystal orientation retrieved. At sub-wavelength scale, we were able to isolate the electro-optical modulation of light scattered by isolated 150nm size KTiOP04 (KTP) nanoparticles. Using the angular dependency of the Pockels response to the polarization of light we could determine the a priori random, spatial orientation of the nanocrystal. Such electric-field nano-probe configuration could find its way in various applications. In the case of biological entities such as neurons, information is transmitted via an electric field signal, propagating through the plasmid membrane. We concentrated first on a model artificial membrane doped with the DI-8-ANEPPS nonlinear dye, evidencing for the first time a Pockels electro-optical response. A relatively high sensitivity to the electric field allows to envision interesting applications in living cells. Experiences performed with PC 12 cells have shown an optical response that reflects the electric field spatial distribution. This work demonstrates that the electro-optical microscopy is emerging as a new powerful tool for sub-wavelength investigation of electro-optical properties in physics and biology.

الإتاحة: http://www.theses.fr/2010DENS0036/documentTest

المؤلفون: Valades-Cruz, Cesar Augusto, Leconte, Ludovic, Fouché, Gwendal, Blanc, Thomas, van Hille, Nathan, Fournier, Kevin, Laurent, Tao, Gallean, Benjamin, Deslandes, François, Hajj, Bassam, Faure, Emmanuel, Argelaguet, Ferran, Trubuil, Alain, Isenberg, Tobias, Masson, Jean-Baptiste, Salamero, Jean, Kervrann, Charles

المساهمون: Space-timE RePresentation, Imaging and cellular dynamics of molecular COmplexes (SERPICO), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Biologie Cellulaire et Cancer, Institut Curie Paris -Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), 3D interaction with virtual environments using body and mind (Hybrid), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-RÉALITÉ VIRTUELLE, HUMAINS VIRTUELS, INTERACTIONS ET ROBOTIQUE (IRISA-D5), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT), Laboratoire Physico-Chimie Curie Institut Curie (PCC), Institut Curie Paris -Institut de Chimie - CNRS Chimie (INC-CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Image & Interaction (LIRMM, Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Mathématiques et Informatique Appliquées du Génome à l'Environnement Jouy-En-Josas (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Analysis and Visualization (AVIZ), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Interaction avec l'Humain (IaH), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Décision et processus Bayesiens - Decision and Bayesian Computation, Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), ANR-11-LABX-0038,CelTisPhyBio,Des cellules aux tissus: au croisement de la Physique et de la Biologie(2011), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-10-LABX-0073,REVIVE,Stem Cells in Regenerative Biology and Medicine(2010), ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019)

المصدر: EISSN: 2673-7647 ; Frontiers in Bioinformatics ; https://inria.hal.science/hal-03790274Test ; Frontiers in Bioinformatics, 2022, 2, pp.997082:1-997082:9. ⟨10.3389/fbinf.2022.997082⟩

مصطلحات موضوعية: multi-dimensional biological data, virtual reality, augmented reality, intracellular imaging, bioimaging, [INFO.INFO-GR]Computer Science [cs]/Graphics [cs.GR], [SDV]Life Sciences [q-bio], [SDV.BC]Life Sciences [q-bio]/Cellular Biology

الوصف: International audience ; Microscopy image observation is commonly performed on 2D screens, which limits human capacities to grasp volumetric, complex, and discrete biological dynamics. With the massive production of multidimensional images (3D + time, multi-channels) and derived images (e.g., restored images, segmentation maps, and object tracks), scientists need appropriate visualization and navigation methods to better apprehend the amount of information in their content. New modes of visualization have emerged, including virtual reality (VR)/ augmented reality (AR) approaches which should allow more accurate analysis and exploration of large time series of volumetric images, such as those produced by the latest 3D + time fluorescence microscopy. They include integrated algorithms that allow researchers to interactively explore complex spatiotemporal objects at the scale of single cells or multicellular systems, almost in a real time manner. In practice, however, immersion of the user within 3D + time microscopy data represents both a paradigm shift in human-image interaction and an acculturation challenge, for the concerned community. To promote a broader adoption of these approaches by biologists, further dialogue is needed between the bioimaging community and the VR&AR developers.

