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CREATIS Laboratory



The Centre de Recherche en Acquisition et Traitement de l’Image pour la Santé - CREATIS (Research Centre for Image Acquisition and Processing for Health) is a multidisciplinary laboratory of 200 people encompassing a wide spectrum of skills in medical imaging. Located in the Auvergne-Rhône-Alpes region, it is playing a major role in the field of health technology. It is renowned for its expertise in magnetic resonance imaging, ultrasound, X-ray, and optics, with related skills in physics, mathematics, computer science and instrumentation. CREATIS holds all the skills needed to optimise each step of the imaging procedure from acquisition to data analysis and medical interpretation. Through a long standing and close collaboration with hospitals, CREATIS is contributing to the development of a personalised and predictive medicine of future by the identification of imaging biomarkers for the early diagnosis, monitoring of diseases, the prediction of its progression and the response to treatment. Ischemic heart diseases, multiple sclerosis, cancer and stroke are among the most widespread diseases and main causes of death or disability that are studied at CREATIS.
 
  • CREATIS_team-MAGICS_illus1
    Intraoperative functional brain mapping based on RGB imaging: detection of activated cortical areas © Charly Caredda, Laurent Mahieu Williame, Raphaël Sablong, Michaël Sdika, Jacques Guyotat and Bruno Montcel
    CREATIS_team-MAGICS_illus1
  • CREATIS_team-MAGICS_illus2
    Ex vivo tractography of a rat brain obtained with mrtrix3, when setting up a multiparametric MRI protocol on the new 11.7T system, for monitoring a demyelinisation/remyelination rat model © Denis Grenier, Fabien Chauveau (CRNL-BioRan), Sophie Gaillard, Olivier Beuf, Françoise Durand Dubief, Hélène Ratiney
    CREATIS_team-MAGICS_illus2
    Ex vivo tractography of a rat brain obtained with mrtrix3, when setting up a multiparametric MRI protocol on the new 11.7T system, for monitoring a demyelinisation/remyelination rat model (axial view, pulsed-gradient spin echo, 12 b-values, 3 hours acquisition time, 0.125x0.125 mm2 in plane pixel size, 25 slices with a thickness of 0.45 mm) resonance and optICS: from measure to biomarker]
  • CREATIS_MYRIAD_illus1
    Supervised segmentation of a patient's MRI sequence and 3D reconstruction via the Boltzmann network method of a cerebral stent implanted in a patient to treat a cerebral aneurysm. © Source: CSC doctoral thesis by Ge Fei under the supervision of Guy Courbebaisse (CREATIS-INSA Lyon-2020)
    CREATIS_MYRIAD_illus1
  • CREATIS_MYRIAD_illus2
    Supervised segmentation of a patient's MRI sequence and 3D reconstruction via Boltzmann's network method of a patient's skull in which a giant cerebral aneurysm has been detected © Source: CSC doctoral thesis by Ge Fei under the supervision of Guy Courbebaisse (CREATIS-INSA Lyon-2020)
    CREATIS_MYRIAD_illus2
  • CREATIS_team-MYRIAD_illus3
    Pulmonary vascular segmentation of a chest CT-angiography (iodine contrast) in a Covid-19 patient (COVID-CTPRED cohort, CHU Saint-Etienne, Clinical Trials N°: NCT04377685) © Titouan Poquillon, Odyssée Merveille, Pierre Croisille, Carole Frindel
    CREATIS_team-MYRIAD_illus3
  • CREATIS_team-TOMORADIO_illus1
    Segmentation of osteons in a 3D image of human cortical bone (synchrotron micro-CT, voxel size 0.7µm): Green: edge of osteons, Grey: Havers' channels, Yellow: osteocyte lacunae, Red: micro-cracks © R Gauthier, C Olivier, M Langer, F Peyrin / D Mitton (IFSTTAR), H Follet (LYOS)
    CREATIS_team-TOMORADIO_illus1
  • CREATIS_team-ULTIM_illus1
    Plane wave imaging for high-frame-rate echography. A 3-D simulation with SIMUS © Damien GARCIA
    CREATIS_team-ULTIM_illus1
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NATIONAL AND INTERNATIONAL COLLABORATIONS AND NETWORKS
CREATIS strongly contributes to the coordination or is significantly involved in large research projects at the regional scale:
  • LabEx PRIMES (Physics Radiobiology Medical Imaging and Simulation) created in 2012;
  • Labex CeLyA (Lyon Acoustics Centre) includes all public research stakeholders in acoustics on the Lyon Saint-Etienne site;
  • IngeLySE is the federation of CNRS research in engineering from Lyon and Saint-Etienne;
  • FIL (Federation of informatics at Lyon).
CREATIS is co-leading an International Research project METISLAB with China for the period 2019-2023. Recently, a Cultural and Scientific Collaboration Agreement between University of Florence and UCBL1 was signed in the field of ultrasound and medical imaging. The international activities is materialized by collaboration at the European level within several European projects or bi-national ANR project. CREATIS has very fruitful international collaborations with 60 collaborations in 21 countries. CREATIS is mainly co-publishing with Italy (8.6%), USA (8.4%), Germany (8.0%), China (7.9%), Belgium (7.4%), UK (6.6%), Switzerland 5(.3%) and Canada (4.9%).


