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Thomas Grenier

Assistant professor at INSA LYON Electrical Engineering department CREATIS
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### Laboratoire de recherche CREATIS, Unité CNRS UMR 5220 – INSERM U1206 – Université Lyon 1 – INSA Lyon - Université Jean Monnet Saint-Etienne **Adresse du laboratoire** CREATIS, UMR CNRS 5220, Inserm U1206 Bât.Léonard de Vinci, INSA-Lyon 21 Av. Jean Capelle O 69621 Villeurbanne Cedex, France Tel : 04 72 43 64 70 E-mail : thomas.grenier[@creatis.insa-lyon.fr] ### Diplômes * 2023 : **HDR**, Université de Lyon, INSA Lyon, *Approches non-supervisées et supervisées de filtrage et segmentation pour l’analyse longitudinale en imagerie médicale* * 2005 : **Thèse,** INSA Lyon, France. *Espaces des caractéristiques et paramètres d’échelle pour le filtrage et la segmentation d’image.* * 2001 : Master, DEA St-Etienne, France. *«Transformée en cercle et généralisation ».* * 2001 : Ingénieur ISTASE St-Etienne, France. ### Statut actuel Depuis 2006: Maître de Conférences HDR (hors classe) 61ème section, à INSA-Lyon France : CREATIS/département Génie Electrique de l’INSA Lyon. ### Responsabilités actuelles Depuis 2009: responsable de la communication au département Génie Electrique et des systèmes d'information. Responsable de l'option Traitement des signaux et des Images en 5ème année du département Génie Electrique. Co-responsable du work-package formation du Labex PRIMES (salle de formation, écoles d'été internationale en Deep learning pour l'imagerie médicale) Elu au Conseil de département du département Génie Electrique ### Domaines académiques * Informatique: algorithmes, microcontrôleur, UML, C/C++. * Traitement du Signal: Théorie de l’Information, Filtrage de signal, Traitement d’images, Digital Image Processor (DSP). ### Domaines de recherche * Filtrage et segmentation d’images médicales, Clustering et analyse de données spatio-temporelles * méthodes : Apprentissage profond
Research Lab CREATIS, Unité CNRS UMR 5220 – INSERM U1206 – Université Lyon 1 – INSA Lyon - Université Jean Monnet Saint-Etienne Addresse CREATIS, UMR CNRS 5220, Inserm U1206 Bât. Blaise Pascal, INSA 69621 Villeurbanne Cedex, France Tel : 04 72 43 64 70 Fax : 04 72 43 63 12 E-mail : thomas.grenier[@creatis.insa-lyon.fr](mailto:remy.prost@creatis.insa-lyon.fr) Education and Qualifications 2005 :** PhD, INSA Lyon, France. *« Features and scale space for image filtering and segmentation. ».* 2001 : Master degree, St-Etienne, France. *«Circle transforsm and gereliazation ».* 2001 : Enginer degree ISTASE St-Etienne, France. Actual employement Since 2006: Assistant professor at INSA-Lyon France, within CREATIS and Electrical Engineering department. Academic skills Computer Science: algorithms, microcontroler, UML, C/C++. Signal processing: Information theorie, Image Processing, Digital Image Processor (DSP). Research topics Image segmentation based on region growing, mean-shift and deep learning. Clustering and spatiotemporal medical data analysis (*mean shift, DNN)*.

Publications

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Multiple Sclerosis Clinical Forms Classification Study with Graph Convolutional Networks

Enyi Chen , Berardino Barile , Françoise Durand-Dubief , Thomas Grenier , Dominique Sappey-Marinier
Frontiers in Neuroscience, inPress, ⟨10.3389/fnins.2023.1268860⟩
Journal articles hal-04373468v1
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A Weakly Supervised Gradient Attribution Constraint for Interpretable Classification and Anomaly Detection

