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Perrine Paul-Gilloteaux

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I'm a CNRS Research Engineer, specialized in computer vision and bio image analysis. After my electrical engineering studies, with a computer vision option, I did my PhD with a company (Medtronic Surgical Navigation, Boulder USA) and the ViSages team (INRIA, INSERM, CNRS) under the supervision of Dr. Pierre Jannin. I was working on the tracking of deformations of the brain during craniotomy in brain surgery, in order to relocate information from different exams of the patient , in particular indicated functional areas, such as language or motor area of the brain and to display them in the surgical microscope. For this, I was creating stereoscopic reconstruction from the surgical microscope binocular, and I developed a new method for the tracking of surface deformation, based on an hybrid approach of point cloud registration and of video tracking. I did a first postdoc as experienced Researcher in a Marie-Curie network, ARIS\*ER to work on augmented reality in surgery, and in particular the segmentation of tumors in ultrasound based on wavelet analysis of the ultrasound raw signal. I then got a post-doc position in Maynooth, Ireland (close to Dublin), in the Hamilton Institute which is an applied mathematics institute. I was in the Systems Biology group, where I've developed with my colleagues an intelligent fluorescent microscope, taking the decision of the area to image and of the frequency of acquisition, based on real time analysis of the image content (cell segmentation and cell tracking). In 2010, I joined the CNRS as research Engineer in the PICT IBISA cell and tissue microscopy facility in Institut Curie, Paris, France. My job was to support the biologists in image analysis, by adapting existing sofwtare or developping new methods. In June 2015, I've joined the [Structure Federative de Recherche in Health](https://sfrsante.univ-nantes.fr/) of Nantes (France), where I work for the facility, and on my own research activities I am now leading R&D activities in multimodal image analysis, through the [ANR CROCOVAL](https://anrcrocoval.github.io/) , and heading [MicroPICell](https://micropicell.univ-nantes.fr/), a microscopy facility performing services and R& D in histology, photonic microscopy and image analysis and management. I am one of the co-funder of COST action [NEUBIAS](http://www.neubias.org), for which I lead the group creating [biii.eu](http://www.biii.eu) and [edam bio imaging](https://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING?p=classes) and is part of the core group managing the full network, and vice chair and the [COMULIS](https://www.comulis.eu/) COST action.

Research domains


Publications

Image document

Bioimage informatics: Investing in software usability is essential

Perrine Paul-Gilloteaux
PLoS Biology, 2023, 21 (7), pp.e3002213. ⟨10.1371/journal.pbio.3002213⟩
Journal articles hal-04175990v1
Image document

Visualizing enteric nervous system activity through dye-free dynamic full-field optical coherence tomography

Tony Durand , Perrine Paul-Gilloteaux , Michalina Gora , Lara Laboudie , Emmanuel Coron
Communications Biology, 2023, 6 (1), pp.236. ⟨10.1038/s42003-023-04593-9⟩
Journal articles hal-04013867v1
Image document

Multimodality imaging and transcriptomics to phenotype mitral valve dystrophy in a unique knock-in Filamin-A rat model

Constance Delwarde , Claire Toquet , Pascal Aumond , Amir Hossein Kayvanjoo , Adrien Foucal
Cardiovascular Research, 2022, 119 (3), pp.759-771. ⟨10.1093/cvr/cvac136⟩
Journal articles hal-03765601v1

A time-lapse embryo dataset for morphokinetic parameter prediction

Tristan Gomez , Magalie Feyeux , Justine Boulant , Nicolas Normand , Laurent David
Data in Brief, 2022, pp.108258. ⟨10.1016/j.dib.2022.108258⟩
Journal articles hal-03667158v1

Sample preparation and image registration for correlative cryo-FM and cryo-FIB-SEM of plunge-frozen mammalian cells

Nadav Scher , Katya Rechav , Perrine Paul-Gilloteaux , Ori Avinoam
STAR Protocols, 2022, 3 (1), pp.101142. ⟨10.1016/j.xpro.2022.101142⟩
Journal articles hal-03745072v1
Image document

A flexible open-source processing workflow for multiplexed fluorescence imaging based on cycles

Guillaume Potier , Aurélie Doméné , Perrine Paul-Gilloteaux
F1000Research, 2022, 11, pp.1121. ⟨10.12688/f1000research.124990.1⟩
Journal articles hal-03791824v1
Image document

Bioimage analysis workflows: community resources to navigate through a complex ecosystem

Perrine Paul-Gilloteaux , Sébastien Tosi , Jean-Karim Hériché , Alban Gaignard , Hervé Ménager
F1000Research, 2021, 10, pp.320. ⟨10.12688/f1000research.52569.1⟩
Journal articles hal-03208600v1

Protocol for image registration of correlative soft X-ray tomography and super-resolution structured illumination microscopy images

Nina Vyas , Stephan Kunne , Thomas Fish , Ian Dobbie , Maria Harkiolaki
STAR Protocols, 2021, 2 (2), pp.100529. ⟨10.1016/j.xpro.2021.100529⟩
Journal articles hal-03223460v1
Image document

An LDV based method to quantify the error of PC-MRI derived Wall Shear Stress measurement

Marco Castagna , Sébastien Levilly , Perrine Paul-Gilloteaux , Saïd Moussaoui , Jean-Marc Rousset
Scientific Reports, 2021, 11 (1), pp.4112. ⟨10.1038/s41598-021-83633-y⟩
Journal articles hal-03149044v1
Image document

REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology

Ugis Sarkans , Wah Chiu , Lucy Collinson , Michele Darrow , Jan Ellenberg
Nature Methods, 2021, ⟨10.1038/s41592-021-01166-8⟩
Journal articles hal-03232628v1

In situ fiducial markers for 3D correlative cryo-fluorescence and FIB-SEM imaging

Nadav Scher , Katya Rechav , Perrine Paul-Gilloteaux , Ori Avinoam
iScience, 2021, 24 (7), pp.102714. ⟨10.1016/j.isci.2021.102714⟩
Journal articles hal-03278159v1

QUAREP‐LiMi: A community‐driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