RESEARCH TEAMS INVOLVED IN THE MANUTEH-SLEIGHT GRADUATE SCHOOL

Modeling & analYsis foR medIcal imAging and Diagnosis - MYRIAD

The MYRIAD team was created in 2019 from the merging of two previous teams MOTIVATE and Images & models. The goal is to develop innovative methodology on medical image analysis and modeling for heart, lung and brain applications. One particularity of the team is to gather scientific members and clinicians around targeted medical applications. The objectives are to progress in the understanding of patho-physiological processes, to better answer well-defined clinical questions, to improve diagnosis and patient follow-up, including the impact of a given treatment.
Main research axes are:
  • Machine learning for medical data analysis
  • Modeling and simulations
  • Innovations in brain, cardiovascular and lung applications
  • CREATIS_MYRIAD_illus1
    Supervised segmentation of a patient's MRI sequence and 3D reconstruction via the Boltzmann network method of a cerebral stent implanted in a patient to treat a cerebral aneurysm. © Source: CSC doctoral thesis by Ge Fei under the supervision of Guy Courbebaisse (CREATIS-INSA Lyon-2020)
    CREATIS_MYRIAD_illus1
  • CREATIS_MYRIAD_illus2
    Supervised segmentation of a patient's MRI sequence and 3D reconstruction via Boltzmann's network method of a patient's skull in which a giant cerebral aneurysm has been detected © Source: CSC doctoral thesis by Ge Fei under the supervision of Guy Courbebaisse (CREATIS-INSA Lyon-2020)
    CREATIS_MYRIAD_illus2
  • CREATIS_team-MYRIAD_illus3
    Pulmonary vascular segmentation of a chest CT-angiography (iodine contrast) in a Covid-19 patient (COVID-CTPRED cohort, CHU Saint-Etienne, Clinical Trials N°: NCT04377685) © Titouan Poquillon, Odyssée Merveille, Pierre Croisille, Carole Frindel
    CREATIS_team-MYRIAD_illus3
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PUBLICATIONS
  • Qin Y., Zheng H., Huang X., Yang J. and Zhu Y. M. (2019).«Pulmonary nodule segmentation with CT sample synthesis using adversarial networks». Med Phys, 46(3): 1218-1229
  • Franchi A., Valette S., Agier R., Prost R., Kéchichan R., Fanton L. (2019). « The prospects for application of computational anatomy in forensic anthropology for sex determination ». Forensic Science International, 297:156-160
  • Seners P., Delepierre J., Turc G., Henon H., Piotin M., Arquizan C., Cho T. H., Lapergue B., Cottier J. P., Richard S., Legrand L., Bricout N., Mazighi M., Dargazanli C., Nighoghossian N., Consoli A., Debiais S., Bracard S.,
  • Naggara O., Leclerc X., Obadia M., Costalat V., Berthezene Y., Tisserand M., Narata A. P., Gory B., Mas J. L., Oppenheim C., Baron J. C. and Collaborators P.-R. (2019).«Thrombus Length Predicts Lack of Post Thrombolysis Early Recanalization in Minor Stroke With Large Vessel Occlusion». Stroke, 50(3): 761-764
  • Bernard O., Lalande A., Zotti C., Cervenansky F., Yang X., Heng P.- A. H., Cetin I., Lekadir K., Camara O., Ballester M. A. G., Sanroma G., Napel S., Petersen S., Tziritas G., Grinias E., Khened M. H., Kollerathu V. A. H., Krishnamurthi G. H., Rohé M.-M. H., Pennec X., Sermesant M., Isensee F., Jager P., Maier-Hein K. H., Full P., Wolf I., Engelhardt S. H., Baumgartner C. H., Koch L. H., Wolterink J., Isgum I., Jang Y., Hong Y. H., Patravali J., Jain S. H., Humbert O. H., Jodoin P.-M. (2018). « Deep Learning Techniques for Automatic MRI Cardiac Multi-structures Segmentation and Diagnosis: Is the Problem Solved? ». IEEE Transactions on Medical Imaging, 37(11):2514-2525
  • Duchateau N., Sermesant M., Delingette H. and Ayache N. (2018).«Model-Based Generation of Large Databases of Cardiac Images: Synthesis of Pathological Cine MR Sequences From Real Healthy Cases». IEEE Trans Med Imaging, 37(3): 755-766
More about the MYRIAD team's work