Valentine Wargnier-Dauchelle , Thomas Grenier , Françoise Durand-Dubief , François Cotton , Michaël Sdika
IEEE Transactions on Medical Imaging, 2023, ⟨10.1109/TMI.2023.3282789⟩
Journal articles hal-04110698v2
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Deep learning detection of nanoparticles and multiple object tracking of their dynamic evolution during in situ ETEM studies

Khuram Faraz , Thomas Grenier , Christophe Ducottet , Thierry Epicier
Scientific Reports, 2022, 12 (1), pp.2484. ⟨10.1038/s41598-022-06308-2⟩
Journal articles hal-03578102v1
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Pesticide-Free Robotic Control of Aphids as Crop Pests

Virginie Lacotte , Duc Toan Nguyen , Javier Diaz Sempere , Vivien Novales , Vincent Dufour
AgriEngineering, 2022, 4 (4), pp.903-921. ⟨10.3390/agriengineering4040058⟩
Journal articles hal-03806585v2

Deep learning in veterinary medicine, an approach based on CNN to detect pulmonary abnormalities from lateral thoracic radiographs in cats

Léo Dumortier , Florent Guépin , Marie Laure Delignette-Muller , C. Boulocher , Thomas Grenier
Scientific Reports, 2022, 12 (1), pp.11418. ⟨10.1038/s41598-022-14993-2⟩
Journal articles hal-03727944v1
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PET image enhancement using artificial intelligence for better characterization of epilepsy lesions

Anthime Flaus , Tahya Deddah , Anthonin Reilhac , Nicolas De Leiris , Marc Janier
Frontiers in Medicine, 2022, 9, pp.1042706. ⟨10.3389/fmed.2022.1042706⟩
Journal articles hal-03880659v1
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Quantitative Magnetic Resonance Imaging Assessment of the Quadriceps Changes during an Extreme Mountain Ultramarathon

Hoai-Thu Nguyen , Thomas Grenier , Benjamin Leporq , Caroline Le Goff , Benjamin Gilles
Medicine and Science in Sports and Exercise, 2021, 53 (4), pp.869-881. ⟨10.1249/mss.0000000000002535⟩
Journal articles hal-02998029v1

Development of normal pressure hydrocephalus following post-traumatic external hydrocephalus in an adult patient

Romain Manet , Laurent Gergelé , Thomas Grenier , Zofia Czosnyka , Marek Czosnyka
British Journal of Neurosurgery, 2020, pp.1-4. ⟨10.1080/02688697.2020.1738340⟩
Journal articles hal-02998015v1
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LU-Net: A Multistage Attention Network to Improve the Robustness of Segmentation of Left Ventricular Structures in 2-D Echocardiography

Sarah Leclerc , Erik Smistad , Andreas Ostvik , Frédéric Cervenansky , Florian Espinosa
IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, 2020, 67 (12), pp.2519-2530. ⟨10.1109/TUFFC.2020.3003403⟩
Journal articles hal-03149347v1
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A Pilot Study on Convolutional Neural Networks for Motion Estimation From Ultrasound Images

Ewan Evain , Faraz Khuram , Thomas Grenier , Damien Garcia , Mathieu de Craene
IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, 2020, 67 (12), pp.2565-2573. ⟨10.1109/TUFFC.2020.2976809⟩
Journal articles hal-03027193v1
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New OFSEP recommendations for MRI assessment of multiple sclerosis patients: Special consideration for gadolinium deposition and frequent acquisitions

Stephane Kremer , Salem Hannoun , Fabrice Bonneville , Francoise Durand-Dubief , Thomas Tourdias
Journal de Neuroradiologie / Journal of Neuroradiology, 2020, 47 (4), pp.250-258. ⟨10.1016/j.neurad.2020.01.083⟩
Journal articles hal-02570313v1
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Fast electron tomography: Applications to beam sensitive samples and in situ TEM or operando environmental TEM studies

Siddardha Koneti , Lucian Roiban , Florent Dalmas , Cyril Langlois , Anne-Sophie Gay
Materials Characterization, 2019, 151, pp.480-495. ⟨10.1016/j.matchar.2019.02.009⟩
Journal articles hal-02151235v1
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Automatic myocardial ischemic lesion detection on magnetic resonance perfusion weighted imaging prior perfusion quantification: A pre-modeling strategy