Glyn Nelson , Ulrike Boehm , Steve Bagley , Peter Bajcsy , Johanna Bischof
Journal of Microscopy, 2021, 284 (1), pp.56-73. ⟨10.1111/jmi.13041⟩
Journal articles hal-03745112v1
Image document

Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists

Gabriel Martins , Fabrice Cordelières , Julien Colombelli , Rocco D’antuono , Ofra Golani
F1000Research, 2021, 10, pp.334. ⟨10.12688/f1000research.25485.1⟩
Journal articles hal-03214896v1
Image document

Towards Quantitative Evaluation of Wall Shear Stress from 4D Flow Imaging

Sébastien Levilly , Marco Castagna , Jérôme Idier , Félicien Bonnefoy , David Le Touzé
Magnetic Resonance Imaging, 2020
Journal articles hal-02564861v1

Imagerie tri-dimensionnelle d’échantillons par une technique de serial block face imaging amovible

Marine Malloci , Stéphanie Blandin , Philippe Hulin , Paul Dorval , Steven Nedellec
Revue Française d'Histotechnologie, 2020, 32 (1), pp.187-197
Journal articles hal-03196150v1
Image document

Kinetics of Plasmodium midgut invasion in Anopheles mosquitoes

Gloria Volohonsky , Perrine Paul-Gilloteaux , Jitka Štáfková , Julien Soichot , Jean Salamero
PLoS Pathogens, 2020, 16 (9), ⟨10.1371/journal.ppat.1008739⟩
Journal articles hal-03093938v1

Development of automated annotation software for human embryo morphokinetics

M Feyeux , A Reignier , M Mocaer , J Lammers , D Meistermann
Human Reproduction, 2020, ⟨10.1093/humrep/deaa001⟩
Journal articles hal-02509917v1
Image document

The NEUBIAS Gateway: a hub for bioimage analysis methods and materials

Beth Cimini , Simon Nørrelykke , Marion Louveaux , Nataša Sladoje , Perrine Paul-Gilloteaux
F1000Research, 2020, 9, pp.613. ⟨10.12688/f1000research.24759.1⟩
Journal articles hal-02903660v1

BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows

Ulysse Rubens , Romain Mormont , Lassi Paavolainen , Volker Bäcker , Benjamin Pavie
Patterns, 2020, 1, pp.100040. ⟨10.1016/j.patter.2020.100040⟩
Journal articles hal-02799349v1
Image document

3D Correlative Cryo-Structured Illumination Fluorescence and Soft X-ray Microscopy Elucidates Reovirus Intracellular Release Pathway

Ilias Kounatidis , Megan Stanifer , Michael Phillips , Perrine Paul-Gilloteaux , Xavier Heiligenstein
Journal articles hal-02886173v1
Image document

Correlated Multimodal Imaging in Life Sciences: Expanding the Biomedical Horizon

Andreas Walter , Perrine Paul-Gilloteaux , Birgit Plochberger , Ludek Sefc , Paul Verkade
Frontiers in Physics, 2020, 8, ⟨10.3389/fphy.2020.00047⟩
Journal articles hal-02539357v1
Image document

Automatic Registration of Correlative Microscopies with Error Assessment and Applications for the Optimization of Multimodal Acquisitions.

Guillaume Potier , Romain Capoulade , Jean Mérot , Frédéric Lavancier , Xavier Heiligenstein
Microscopy and Microanalysis, 2019, 25 (S2), pp.1020-1021. ⟨10.1017/S143192761900583X⟩
Journal articles hal-02267554v1
Image document

In-vitro validation of 4D flow MRI measurements with an experimental pulsatile flow model

A. David , D. Le Touzé , K. Warin-Fresse , P. Paul-Gilloteaux , F. Bonnefoy
Diagnostic and Interventional Imaging, 2019, 100 (1), pp.17-23. ⟨10.1016/j.diii.2018.08.012⟩
Journal articles hal-02267542v1

EP-1998: In silico modelling of the impact of the fractionation for hypofractionated prostate treatments

G. Delpon , J. N'Guessan , Perrine Paul-Gilloteaux , K. Clément-Colmou , V. Potiron
Radiotherapy & Oncology, 2018, 127 (S2), pp.S1086-S1087. ⟨10.1016/S0167-8140(18)32307-7⟩
Journal articles hal-02736053v1
Image document

LINC complex-Lis1 interplay controls MT1-MMP matrix digest-on-demand response for confined tumor cell migration

Elvira Infante , Alessia Castagnino , Robin Ferrari , Pedro Monteiro , Sonia Agüera-González
Nature Communications, 2018, 9 (1), ⟨10.1038/s41467-018-04865-7⟩
Journal articles hal-02267545v1
Image document

Human Motor Thalamus Reconstructed in 3D from Continuous Sagittal Sections with Identified Subcortical Afferent Territories

Igor Ilinsky , Andreas Horn , Perrine Paul-Gilloteaux , Pierre Gressens , Catherine Verney
eNeuro, 2018, 5 (3), pp.ENEURO.0060-18.2018. ⟨10.1523/ENEURO.0060-18.2018⟩
Journal articles hal-02267562v1

eC-CLEM: A multidimension, multimodel software to correlate intermodal images with a focus on light and electron microscopy.

