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Perrine Paul-Gilloteaux

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Présentation

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.

Domaines de recherche


Publications

48812
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⟩
Article dans une revue hal-04013867v1
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⟩
Article dans une revue hal-04175990v1
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⟩
Article dans une revue hal-03765601v1

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⟩
Article dans une revue hal-03745072v1
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⟩
Article dans une revue 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⟩
Article dans une revue hal-03278159v1

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⟩
Article dans une revue hal-03223460v1
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
Article dans une revue hal-02886173v1

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
Article dans une revue hal-03196150v1
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⟩
Article dans une revue 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⟩
Article dans une revue hal-02267554v1

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
Communication dans un congrès 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
Communication dans un congrès hal-04217188v1

Linking and analyzing correlative datasets

Perrine Paul-Gilloteaux
ALL-HANDS NODES MEETINg&MORE, iNext DISCOVERY, Apr 2023, Heidelberg, Germany
Communication dans un congrès hal-04217201v1

Image analysis tools and applications for correlative microscopy

Perrine Paul-Gilloteaux
Séminaire de l'Institut de Génétique & Développement de Rennes, Apr 2023, Rennes, France
Communication dans un congrès 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
Communication dans un congrès 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
Communication dans un congrès 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
Communication dans un congrès 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
Communication dans un congrès hal-04217262v1

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
Communication dans un congrès 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⟩
Communication dans un congrès 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
Communication dans un congrès hal-04219791v1

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
Communication dans un congrès hal-04214182v1

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
Communication dans un congrès hal-03039114v1

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
Communication dans un congrès hal-04214173v1

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
Communication dans un congrès hal-04219534v1

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
Communication dans un congrès 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
Communication dans un congrès 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
Communication dans un congrès hal-02745967v1

Introduction to Correlation Software in CLEM

Perrine Paul-Gilloteaux
Correlated Multimodal Imaging Conference, Nov 2019, Vienne, Austria
Communication dans un congrès hal-02744299v1

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⟩
Chapitre d'ouvrage hal-03232548v1