Clément Daviller , Thomas Grenier , Hélène Ratiney , Michaël Sdika , Pierre Croisille
Computers in Biology and Medicine, 2019, 110, pp.108-119. ⟨10.1016/j.compbiomed.2019.05.001⟩
Journal articles hal-02135018v1

Corrigendum to “Automatic myocardial ischemic lesion detection on magnetic resonance perfusion weighted imaging prior perfusion quantification: A pre-modeling strategy” [Comput. Biol. Med. 110 (2019) 108–119]

Clément Daviller , Thomas Grenier , Hélène Ratiney , Michaël Sdika , Pierre Croisille
Computers in Biology and Medicine, 2019, 114, pp.103455. ⟨10.1016/j.compbiomed.2019.103455⟩
Journal articles hal-03009072v1
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Deep Learning for Segmentation using an Open Large-Scale Dataset in 2D Echocardiography

Sarah Leclerc , Erik Smistad , Joao Pedrosa , Andreas Ostvik , Fréderic Cervenansky
IEEE Transactions on Medical Imaging, 2019, 38 (9), pp.2198-2210. ⟨10.1109/TMI.2019.2900516⟩
Journal articles hal-02054458v1

Very Fast Tomography in the (E)TEM to Probe Dynamics in Materials during Operando and In Situ Experiments

Thierry Epicier , Hussein Banjak , Anne-Sophie Gay , Thomas Grenier , Sid Koneti
Microscopy and Microanalysis, 2018, 24 (S1), pp.1814 - 1815. ⟨10.1017/S1431927618009558⟩
Journal articles hal-01934140v1
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Spatial and spectral regularization to discriminate tissues using multispectral photoacoustic imaging

Aneline Dolet , Francois Varray , Simon Mure , Thomas Grenier , Yubin Liu
EURASIP Journal on Advances in Signal Processing, 2018, 2018 (1), pp.39. ⟨10.1186/s13634-018-0554-8⟩
Journal articles hal-01909562v1

Evaluation of noise and blur effects with SIRT-FISTA-TV reconstruction algorithm: Application to fast environmental transmission electron tomography

Hussein Banjak , Thomas Grenier , Thierry Epicier , Siddardha Koneti , Lucian Roiban
Ultramicroscopy, 2018, 189, pp.109 - 123. ⟨10.1016/j.ultramic.2018.03.022⟩
Journal articles hal-01812662v1

Rapid Tomography in Environmental TEM: How Fast Can We Go to Follow the 3D Evolution of Nanomaterials in situ?

Lucian Roiban , Sid Koneti , Khan Tran , Yue-Meng Feng , Thomas Grenier
Microscopy and Microanalysis, 2016, 22 (S5), pp.8 - 9. ⟨10.1017/S143192761601206X⟩
Journal articles hal-01612810v1

Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification

S. Mure , T. Grenier , D. Meier , C. R. G. Guttmann , H. Benoit-Cattin
Pattern Recognition Letters, 2015, 68 (Part), pp.48-55. ⟨10.1016/j.patrec.2015.07.021⟩
Journal articles hal-01206150v1

Le modèle International de l'INSA de Lyon : au-delà de l’échange académique

Jérôme Dupuy , Thalia Darnanville , Fabrice Valois , Nina Arnesen , Marie-Pierre Favre
Journal sur l'enseignement des sciences et technologies de l'information et des systèmes, 2011, 10, pp.1009. ⟨10.1051/j3ea/2011009⟩
Journal articles hal-01986032v1

Region Growing: When Simplicity Meets Theory - Region Growing Revisited in Feature Space and Variational Framework