Xavier Heiligenstein , Perrine Paul-Gilloteaux , Graça Raposo , Jean Salamero
Methods in Cell Biology, 2018, pp.335-352. ⟨10.1016/bs.mcb.2017.03.014⟩
Journal articles hal-01712180v1

L. fermentum CECT 5716 prevents stress-induced intestinal barrier dysfunction in newborn rats

T. Vanhaecke , P. Aubert , P. Grohard , Thierry Durand , P. Hulin
Neurogastroenterology & Motility, 2017, 29 (8), ⟨10.1111/nmo.13069⟩
Journal articles hal-01712194v1

eC-CLEM: Flexible Multidimensional Registration Software for Correlative Microscopies with Refined Accuracy Mapping

Xavier Heiligenstein , Perrine Paul-Gilloteaux , Martin Belle , Graca Raposo , Jean Salamero
Microscopy and Microanalysis, 2017, 23 (S1), pp.360-361. ⟨10.1017/S1431927617002483⟩
Journal articles hal-02735782v1

eC-CLEM: flexible multidimensional registration software for correlative microscopies

Perrine Paul-Gilloteaux , Xavier Heiligenstein , Martin Belle , Marie-Charlotte Domart , Banafshe Larijani
Nature Methods, 2017, 14 (2), pp.102 - 103. ⟨10.1038/nmeth.4170⟩
Journal articles hal-01712184v1
Image document

Optimizing radiotherapy protocols using computer automata to model tumour cell death as a function of oxygen diffusion processes

Perrine Paul-Gilloteaux , Vincent Potiron , Grégory Delpon , Stéphane Supiot , Sophie Chiavassa
Scientific Reports, 2017, 7 (1), pp.2280. ⟨10.1038/s41598-017-01757-6⟩
Journal articles inserm-01550008v1

Direct interaction between exocyst and Wave complexes promotes cell protrusions and motility.

Marco Biondini , Amel Sadou-Dubourgnoux , Perrine Paul-Gilloteaux , Giulia Zago , Melis D Arslanhan
Journal of Cell Science, 2016, 129 (20), pp.3756-3769. ⟨10.1242/jcs.187336⟩
Journal articles hal-01452011v1

Control of the collective migration of enteric neural crest cells by the Complement anaphylatoxin C3a and N-cadherin

Florence Bondon Bondon Broders , Florence Broders-Bondon , Perrine Paul-Gilloteaux , Elodie Gazquez , Julie Heysch
Developmental Biology, 2016, 414 (1), pp.85-99. ⟨10.1016/j.ydbio.2016.03.022⟩
Journal articles hal-03043888v1

Endothelin-3 stimulates cell adhesion and cooperates with β1-integrins during enteric nervous system ontogenesis

Florence Bondon Bondon Broders , Elodie Gazquez , Yuli Watanabe , Florence Broders-Bondon , Perrine Paul-Gilloteaux
Scientific Reports, 2016, 6 (1), ⟨10.1038/srep37877⟩
Journal articles hal-03043883v1

Control of the collective migration of enteric neural crest cells by the Complement anaphylatoxin C3a and N-cadherin

Florence Broders-Bondon , Perrine Paul-Gilloteaux , Elodie Gazquez , Julie Heysch , Matthieu Piel
Developmental Biology, 2016, 414 (1), pp.85 - 99. ⟨10.1016/j.ydbio.2016.03.022⟩
Journal articles hal-01712198v1
Image document

Endothelin-3 stimulates cell adhesion and cooperates with β1-integrins during enteric nervous system ontogenesis

Elodie Gazquez , Yuli Watanabe , Florence Broders-Bondon , Perrine Paul-Gilloteaux , Julie Heysch
Scientific Reports, 2016, 6, pp.37877. ⟨10.1038/srep37877⟩
Journal articles hal-01426076v1
Image document

Myosin 1b functions as an effector of EphB signaling to control cell repulsion

Marie-Thérèse Prospéri , Priscilla Lépine , Florent Dingli , Perrine Paul-Gilloteaux , René Martin
Journal of Cell Biology, 2015, 210 (2), pp.347 - 361. ⟨10.1083/jcb.201501018⟩
Journal articles hal-01712201v1

Quantitative analysis of flagellar proteins in Drosophila sperm tails.

Teresa Mendes Maia , Perrine Paul-Gilloteaux , Renata Basto
Methods in Cell Biology, 2015, pp.263-78. ⟨10.1016/bs.mcb.2015.01.003⟩
Journal articles hal-01712207v1
Image document

Recycling Endosome Tubule Morphogenesis from Sorting Endosomes Requires the Kinesin Motor KIF13A

Cédric Delevoye , Stephanie Miserey-Lenkei , Guillaume Montagnac , Floriane Gilles-Marsens , Perrine Paul-Gilloteaux
Cell Reports, 2014, 6 (3), pp.445-454. ⟨10.1016/j.celrep.2014.01.002⟩
Journal articles hal-02735329v1

Fast high-resolution 3D total internal reflection fluorescence microscopy by incidence angle scanning and azimuthal averaging.

Jérôme Boulanger , Charles Gueudry , Daniel Münch , Bertrand Cinquin , Perrine Paul-Gilloteaux
Proceedings of the National Academy of Sciences of the United States of America, 2014, 111 (48), pp.17164-9
Journal articles hal-01133826v1
Image document

The CryoCapsule: Simplifying Correlative Light to Electron Microscopy

Xavier Heiligenstein , Jérôme Heiligenstein , Cédric Delevoye , Ilse Hurbain , Sabine Bardin
Traffic, 2014, 15 (6), pp.700 - 716. ⟨10.1111/tra.12164⟩
Journal articles hal-01712232v1
Image document

Septin6 and Septin7 GTP Binding Proteins Regulate AP-3- and ESCRT-Dependent Multivesicular Body Biogenesis

Sofia Traikov , Christoph Stange , Thomas Wassmer , Perrine Paul-Gilloteaux , Jean Salamero
PLoS ONE, 2014, 9 (11), pp.e109372. ⟨10.1371/journal.pone.0109372⟩
Journal articles hal-01712221v1
Image document

Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut

Maia Chanrion , Inna Kuperstein , Cédric Barrière , Fatima El Marjou , David Cohen
Nature Communications, 2014, 5, pp.5005. ⟨10.1038/ncomms6005⟩
Journal articles hal-01712223v1
Image document

Control of MT1-MMP transport by atypical PKC during breast-cancer progression

Carine Rossé , Catalina Lodillinsky , Laetitia Fuhrmann , Maya Nourieh , Pedro Monteiro
Proceedings of the National Academy of Sciences of the United States of America, 2014, 111 (18), pp.E1872 - E1879. ⟨10.1073/pnas.1400749111⟩
Journal articles hal-01712228v1
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Objective comparison of particle tracking methods