Ultrasound Imaging - ULTIM

ULTIM research focuses on physical and signal interaction for ultrasound imaging systems and the development of methods to extract relevant parameters from images/signals to characterise biological tissues. The ULTIM team covers all stages of the development of ultrasound imaging techniques, from sensor to patient. The control of the device of acquisition allows the team to act on the image formation process. The radio frequency (RF) images and customised images are beamformed with the raw signals directly provided by the ultrasound probe. The image formation is adapted to the methods which the team develops. Mutually, the methods take into account the spatiotemporal impulse response of the imaging system and the beamformed image properties. The methods that ULTIM develops lean on physical models to estimate the parameters of elasticity, viscosity, non-linearity, scattering, anisotropy, etc. of biological media. Whenever possible, the methods are developed to operate in real time, ie the rate of acquisition of images by the system and are extended to 3D data.

ULTIM's main research axes
  • Ultrasound imaging for cancer detection and therapy follow up
  • Ultrasound imaging for cardiac imaging
  • Doppler and vascular motion imaging
  • Novel methods and instruments for ultrasound imaging
  • CREATIS_team-ULTIM_illus1
    Plane wave imaging for high-frame-rate echography. A 3-D simulation with SIMUS © Damien GARCIA
    CREATIS_team-ULTIM_illus1
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PUBLICATIONS
  • Franceschini E., Escoffre JM., Novell A., Auboire L., Mendes V., Benane Y., Bouakaz A., Basset O. Quantitative ultrasound in ex vivo fibrotic rabbit livers. Ultrasound in Medicine and Biology, Elsevier, 2019. hal-02143906
  • Faurie J., Baudet M., Porée J., Cloutier G., Tournoux F., Garcia D. (2019). « Coupling myocardium and vortex dynamics in diverging-wave echocardiography ». IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control
  • Garcia-2019-PLoS ONE Garcia D., Harbaoui B., Van De Hoef T., Meuwissen M., Nijjer S., Echavarria-Pinto M., Davies J., Piek J., Lantelme P., De Rosa S. (2019). « Relationship between FFR, CFR and coronary microvascular resistance – Practical implications for FFR-guided percutaneous coronary intervention ». PLoS ONE, 14(1):e0208612
  • Lantelme P., Eltchaninoff H., Rabilloud M., Souteyrand G., Dupré M., Spaziano M., Becle C., Riche B., Durand E., Bouvier E., Dacher J.-N., Courand P., Cassagnes L., Dávila Serrano E. E., Motreff P., Boussel L., Lefèvre T., Harbaoui B. (2019). « Development of a Risk Score Based on Aortic Calcification to Predict 1-Year Mortality After Transcatheter Aortic Valve Replacement ». JACC: Cardiovascular Imaging, 12(1):123-132
  • Benane Y., Bujoreanu D. J., Lavarello R., Varray F., Escoffre J.-M. J., Novell A., Cachard C., Basset O. (2018). « Experimental Implementation of a Pulse Compression Technique Using Coherent Plane-Wave Compounding ». IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, 65(6):1025-1036