C. Revol-Muller , T. Grenier , J.-L. Rose , A. Pacureanu , F. Peyrin
G. Csurka, M. Kraus, R. S. Laramee, P. Richard, J. Braz. Communications in Computer and Information Science Computer Vision, Imaging and Computer Graphics. Theory and Application, Springer, pp.426-444, 2013, 978-3-642-38241-3. ⟨10.1007/978-3-642-38241-3_29⟩
Book sections hal-00828473v1
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Comparative analysis of three advanced deep learning algorithms for Multiple Sclerosis lesion segmentation in FLAIR MRI

Yi Zhu , Thomas Grenier , C. Revol-Muller
IEEE ICSP’24 & 5th Sino-French Workshop 2024 “Medical Image Analysis and AI (MAI)”, IEEE Beijing Section, Beijing Jiaotong University, and Soochow University, Oct 2024, Suzhou, China, France
Conference papers hal-04767216v1
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Constrained non-negative networks for a more explainable and interpretable classification

Valentine Wargnier-Dauchelle , Thomas Grenier , Françoise Durand-Dubief , François Cotton , Michaël Sdika
Medical Imaging with Deep Learning, Jul 2024, Paris, France
Conference papers hal-04561860v1
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An unexpected confounder: how brain shape can be used to classify MRI scans ?

Valentine Wargnier-Dauchelle , Thomas Grenier , Michaël Sdika
Medical Imaging with Deep Learning, Jul 2024, Paris, France
Conference papers hal-04561863v1
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Deep learning for bone segmentation: towards automating failure load simulations

Emile Saillard , Marc Gardegaront , François Bermond , David Mitton , Jean-Baptiste Pialat
48e Congrès de la Société de Biomécanique, Oct 2023, Grenoble, France. pp.S27-S29
Conference papers hal-04288748v1
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Long-term follow-up of a LPC animal model using Optimal control MRI contrast targeting short T2 components

Claire Lemoine , Thomas Grenier , Eric van Reeth van Reeth , Hoai-Thu Nguyen , Benoît Vernier
ESMRMB 2023, Oct 2023, Basel, Switzerland
Conference papers hal-04446089v1
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Impact of MR sequences choice on deep learning segmentation of muscles

Maylis Jouvencel , Hoai-Thu Nguyen , Magalie Viallon , P Croisille , Thomas Grenier
2022 16th IEEE International Conference on Signal Processing (ICSP), Oct 2022, Beijing, China. pp.420-425, ⟨10.1109/ICSP56322.2022.9965354⟩
Conference papers hal-03919414v1
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Evaluation de l'apport d'irm de contraste générée par contrôle optimal pour l'étude du processus de demyelinisation/remyelinisation chez le rat a 11.7t

Claire Lemoine , Thomas Grenier , Eric van Reeth van Reeth , Hoai-Thu Nguyen , Benoît Vernier
RITS 2022, May 2022, Brest, France
Conference papers hal-04444875v1

UNet based automatic femur segmentation with few annotated data for bone fracture prediction: from pre-processing to segmentation assessments

Emile Saillard , Cyrille Confavreux , Marc Gardegaront , David Jicquel , Stéphane Cadot
Medical Image Analysis and Artificial Intelligence, 2nd Sino French Workshop, Oct 2021, Online, France. 2p
Conference papers hal-03406187v1
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A More Interpretable Classifier for Multiple Sclerosis

Valentine Wargnier-Dauchelle , Thomas Grenier , Françoise Durand-Dubief , François Cotton , Michaël Sdika
International Symposium on Biomedical Imaging (ISBI), Apr 2021, Nice, France. ⟨10.1109/ISBI48211.2021.9434074⟩
Conference papers hal-03212945v1
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A machine Learning pipeline to track dynamics of a population of nanoparticles during in situ Environmental Transmission Electron Microscopy in gases

Khuram Faraz , Thomas Grenier , Christophe Ducottet , Thierry Epicier
M&M2021, Microscopy Society of America (MSA), Aug 2021, Pittsburgh (virtual), United States. pp.2236-2237, ⟨10.1017/S1431927621008060⟩
Conference papers hal-03271239v1