Nicolas Chenouard , Ihor Smal , Fabrice de Chaumont , Martin Maska , Ivo F. Sbalzarini
Nature Methods, 2014, 11 (3), pp.281-289. ⟨10.1038/nmeth.2808⟩
Journal articles hal-00932869v1

Sox10 and Itgb1 interaction in enteric neural crest cell migration

Yuli Watanabe , Florence Broders-Bondon , Viviane Baral , Perrine Paul-Gilloteaux , Veronique Pingault
Developmental Biology, 2013, 379 (1), pp.92 - 106. ⟨10.1016/j.ydbio.2013.04.013⟩
Journal articles hal-01712242v1

Endosomal WASH and exocyst complexes control exocytosis of MT1-MMP at invadopodia

Pedro Monteiro , Carine Rossé , Antonio Castro-Castro , Marie Irondelle , Emilie Lagoutte
Journal of Cell Biology, 2013, 203 (6), pp.1063 - 1079. ⟨10.1083/jcb.201306162⟩
Journal articles hal-01712237v1

Centrosome amplification causes microcephaly

Véronique Marthiens , Maria Rujano , Carole Pennetier , Sarah Tessier , Perrine Paul-Gilloteaux
Nature Cell Biology, 2013, 15 (7), pp.731 - 740. ⟨10.1038/ncb2746⟩
Journal articles hal-01712239v1

The first World Cell Race (vol 22, pg R673, 2012)

Paolo Maiuri , Emmanuel Terriac , Perrine Paul-Gilloteaux , Timothee Vignaud , Krista Mcnally
Current Biology - CB, 2013, 23 (1), pp.97. ⟨10.1016/j.cub.2012.12.015⟩
Journal articles hal-03304887v1

Centrosome amplification causes microcephaly

Véronique Marthiens , Maria Rujano , Carole Pennetier , Sarah Tessier , Perrine Paul-Gilloteaux
Nature Cell Biology, 2013, 15 (7), pp.731-740. ⟨10.1038/ncb2746⟩
Journal articles hal-03453019v1

Sox10 and Itgb1 interaction in enteric neural crest cell migration

Florence Bondon Bondon Broders , Yuli Watanabe , Florence Broders-Bondon , Viviane Baral , Perrine Paul-Gilloteaux
Developmental Biology, 2013, 379 (1), pp.92-106. ⟨10.1016/j.ydbio.2013.04.013⟩
Journal articles hal-03043892v1
Image document

Software for drift compensation, particle tracking and particle analysis of high-speed atomic force microscopy image series †

Mohamed Husain , Thomas Boudier , Perrine Paul-Gilloteaux , Ignacio Casuso , Simon Scheuring
Journal of Molecular Recognition, 2012, 25 ((5)), pp.292-8. ⟨10.1002/jmr.2187⟩
Journal articles inserm-01363229v1

The first World Cell Race.

Paolo Maiuri , Emmanuel Terriac , Perrine Paul-Gilloteaux , Timothée Vignaud , Krista Mcnally
Current Biology - CB, 2012, 22 (17), pp.R673-5. ⟨10.1016/j.cub.2012.07.052⟩
Journal articles hal-00744751v1

Complete Lateral and Angular Diffusion and Protein-Protein Interaction Description of a Membrane Protein

Ignacio Casuso , Jean-Pierre Duneau , Mohamed Chami , Perrine Paul-Gilloteaux , Mohamed Husain
Biophysical Journal, 2012, 102 (3), pp.413a-414a. ⟨10.1016/j.bpj.2011.11.2261⟩
Journal articles hal-02735811v1
Image document

Characterization of the motion of membrane proteins using high-speed atomic force microscopy

Ignacio Casuso , Jonathan Khao , Mohamed Chami , Perrine Paul-Gilloteaux , Mohamed Husain
Nature Nanotechnology, 2012, 7, pp.525-529. ⟨10.1038/nnano.2012.109⟩
Journal articles inserm-01363192v1

N-cadherin and β1-integrins cooperate during the development of the enteric nervous system

Florence Broders-Bondon , Perrine Paul-Gilloteaux , Camille Carlier , Glenn Radice , Sylvie Dufour
Developmental Biology, 2012, 364 (2), pp.178 - 191. ⟨10.1016/j.ydbio.2012.02.001⟩
Journal articles hal-01712255v1

ATAT1/MEC-17 acetyltransferase and HDAC6 deacetylase control a balance of acetylation of alpha-tubulin and cortactin and regulate MT1-MMP trafficking and breast tumor cell invasion

Antonio Castro-Castro , Carsten Janke , Guillaume Montagnac , Perrine Paul-Gilloteaux , Philippe Chavrier
European Journal of Cell Biology, 2012, 91 (11-12), pp.950 - 960. ⟨10.1016/j.ejcb.2012.07.001⟩
Journal articles hal-01712252v1

N-cadherin and β1-integrins cooperate during the development of the enteric nervous system

Florence Bondon Bondon Broders , Florence Broders-Bondon , Perrine Paul-Gilloteaux , Camille Carlier , Glenn Radice
Developmental Biology, 2012, 364 (2), pp.178-191. ⟨10.1016/j.ydbio.2012.02.001⟩
Journal articles hal-03043897v1

Automatic noise quantification for confocal fluorescence microscopy images

Perrine Paul , Heiko Duessmann , Tytus Bernas , Heinrich Huber , Dimitrios Kalamatianos
Computerized Medical Imaging and Graphics, 2010, 34 (6), pp.426-434. ⟨10.1016/j.compmedimag.2010.04.001⟩
Journal articles hal-02735528v1

ALISSA: an automated live-cell imaging system for signal transduction analyses

Jakub Wenus , Heiko Dussmann , Perrine Paul , Dimitrios Kalamatianos , Markus Rehm
Biotechniques, 2009, 47 (6), pp.1033-1040. ⟨10.2144/000113247⟩
Journal articles hal-02735355v1
Image document

A surface registration method for quantification of intraoperative brain deformations in image-guided neurosurgery.