العلاقة: hal-03790274; https://inria.hal.science/hal-03790274Test; https://inria.hal.science/hal-03790274/documentTest; https://inria.hal.science/hal-03790274/file/fbinf-02-997082.pdfTest

الإتاحة: https://doi.org/10.3389/fbinf.2022.997082Test
https://inria.hal.science/hal-03790274Test
https://inria.hal.science/hal-03790274/documentTest
https://inria.hal.science/hal-03790274/file/fbinf-02-997082.pdfTest

المؤلفون: Guérinot, Corentin, Marcon, Valentin, Godard, Charlotte, Blanc, Thomas, Verdier, Hippolyte, Planchon, Guillaume, Raimondi, Francesca, Boddaert, Nathalie, Alonso, Mariana, Sailor, Kurt, Lledo, Pierre-Marie, Hajj, Bassam, El Beheiry, Mohamed, Masson, Jean-Baptiste

المساهمون: Décision et processus Bayesiens - Decision and Bayesian Computation, Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Perception et Mémoire / Perception and Memory, Collège Doctoral, Sorbonne Université (SU), Université Paris Sciences et Lettres (PSL), Laboratoire Physico-Chimie Curie Institut Curie (PCC), Institut Curie Paris -Institut de Chimie - CNRS Chimie (INC-CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Hôpital Necker - Enfants Malades AP-HP, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), We acknowledge funding from the Institut Pasteur, the Institut Curie, the Paris Science lettre (PSL) University, the sponsorships of CRPCEN, Gilead Science and foundation EDF, the INCEPTION project (PIA/ANR-16-CONV-0005, OG), the LabEx “Revive” (ANR-10-LABX-73), the programme d’investissement d’avenir supported by L’Agence Nationale de la Recherche ANR-19-P3IA-0001 Institut 3IA Prairie and the support of the AVIRON grant from the Région Ile-de-France (DIM-ELICIT). We acknowledge funding from the Fondation pour la recherche médicale (FRM, DEI20151234398), the Agence National de la recherche (ANR-19-CE42-0003-01), the LabEx CelTisPhyBio (ANR-10-LBX-0038, ANR-10-IDEX-0001-02) and the Institut Curie. We recognize the support of France-BioImaging infrastructure grant ANR-10-INBS-04 (Investments for the future). We acknowledge the financial support of the Agence pour la Recherche sur le Cancer (ARC Foundation), DIM ELICIT and from ITMO Cancer of Aviesan on funds administered by Inserm (grant No. 20CP092-00)., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-10-LABX-0073,REVIVE,Stem Cells in Regenerative Biology and Medicine(2010), ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019), ANR-11-LABX-0038,CelTisPhyBio,Des cellules aux tissus: au croisement de la Physique et de la Biologie(2011), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010)

المصدر: EISSN: 2673-7647 ; Frontiers in Bioinformatics ; https://hal.science/hal-03795778Test ; Frontiers in Bioinformatics, 2022, 1, pp.777101. ⟨10.3389/fbinf.2021.777101⟩

مصطلحات موضوعية: virtual reality, cloud computation, one-shot learning, inference, human-in-the-loop, MRI, CT-scan, [INFO]Computer Science [cs]

الوصف: International audience ; Three-dimensional imaging is at the core of medical imaging and is becoming a standard in biological research. As a result, there is an increasing need to visualize, analyze and interact with data in a natural three-dimensional context. By combining stereoscopy and motion tracking, commercial virtual reality (VR) headsets provide a solution to this critical visualization challenge by allowing users to view volumetric image stacks in a highly intuitive fashion. While optimizing the visualization and interaction process in VR remains an active topic, one of the most pressing issue is how to utilize VR for annotation and analysis of data. Annotating data is often a required step for training machine learning algorithms. For example, enhancing the ability to annotate complex three-dimensional data in biological research as newly acquired data may come in limited quantities. Similarly, medical data annotation is often time-consuming and requires expert knowledge to identify structures of interest correctly. Moreover, simultaneous data analysis and visualization in VR is computationally demanding. Here, we introduce a new procedure to visualize, interact, annotate and analyze data by combining VR with cloud computing. VR is leveraged to provide natural interactions with volumetric representations of experimental imaging data. In parallel, cloud computing performs costly computations to accelerate the data annotation with minimal input required from the user. We demonstrate multiple proof-of-concept applications of our approach on volumetric fluorescent microscopy images of mouse neurons and tumor or organ annotations in medical images.