Un Classifieur plus Interprétable pour la SEP

Valentine Wargnier-Dauchelle , Thomas Grenier , Françoise Durand-Dubief , François Cotton , Michaël Sdika
Congrès Société Française de Résonance Magnétique en Biologie et Médecine (SFRMBM), Sep 2021, Lyon, France
Conference papers hal-03212961v1

A Duplex Pipeline for the Generation of Realistic Echocardiographic Sequences with Doppler Imaging

Yunyun Sun , Khuram Faraz , Thomas Grenier , Patrick Clarysse , Damien Garcia
2020 IEEE International Ultrasonics Symposium (IUS), Sep 2020, Las Vegas, United States. pp.1-4, ⟨10.1109/IUS46767.2020.9251845⟩
Conference papers hal-03538705v1

A Duplex Pipeline for the Generation of Realistic Echocardiographic Sequences with Doppler Imaging

Yunyun Sun , Khuram Faraz , Thomas Grenier , Patrick Clarysse , Damien Garcia
2020 IEEE International Ultrasonics Symposium (IUS), Sep 2020, Las Vegas, United States. pp.1-4, ⟨10.1109/IUS46767.2020.9251845⟩
Conference papers hal-03149351v1
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Deep Learning Segmentation in 2D echocardiography using the CAMUS dataset : Automatic Assessment of the Anatomical Shape Validity

Sarah Leclerc , Erik Smistad , Andreas Ostvik , Frederic Cervenansky , Florian Espinosa
International conference on Medical Imaging with Deep Learning (MIDL 2019), Jul 2019, London, United Kingdom
Conference papers hal-02395245v1

Evaluation of local changes in femoral bone marrow during a mountain ultra-marathon with quantitative MRI

Hoai-Thu Nguyen , Thomas Grenier , Benjamin Leporq , Loïc Bey , Magalie Viallon
ISMRM, May 2019, Montréal, Canada
Conference papers hal-03006651v1
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Exploiting GPUs on distributed infrastructures for medical imaging applications with VIP and DIRAC

Sorina Camarasu-Pop , Carole Lartizien , Thomas Grenier , Axel Bonnet , Pascal Wassong
42nd international convention on information and communication technology, electronics and microelectronics, May 2019, Opatija, Croatia. pp.190-195, ⟨10.23919/mipro.2019.8757075⟩
Conference papers hal-02327867v1

Very Fast Acquisition of Tilt series in Environmental TEM Tomography: Tips and Tricks

Thierry Epicier , Thomas Grenier , Hussein Banjak , Voichita Maxim , Siddardha Koneti
XVIème colloque de la Société Française des Microscopies, Société Française des Microscopies (SFµ), Jul 2019, Poitiers, France
Conference papers hal-02378507v1
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RU-Net: A refining segmentation network for 2D echocardiography

Sarah Leclerc , Erik Smistad , Thomas Grenier , Carole Lartizien , Andreas Ostvik
2019 IEEE International Ultrasonics Symposium (IUS), Oct 2019, Glasgow, France. pp.1160-1163, ⟨10.1109/ULTSYM.2019.8926158⟩
Conference papers hal-02570017v1

Robust multi-atlas MRI segmentation with corrective learning for quantification of local quadriceps muscles inflammation changes during a longitudinal study in athletes

Hoai-Thu Nguyen , P. Croisille , Magalie Viallon , Charles de Bourguignon , Rémi Grange
ISMRM, Jun 2018, Paris, France
Conference papers hal-03006643v1

Deep Learning Applied to Multi-Structure Segmentation in 2D Echocardiography: A Preliminary Investigation of the Required Database Size

Sarah Leclerc , Erik Smistad , Thomas Grenier , Carole Lartizien , Andreas Ostvik
2018 IEEE International Ultrasonics Symposium (IUS), Oct 2018, Kobe, France. pp.1-4, ⟨10.1109/ULTSYM.2018.8580136⟩
Conference papers hal-02093095v1

Quantification of multispectral photoacoustic images: unsupervised unmixing methods comparison