Perrine Paul , Xavier Morandi , Pierre Jannin
IEEE Transactions on Information Technology in Biomedicine, 2009, 13 (6), pp.976-83. ⟨10.1109/TITB.2009.2025373⟩
Journal articles inserm-00546498v1
Image document

Augmented virtuality based on stereoscopic reconstruction in multimodal image-guided neurosurgery: methods and performance evaluation.

Perrine Paul , Oliver J. Fleig , Pierre Jannin
IEEE Transactions on Medical Imaging, 2005, 24 (11), pp.1500-11. ⟨10.1109/TMI.2005.857029⟩
Journal articles inserm-00136469v1

Linking and analyzing correlative datasets

Perrine Paul-Gilloteaux
ALL-HANDS NODES MEETINg&MORE, iNext DISCOVERY, Apr 2023, Heidelberg, Germany
Conference papers hal-04217201v1

France Bio Imaging : setting up image data management solutions at the national level

Perrine Paul-Gilloteaux
BioImaging and the European Open Science Cloud, EOSC-Life, Apr 2023, Heidelberg, Germany
Conference papers hal-04217222v1

Correlative microscopies : image registration for clem and for deep learning What can bring error estimation ?

Perrine Paul-Gilloteaux
Colloque Français d'Intelligence Artificielle en Imagerie Biomédicale, Instituts 3IA MIAI, 3IA Cote d'Azur et PRAIRIE, Mar 2023, Paris, France
Conference papers hal-04217245v1

Correlative microscopies : comulisglobe and news from ec-clem

Perrine Paul-Gilloteaux
France BioImaging CLEM day: What's new in multimodal imaging, Mar 2023, Paris, France
Conference papers hal-04217188v1

Image analysis tools and applications for correlative microscopy

Perrine Paul-Gilloteaux
Séminaire de l'Institut de Génétique & Développement de Rennes, Apr 2023, Rennes, France
Conference papers hal-04217158v1

Development of correlation software for Correlative cryo light Soft X-Ray Tomography : example of 3d correlative cryo-structured illumination fluorescence and soft x-ray microscopy to ellucidate reovirus intracellular release pathway

Perrine Paul-Gilloteaux
INSTRUCT Soft X-ray Tomography workshop, Sep 2023, Didcot, United Kingdom
Conference papers hal-04217085v1

Correlative microscopies: image registration for CLEM and for Deep Learning

Perrine Paul-Gilloteaux
Crick BioImage Analysis Symposium (CBIAS), Nov 2022, Londres (London), United Kingdom
Conference papers hal-04217278v1

La tomographie par cohérence optique plein champ : un nouvel outil de microscopie optique dynamique pour l'analyse du système nerveux entérique

T Durand , L Laboudie , Perrine Paul-Gilloteaux , Isabelle Neveu , Philippe Naveilhan
JFHOD, Mar 2022, Paris, France
Conference papers hal-03548856v1

Image processing and analysis in clem : methods and pitfalls

Perrine Paul-Gilloteaux
Symposium on recent developments in cellular electron microscopy, AVIESAN ITMO MOLECULAR AND STRUCTURAL BASIS OF LIFE SCIENCES, Mar 2022, Paris, France
Conference papers hal-04217262v1

Méthodes et écueils du traitement des images issues de microscopie corrélative

Perrine Paul-Gilloteaux
6eme rencontre des microscopistes clermontois, Igred et Inrae, Oct 2021, Clermont-Ferrand, France
Conference papers hal-04214182v1

A FULL 3D CORRELATIVE IMAGING WORKFLOW: CHALLENGES IN COMPUTER VISION

Perrine Paul-Gilloteaux , Nina Vyas , Guillaume Potier , Stephan Kunne , Thomas M Fish
IEEE ISBI 2021 (VIRTUAL)., Apr 2021, Nice, France
Conference papers hal-03258718v1
Image document

A Registration Error Estimation Framework for Correlative Imaging

Guillaume Potier , Frederic Lavancier , Stephan Kunne , Perrine Paul-Gilloteaux
2021 IEEE International Conference on Image Processing (ICIP), Sep 2021, Anchorage, United States. pp.131-135, ⟨10.1109/ICIP42928.2021.9506474⟩
Conference papers hal-03327500v1

EcClemv2: A new version of a flexible software for correlative workflows

Perrine Paul-Gilloteaux , Guillaume Potier , Frédéric Lavancier
COMULIS Conference, Sep 2021, Gothenburg, Sweden
Conference papers hal-04219791v1

French gastronomy and bio image analysis workflows

Perrine Paul-Gilloteaux
Virtual Analytical and Quantitative Microscopy, May 2020, Woods Hole, United States
Conference papers hal-02736886v1

Leveraging Molecular and Cellular Fiducial Markers for Correlative Bio-Imaging

Chidinma Okolo , Ilias Kounatidis , Thomas Fish , Perrine Paul-Gilloteaux , Ian Dobbie
Quantitative BioImaging, Jan 2020, Oxford, United Kingdom
Conference papers hal-04219534v1

Cross-modal registration using point clouds and graph-matching in the context of correlative microscopies

Stephan Kunne , Guillaume Potier , Jean Merot , Perrine Paul-Gilloteaux
iTWIST : international Traveling Workshop on Interactions between low-complexity data models and Sensing Techniques, Dec 2020, Nantes, France
Conference papers hal-03039114v1

Le dorica castra des images

Perrine Paul-Gilloteaux , Laurence Dubreil
Nuit Blanche des Chercheurs, Feb 2020, Nantes, France
Conference papers hal-02509532v1

Quantification: extracting quantitative information from correlated multimodal dataset

Perrine Paul-Gilloteaux
IMAGE PROCESSING FOR CORRELATED AND MULTIMODAL IMAGING TECHNIQUES, VIB Training, Oct 2020, Ghent, Belgium
Conference papers hal-04214173v1

Interdisciplinarity in a (still short) carreer: living and contributing to the creation of a new research field in biomedical image informatics.