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/36303792; hal-03795778; https://hal.science/hal-03795778Test; https://hal.science/hal-03795778/documentTest; https://hal.science/hal-03795778/file/2022_B_FrontiersInBioinformatics_annotations.pdfTest; PUBMED: 36303792; PUBMEDCENTRAL: PMC9580868

الإتاحة: https://doi.org/10.3389/fbinf.2021.777101Test
https://hal.science/hal-03795778Test
https://hal.science/hal-03795778/documentTest
https://hal.science/hal-03795778/file/2022_B_FrontiersInBioinformatics_annotations.pdfTest

المؤلفون: Blanc, Thomas, Verdier, Hippolyte, Regnier, Louise, Planchon, Guillaume, Guérinot, Corentin, El Beheiry, Mohamed, Masson, Jean-Baptiste, Hajj, Bassam

المساهمون: Laboratoire Physico-Chimie Curie Institut Curie (PCC), Institut Curie Paris -Institut de Chimie - CNRS Chimie (INC-CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Décision et processus Bayesiens - Decision and Bayesian Computation, Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Collège Doctoral, We acknowledge funding from the Fondation pour la recherche médicale (FRM, DEI20151234398), the Agence National de la recherche (ANR-19-CE42-0003-01), the LabEx CelTisPhyBio (ANR-11-LABX-0038, ANR-10-IDEX-0001-02), and the Institut Curie. We recognize the support of France-BioImaging infrastructure grant ANR-10-INBS-04 (Investments for the future). We acknowledge the financial support of the Agence pour la Recherche sur le Cancer (ARC Foundation), DIM ELICIT and from ITMO Cancer of Aviesan on funds administered by Inserm (grant N° 20CP092-00). We acknowledge funding from the Institut Pasteur, the Institut Curie, the Paris Science lettre (PSL) University, the sponsorships of CRPCEN, Gilead Science and foundation EDF, the INCEPTION project (PIA/ANR-16-CONV-0005, OG), the programme d’investissement d’avenir supported by L’Agence Nationale de la Recherche ANR-19-P3IA-0001 Institut 3IA Prairie and the support of the AVIRON grant from the Région Ile-de-France (DIM-ELICIT)., ANR-19-CE42-0003,VISION,Excitation et imagerie super-résolution volumétrique confinée à basse température : étude de l'architecture du chromosome durant l'expression des gènes(2019), ANR-11-LABX-0038,CelTisPhyBio,Des cellules aux tissus: au croisement de la Physique et de la Biologie(2011), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019)

المصدر: EISSN: 2673-7647 ; Frontiers in Bioinformatics ; https://hal.science/hal-03795768Test ; Frontiers in Bioinformatics, 2022, 1, ⟨10.3389/fbinf.2021.775379⟩

مصطلحات موضوعية: virtual reality, point clouds, inference, microscopy, human in the loop, 3D maps, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], [SDV]Life Sciences [q-bio]

الوصف: International audience ; Multiple fields in biological and medical research produce large amounts of point cloud data with high dimensionality and complexity. In addition, a large set of experiments generate point clouds, including segmented medical data or single-molecule localization microscopy. In the latter, individual molecules are observed within their natural cellular environment. Analyzing this type of experimental data is a complex task and presents unique challenges, where providing extra physical dimensions for visualization and analysis could be beneficial. Furthermore, whether highly noisy data comes from single-molecule recordings or segmented medical data, the necessity to guide analysis with user intervention creates both an ergonomic challenge to facilitate this interaction and a computational challenge to provide fluid interactions as information is being processed. Several applications, including our software DIVA for image stack and our platform Genuage for point clouds, have leveraged Virtual Reality (VR) to visualize and interact with data in 3D. While the visualization aspects can be made compatible with different types of data, quantifications, on the other hand, are far from being standard. In addition, complex analysis can require significant computational resources, making the real-time VR experience uncomfortable. Moreover, visualization software is mainly designed to represent a set of data points but lacks flexibility in manipulating and analyzing the data. This paper introduces new libraries to enhance the interaction and human-in-theloop analysis of point cloud data in virtual reality and integrate them into the open-source platform Genuage. We first detail a new toolbox of communication tools that enhance user experience and improve flexibility. Then, we introduce a mapping toolbox allowing the representation of physical properties in space overlaid on a 3D mesh while maintaining a point cloud dedicated shader. We introduce later a new and programmable video capture tool in VR ...