Aneline Dolet , Rita Ammanouil , Thomas Grenier , Cédric Richard , Piero Tortoli
IEEE International Ultrasonic Symposium 2018, 2018, Kobe, Japan
Conference papers hal-01957861v1
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A fully Automatic and Multi-Structural Segmentation of the Left Ventricle and the Myocardium on Highly Heterogeneous 2D Echocardiographic Data

Sarah Leclerc , Thomas Grenier , Florian Espinoza , Olivier Bernard
2017 IEEE International Ultrasonic Symposium (IUS), Sep 2017, Washington, DC, United States. ⟨10.1109/ULTSYM.2017.8092632⟩
Conference papers hal-01609235v1

Unsupervised spatiotemporal video clustering a versatile mean-shift formulation robust to total object occlusions

Simon Mure , Thomas Grenier , Hugues Benoit-Cattin
The 41st IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP 2016), Mar 2016, Shanghai, China. pp.1536-1540, ⟨10.1109/ICASSP.2016.7471934⟩
Conference papers hal-01433000v1

New insight in perivenular lesion formation in multiple sclerosis on weekly susceptibility weighted images

S. Mure , C. R. G. Guttmann , T. Grenier , H. Benoit-Cattin , F. Cotton
24th annual meeting and exhibition ISMRM 2016, May 2016, Singapour, Singapore. pp.Abstract #1290
Conference papers hal-01452997v1

Classification of multiple sclerosis lesion evolution patterns a study based on unsupervised clustering of asynchronous time-series

Simon Mure , Thomas Grenier , Charles R G Guttmann , François Cotton , Hugues Benoit-Cattin
IEEE 13th International Symposium on Biomedical Imaging (ISBI 2016), Apr 2016, Prague, Czech Republic. ⟨10.1109/ISBI.2016.7493509⟩
Conference papers hal-01432982v1

Analyse dynamique hebdomadaire du développement péri-veinulaire des lésions actives de SEP par imagerie de susceptibilité magnétique

Roxana Ameli , Simon Mure , Charles R G Guttmann , Thomas Grenier , Hugues Benoit-Cattin
43rd Congress of the SFNR, Mar 2016, Paris, France. pp.91-93, ⟨10.1016/j.neurad.2016.01.056⟩
Conference papers hal-01432957v1

Environmental Transmission Electron Tomography: fast 3D analysis of nano-materials

Siddardha Koneti , Lucian Roiban , Voichita Maxim , Thomas Grenier , Priscilla Avenier
European Microscopy Congress, Aug 2016, Lyon, France. pp.29-30, ⟨10.1002/9783527808465.EMC2016.6438⟩
Conference papers hal-01871240v1

Spatial and spectral regularization for multispectral photoacoustic image clustering

Aneline Dolet , François Varray , Simon Mure , Thomas Grenier , Yubin Liu
IEEE International Ultrasonics Symposium (IUS 2016), Sep 2016, Tours, France. ⟨10.1109/ULTSYM.2016.7728439⟩
Conference papers hal-01437840v1

Unsupervised time-series clustering of distorted and asynchronous temporal patterns

Simon Mure , Thomas Grenier , Charles R G Guttmann , Hugues Benoit-Cattin
The 41st IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP 2016), Mar 2016, Shanghai, China. pp.1263-1267, ⟨10.1109/ICASSP.2016.7471879⟩
Conference papers hal-01432897v1

LOCALLY CONTROLLED REGULARIZED SPATIOTEMPORAL ANISOTROPIC DIFFUSION

P. Portejoie , S. Mure , H. Benoit-Cattin , T. Grenier
IEEE International Conference on Image Processing, Sep 2015, Québec, Canada
Conference papers hal-01206168v1

Feature space region growing

C. Revol-Muller , T. Grenier , T. Li , H. Benoit-Cattin
IEEE International Conference On Image Processing, Sep 2012, Orlando, United States. pp.2585 - 2588, ⟨10.1109/ICIP.2012.6467427⟩
Conference papers hal-00830362v1