Perrine Paul-Gilloteaux
Opening conference of Angers Summer schools, Jun 2019, Angers, France
Conference papers hal-02745462v1

Les bases de données images: limitations et aspirations

Perrine Paul-Gilloteaux
Journée partenaire industriel GDR IMABIO, Jun 2019, Paris, France
Conference papers hal-02745126v1

Advanced Image analysis

Perrine Paul-Gilloteaux
Analytical & Quantitative Light Microscopy, May 2019, Woods Hole, United States
Conference papers hal-02736802v1

Introduction to transformations and registrations

Perrine Paul-Gilloteaux , Martin Schorb
High-Accuracy CLEM: Applications at Room Temperature and in cryo, Apr 2019, Heidelberg, Germany
Conference papers hal-02746707v1

Automatic Registration of Correlative Microscopies with Error Assessment and Applications for the Optimization of Multimodal Acquisitions

Perrine Paul-Gilloteaux
SCANDEM 2019, Jun 2019, Gothenburg, Sweden
Conference papers hal-02736339v1

Linking cell scales: methods and software for correlative imaging workflows

Perrine Paul-Gilloteaux
La microscopie électronique pour les sciences du vivant. Journées Scientifiques de l'Université de Nantes, Jun 2019, Nantes, France
Conference papers hal-02745260v1

RECALAGE EN MICROSCOPIES CORRÉLATIVES POUR LA CARACTÉRISATION PHYSIOPATHOLOGIQUE DE LA VALVULOPATHIE

Perrine Paul-Gilloteaux
16eme colloque de la société Française des Microscopies, Jul 2019, Poitiers, France
Conference papers hal-02745967v1

An in Vitro and in Silico Validation Study for PC MRI and Derived Bio‐markers

Marco Castagna , Sébastien Levilly , Perrine Paul-Gilloteaux , Félicien Bonnefoy , Jérôme Idier
31st Society for Magnetic Resonance Angiography conference (SMRA 2019), Aug 2019, Nantes, France
Conference papers hal-03130185v1

NEUBIAS: BIOIMAGE ANALYSTS NETWORK TO SUPPORT LIFE SCIENTISTS THROUGH TRAINING, ONLINE TOOLS REPOSITORIES AND BENCHMARKING DEPLOYMENT FOR BIOIMAGE ANALYSIS WORKFLOWS

Kota Miura , Sebastian Munck , Florian Levet , Gabriel Martins , Fabrice Cordelières
Focus on Microscopy, Apr 2019, Londres, United Kingdom
Conference papers hal-02746229v1

Introduction to Correlation Software in CLEM

Perrine Paul-Gilloteaux
Correlated Multimodal Imaging Conference, Nov 2019, Vienne, Austria
Conference papers hal-02744299v1

Automatic registration for multidimensional correlative microscopies with error assessment and detections of deformations

Perrine Paul-Gilloteaux
International Microscopy Congress, Sep 2018, Sydney, Australia
Conference papers hal-02736564v1

Constructing workflows in Bio Image Analysis

Perrine Paul-Gilloteaux
Analytical & Quantitative Light Microscopy, May 2018, Woods Hole, United States
Conference papers hal-02736843v1

Computer vision methods for multidimensional correlative microscopies: optimizing acquisitions using maths

Perrine Paul-Gilloteaux
Colloqium: Future Microscopy and Analysis, Nov 2018, Ghent, Belgium
Conference papers hal-02736454v1

Computer vision methods for multidimensional correlative microscopies

Perrine Paul-Gilloteaux
Journées communes des GdR MIA et ImaBio "Microscopie et traitement d'image", Nov 2018, Strasbourg, France
Conference papers hal-02736491v1

Bio-image DATA in Life Sciences Research Infrastructures. From SCRATCH to intelligent integrated solutions

Perrine Paul-Gilloteaux
Storage Day, Jan 2018, Paris, France
Conference papers hal-02737009v1

COMULIS, a new network to bridge (pre) clinical imaging and correlative Light Electron microscopy. Focus on multidimensional registration software

Perrine Paul-Gilloteaux
ASCB-EMBO 2018, Dec 2018, San Diego, United States
Conference papers hal-02736408v1

Bio-Imagerie: mathématiques et informatique pour la compréhension du vivant

Perrine Paul-Gilloteaux
Immersion Science, Mar 2018, Ile Tudy, France
Conference papers hal-02736939v1

Introduction to transformations and registrations

Perrine Paul-Gilloteaux , Martin Schorb
High-Accuracy CLEM: Applications at Room Temperature and in cryo, Dec 2017, Heidelberg, Germany
Conference papers hal-02746508v1
Image document

Filtrage spatio-temporel en IRM de flux sanguin 4D

Sébastien Levilly , Jérôme Idier , Félicien Bonnefoy , David Le Touzé , Perrine Paul-Gilloteaux
XXVIème colloque GRETSI sur le Traitement du Signal et des Images, Sep 2017, Juan-Les-Pins, France
Conference papers hal-01720339v1

Gestion et analyse d’images à moyen débit : exemple en microscopie confocale et sur lames virtuelles

Perrine Paul-Gilloteaux
Quand la bio-imagerie rencontre la bio-informatique : vers une intégration des données hétérogènes. Journée d'animation Biogenouest, Oct 2017, Rennes, France
Conference papers hal-02745560v1

Flexible multidimensional registration software for correlative microscopies with refined accuracy mapping: eC-CLEM easy Cell Correlative Light to Electron Microscopy

Perrine Paul-Gilloteaux
Symposium and Workshop on correlative light, electron, and X-ray microscopy, Mar 2017, Harwell, United Kingdom
Conference papers hal-02747152v1

Challenges in image correlation for CLEM (and partial solutions)

Perrine Paul-Gilloteaux
Crick Electron Microscopy Opening Symposium, Jul 2017, Londres, United Kingdom
Conference papers hal-02747126v1

Le recalage d'image sous ICY

Perrine Paul-Gilloteaux , Xavier Heiligenstein
Journée Thématique conjointe sur le repositionnement et la relocalisation/recalage, Nov 2017, Orléans, France
Conference papers hal-02746899v1

Besoins en bio-informatique liés àl’activité de l’infrastructure nationale France Bio Imaging