العلاقة: hal-03795768; https://hal.science/hal-03795768Test; https://hal.science/hal-03795768/documentTest; https://hal.science/hal-03795768/file/2022_A_FrontiersInBioinformatics_Genuage.pdfTest

الإتاحة: https://doi.org/10.3389/fbinf.2021.775379Test
https://hal.science/hal-03795768Test
https://hal.science/hal-03795768/documentTest
https://hal.science/hal-03795768/file/2022_A_FrontiersInBioinformatics_Genuage.pdfTest

المؤلفون: Chauvin, Brieuc, Nakazawa, Koyomi, Beber, Alexandre, Di Cicco, Aurélie, Hajj, Bassam, Iv, François, Mavrakis, Manos, Koenderink, Gijsje, Cabral, João, Trichet, Michaël, Mangenot, Stéphanie, Bertin, Aurélie

المساهمون: Laboratoire Physico-Chimie Curie Institut Curie (PCC), Institut Curie Paris -Institut de Chimie - CNRS Chimie (INC-CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institute of Biotechnology of the Czech Academy of Sciences (IBT / CAS), Czech Academy of Sciences Prague (CAS), Institut FRESNEL (FRESNEL), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Kavli Institute of Nanosciences Delft (KI-NANO), Delft University of Technology (TU Delft), Department of Chemical Engineering London, Imperial College London, Microscopie Electronique IBPS (IBPS-ME), Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Matière et Systèmes Complexes (MSC), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), B. Chauvin is funded by the Ecole Doctorale "ED564: Physique en Ile de France" and Fondation pour lea Recherche Médicale. K. Nakazawa was supported by Sorbonne Université (AAP Emergence). G.H. Koenderink was supported by the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO/OCW) through the ‘BaSyC-Building a Synthetic Cell'. Gravitation grant (024.003.019)., ANR-13-JSV8-0002,SEPTIME,Assemblage et ultrastructure des septines, de la molécule à la cellule(2013), ANR-17-CE13-0014,SEPTIMORF,Rôle des septines dans la morphogenèse des cellules animales(2017), ANR-20-CE11-0014,SeptScort,Interaction spatiale et fonctionnelle entre septines et Escrt pendant la cytocinèse: une approche multi-échelle(2020), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), ANR-11-LABX-0038,CelTisPhyBio,Des cellules aux tissus: au croisement de la Physique et de la Biologie(2011)

المصدر: ISSN: 1940-087X.

مصطلحات موضوعية: [SDV]Life Sciences [q-bio]

الوصف: International audience ; Membrane remodeling occurs constantly at the plasma membrane and within cellular organelles. To fully dissect the role of the environment (ionic conditions, protein and lipid compositions, membrane curvature) and the different partners associated with specific membrane reshaping processes, we undertake in vitro bottom-up approaches. In recent years, there has been keen interest in revealing the role of septin proteins associated with major diseases. Septins are essential and ubiquitous cytoskeletal proteins that interact with the plasma membrane. They are implicated in cell division, cell motility, neuro-morphogenesis, and spermiogenesis, among other functions. It is, therefore, important to understand how septins interact and organize at membranes to subsequently induce membrane deformations and how they can be sensitive to specific membrane curvatures. This article aims to decipher the interplay between the ultra-structure of septins at a molecular level and the membrane remodeling occurring at a micron scale. To this end, budding yeast, and mammalian septin complexes were recombinantly expressed and purified. A combination of in vitro assays was then used to analyze the self-assembly of septins at the membrane. Supported lipid bilayers (SLBs), giant unilamellar vesicles (GUVs), large unilamellar vesicles (LUVs), and wavy substrates were used to study the interplay between septin self-assembly, membrane reshaping, and membrane curvature.

العلاقة: hal-04237668; https://hal.science/hal-04237668Test; https://hal.science/hal-04237668/documentTest; https://hal.science/hal-04237668/file/jove.pdfTest

الإتاحة: https://doi.org/10.3791/63889Test
https://hal.science/hal-04237668Test
https://hal.science/hal-04237668/documentTest
https://hal.science/hal-04237668/file/jove.pdfTest