Perrine Paul-Gilloteaux
Assemblée générale de l'INBS Institut Français de Bioinformatique, Jan 2017, paris, France
Conference papers hal-02747035v1

Cycle de vie des images en microscopie : de l’acquisition au partage des données

Perrine Paul-Gilloteaux
La diversité tumorale à travers les plateformes technologiques franciliennes, Jan 2016, Paris, France
Conference papers hal-02746957v1

Le numérique dans les biotechnologies: exemple de la bio imagerie

Perrine Paul-Gilloteaux
TechnoConférence Pole Image et Réseau #17, Jun 2016, Nantes, France
Conference papers hal-02746143v1

Multiscale and multidimensional Image registration for CLEM : techniques and pitfalls

Perrine Paul-Gilloteaux
High-Accuracy Correlated Light and Electron Microscopy: Applications at Room Temperature and in Cryo, Apr 2016, Heildelberg, Germany
Conference papers hal-02746687v1

Ec-CLEM: an open source plugin for CLEM image and volume registration

Perrine Paul-Gilloteaux
EMBL Workshop: From 3D Light to 3D Electron Microscopy, Mar 2016, Heidelberg, Germany
Conference papers hal-02746474v1

Gestion du cycle de vie des images en microscopie pour la biologie: Extraction de connaissances à partir d’une base de données images

Perrine Paul-Gilloteaux
Séminaire de l'INRA OPEN DATA, Dec 2015, Montpellier, France
Conference papers hal-02908891v1

Methodes de traitement et analyse d’images comme aide à la quantification des biomarqueurs en imagerie: de l’in vitro à la clinique

Perrine Paul-Gilloteaux
Ateliers du DHU2020, Jun 2015, Nantes, France
Conference papers hal-02908867v1

Développement et déploiement d’une base de données image commune : bilan

Perrine Paul-Gilloteaux , Corinne Laplace-Builhé
Imagerie et cancers : optique et imagerie multiphotonique, Sep 2014, Paris, France
Conference papers hal-02746819v1

Computational modeling of the consequences of embryonic neurogenesis disorders

Perrine Paul-Gilloteaux , Renata Basto , Veronique Marthiens
Molecular Biology of The Cell. ASCB, 2013, Nouvelle-Orleans, United States. pp.3775-3775, ⟨10.1091/mbc.E13-10-0584⟩
Conference papers hal-02908946v1

Correlation and variational approaches for motion and diffusion estimation in fluorescence imaging

Denis Fortun , Chen Chen , Perrine Paul-Gilloteaux , François Waharte , Jean Salamero
European Light Microscopy Initiative (ELMI'13), May 2013, Arcachon, France
Conference papers hal-00931593v1

Aggregation of patch-based estimations for illumination-invariant optical flow in live cell imaging

Denis Fortun , Patrick Bouthemy , Perrine Paul-Gilloteaux , Charles Kervrann
ISBI - IEEE International Symposium on Biomedical Imaging, Apr 2013, San-Francisco, United States. pp.660-663, ⟨10.1109/ISBI.2013.6556561⟩
Conference papers hal-00931377v1

Robust parametric stabilization of moving cells with intensity correction in light microscopy image sequences

Solene Ozere , Patrick Bouthemy , Fabien Spindler , Perrine Paul-Gilloteaux , Charles Kervrann
ISBI - IEEE International Symposium on Biomedical Imaging, Apr 2013, San-Francisco, United States. pp.468-471, ⟨10.1109/ISBI.2013.6556513⟩
Conference papers hal-00931371v1

Correlation and variational approaches for motion and diffusion estimation in fluorescence imaging

Denis Fortun , Chen Chen , Perrine Paul-Gilloteaux , François Waharte , Jean Salamero
EUSIPCO 2013 - European Signal Processing Conference, Sep 2013, Marrakech, Morocco. pp.1-5
Conference papers hal-00931408v1

Image Data Base on a microscopy facility: Presentation and use for remote collaborations

Perrine Paul-Gilloteaux
Nouvelles méthodologies en imagerie du vivant, Dec 2012, Lyon, France
Conference papers hal-02746303v1

Developpement des methodes de correlation d images pour l analyse de la mobilite moleculaire dans un systeme biologique complexe spatialement et temporellement

C. Chen , P. Paul-Gilloteaux , T. Vignaud , J. Salamero , F. Waharte
OPTDIAG, May 2012, Paris, France
Conference papers hal-02746408v1

Study of the 3D repartition of vesicles normalized by the distance to the cell periphery

Perrine Paul-Gilloteaux , Elisabetta Padovan , Claire L Hivroz
Focus On Microscopy, Apr 2011, Konstanz, Germany
Conference papers hal-02746059v1

Automatic quality assessment for fluorescence microscopy images

Perrine Paul , Dimitrios Kalamatianos , Heiko Duessmann , Heinrich Huber
2008 8th IEEE International Conference on Bioinformatics and BioEngineering (BIBE), Oct 2008, Athens, France. pp.1-6, ⟨10.1109/BIBE.2008.4696665⟩
Conference papers hal-02735370v1
Image document

Image Guidance in neurosurgical procedures, the "VISAGES" point of view

Christian Barillot , Pierrick Coupé , Bernard Gibaud , Pierre Hellier , Pierre Jannin
4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Apr 2007, Arlington, United States. pp.1056-1059, ⟨10.1109/ISBI.2007.357037⟩
Conference papers inserm-00152147v1
Image document

Knowledge modeling in image guided neurosurgery: application in understanding intra-operative brain shift

Perrine Paul , Xavier Morandi , Pierre Jannin , Julien Cohen-Adad
SPIE Medical Imaging 2006: Visualization, Image-Guided Procedures and Display, Mar 2006, San Diego, United States. ⟨10.1117/12.655752⟩
Conference papers inserm-00147527v1
Image document

A surface registration approach for video-based analysis of intraoperative brain surface deformations

Perrine Paul , Aurélie Quere , Élise Arnaud , Xavier Morandi , Pierre Jannin
Oct 2006, pp.0
Conference papers inserm-00109455v1
Image document

Virtualité augmentée en neurochirurgie guidée par l'image

Perrine Paul , Oliver J. Fleig , Xavier Morandi , Pierre Jannin
2005, pp.99-104
Conference papers inserm-00138138v1

Performance Evaluation of a Stereoscopic Based 3D Surface Localiser for Image-Guided Neurosurgery

Perrine Paul , Oliver J. Fleig , Sabine Tranchant , Pierre Jannin
MICCAI, Sep 2004, Saint-Malo, France. pp.510-517, ⟨10.1007/978-3-540-30136-3_63⟩
Conference papers hal-02735433v1

EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formats (update 2019)

Matúš Kalaš , Laure Plantard , Nataša Sladoje , Joakim Lindblad , Moritz Alexander Kirschmann
3rd NEUBIAS Bioimage Analysis Community Conference 2019, Jun 2020, Luxembourg, Luxembourg
Conference poster hal-02910949v1

EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formats (update 2020)

Matúš Kalaš , Laure Plantard , Nataša Sladoje , Joakim Lindblad , Moritz Alexander Kirschmann
ELIXIR All Hands 2020, Jun 2020, Virtual, United Kingdom
Conference poster hal-02910948v1
Image document

EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formats

Matúš Kalaš , Laure Plantard , Nataša Sladoje , Joakim Lindblad , Moritz Alexander Kirschmann
NEUBIAS, Feb 2019, Luxembourg, Luxembourg. ⟨10.7490/f1000research.1115257.1⟩
Conference poster hal-02267597v1
Image document

Registration and error estimation in correlated multimodal imaging

Guillaume Potier , Stephan Kunne , Frédéric Lavancier , Perrine Paul-Gilloteaux
Correlated Multimodal Imaging Conference, Nov 2019, Vienna, Austria
Conference poster hal-02744368v1
Image document

Analyse d’un échantillon en 3 dimensions par une technique de Serial Block Face Imaging amovible

Marine Malloci , Stéphanie Blandin , Paul Dorval , Philippe Hulin , Pierre-Alix Dancer
AFH 2019, Jun 2019, Strasbourg, France
Conference poster hal-02267585v1
Image document

Spatio-temporal filtering of blood flow in 4D Phase-Contrast MRI

Sébastien Levilly , Jérôme Idier , David Le Touzé , Perrine Paul-Gilloteaux , Félicien Bonnefoy
Society for Magnetic Resonance Angiography, 29th Annual International Conference (SMRA 2017), Oct 2017, Stellenbosch, South Africa. 61, pp.3163 - 3178, 2015
Conference poster hal-01720378v1

Computer-assisted analysis of multimodal image data—perspectives and conclusion

Nataša Sladoje , Joakim Lindblad , Perrine Paul-Gilloteaux
Imaging Modalities for Biological and Preclinical Research: A Compendium, Volume 2, IOP Publishing, 2021, ⟨10.1088/978-0-7503-3747-2ch30⟩
Book sections hal-03232548v1

Workflows and Components of Bioimage Analysis

Kota Miura , Perrine Paul-Gilloteaux , Sébastien Tosi , Julien Colombelli
Bioimage Data Analysis Workflows. Learning Materials in Biosciences. Springer, Cham, pp.1-7, 2020, ⟨10.1007/978-3-030-22386-1_1⟩
Book sections hal-02735486v1
Image document

Resolving the Process of Clathrin Mediated Endocytosis Using Correlative Light and Electron Microscopy (CLEM)

Martin Schorb , Perrine Paul-Gilloteaux
Kota Miura; Nataša Sladoje. Bioimage Data Analysis Workflows, Springer, pp.143-166, 2020, Learning Materials in Biosciences, 978-3-030-22385-4. ⟨10.1007/978-3-030-22386-1_6⟩
Book sections hal-02735825v1

Correlating Data from Imaging Modalities

Perrine Paul-Gilloteaux , Martin Schorb
Correlative Imaging: Focusing on the Future, 1, Wiley, 2019, ⟨10.1002/9781119086420.ch11⟩
Book sections hal-02735744v1

A Biologist-Friendly Method to Analyze Cross-Correlation Between Protrusion Dynamics and Membrane Recruitment of Actin Regulators

Perrine Paul-Gilloteaux , François Waharte , Manish Kumar Singh , Maria Carla Parrini
Methods Mol Biol, pp.279-289, 2018
Book sections hal-02267604v1
Image document

Cell Polarity: Focal Adhesion and Actin Dynamics in Migrating Cells

Perrine Paul-Gilloteaux , Christoph Möhl
Kota Miura. Bioimage Data Analysis, Wiley-VCH, pp.198-218, 2016, 978-3-527-80092-6
Book sections hal-02910995v1
Image document

Bioimage Analysis Tools

Kota Miura , Sébastien Tosi , Christoph Möhl , Chong Zhang , Perrine Paul-Gilloteaux
Kota Miura. Bioimage Data Analysis, Wiley-VCH, 2016, 978-3-527-80092-6
Book sections hal-02910986v1
Image document

Quantitative Evaluation of Multicellular Movements in Drosophila Embryo

Perrine Paul-Gilloteaux , Sébastien Tosi
Kota Miura. Bioimage Data Analysis, Wiley-VCH, 2016, 978-3-527-80092-6
Book sections hal-02910999v1

Quantitative analysis of flagellar proteins in Drosophila sperm tails

Teresa Mendes Maia , Perrine Paul-Gilloteaux , Renata Basto
Methods in Cilia & Flagella, 127, Elsevier, pp.263-278, 2015, Methods in Cell Biology, ⟨10.1016/bs.mcb.2015.01.003⟩
Book sections hal-03453032v1

Microscopy control system and method

Heinrich Huber , Heiko Dussmann , Perrine Paul-Gilloteaux , Jakub Wenus , Dimitrios Kalamatianos
United States, Patent n° : US 2010/0251438 A1. 2010, https://patentimages.storage.googleapis.com/bb/3d/c1/00174666d137a7/US20100251438A1.pdf
Patents hal-02735674v1