Tomographic imaging and therapy with radiation - TOMORADIO

The team develops new algorithmic methods for tomography image reconstruction and simulations for radiation-based imaging, through inverse problem methods and variance reduction techniques for Monte-Carlo simulations. It focuses on innovative imaging systems such as photon-counting spectral CT, X-ray phase-contrast, optical single-pixel camera, Compton camera or proton radiography. The main applications are linked to 3D imaging of bone tissue in osteoarticular research and to advanced radiation therapy and nuclear imaging for cancer treatments, in partnership with biology and clinical collaborators.
The scientific activities of the team are:
  • Inverse problems in imaging
  • Simulation and imaging in radiation therapy
  • Translational research activities
  • CREATIS_team-TOMORADIO_illus1
    Segmentation of osteons in a 3D image of human cortical bone (synchrotron micro-CT, voxel size 0.7µm): Green: edge of osteons, Grey: Havers' channels, Yellow: osteocyte lacunae, Red: micro-cracks © R Gauthier, C Olivier, M Langer, F Peyrin / D Mitton (IFSTTAR), H Follet (LYOS)
    CREATIS_team-TOMORADIO_illus1
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PUBLICATIONS
  • Characterization of a beam-tagging hodoscope for hadrontherapy monitoring Oreste Allegrini, J. P. Cachemiche, C.P.C. Caplan, Bruno Carlus, Xiushan Chen, Sébastien Curtoni, Denis Dauvergne, Rodolphe Della Negra, Marie-Laure Gallin-Martel, J. Hérault, Jean Michel Létang, Christian Morel, Etienne Testa, Yannick Zoccarato Journal of Instrumentation, IOP Publishing, In press
  • Inversion of nonlinear spectral CT pile up model Bruno Sixou International Journal of Tomography and Simulation, CESER Publications, 2021, 34 (1), pp.1-16
  • Impact of the reperfusion status for predicting the final stroke infarct using deep learning Noëlie Debs, Tae-Hee Cho, David Rousseau, Yves Berthezène, Marielle Buisson, Omer Eker, Laura Mechtouff, Norbert Nighoghossian, Michel Ovize, Carole Frindel Neuroimage-Clinical, Elsevier, 2021, 29, pp.102548.
  • Structure and Concept of the Benchmark for Vesselness Filters with focus on Reproducibilty and Future Evaluations Jonas Lamy, Bertrand Kerautret, Odyssée Merveille, Nicolas Passat Reproducible Research in Pattern Recognition (RRPR), 2021, Milan, Italy
More about the TOMORADIO team's work
 

Magnetic resonance and optICS: from measure to biomarker - MAGICS

The goal of the team is to develop new ways of measuring MR and optics based indirect parameters and to search for new biomarkers in a rapid, robust, reproducible and reliable way while handling physiological movements. The biomarkers are sought to come from mechanical, biochemical or structural properties of tissues under investigation. Our aspirations are to combine the physics-based innovations behind the creation of mechanical, biochemical or structural information, from the point of view of acquisition strategies or instrumentation and anchor developments in clinical practice. Our scientific objectives can be summed up in 4 main points:
  1. Going from the proof of concept realized in the previous five years to the application on prelinical and clinical studies
  2. Generating and labeling the physics behind imaging data in order to integrate radiomic and deep learning approaches. This scientific objective will be made in close collaboration with Team MYRIAD. 3) Pursuing upstream developments in acquisition or instrumentation
  3. Supporting typical projects from the team which federate several researchers of the team (Endoluminal MR/optic) or the unit (transversal project TipTop, IDM4, Tumor-ID, MUSIC).
Our team has experience and knowledge in many applied magnetic resonance aspects going from theory of MR physics to medical validation and applications. Bolstered by its experience and taking into account that Magnetic Resonance is a modality that often plays a central role for many biomedical imaging investigations, our team members are involved in most of transversal, inter-team projects.

Main research axes are:
  • New Acquisition strategy using optimization methods
  • Identification of biomarkers through multiparametric quantitative imaging
  • Towards new biomarkers through instrumentation developments
  • CREATIS_team-MAGICS_illus1
    Intraoperative functional brain mapping based on RGB imaging: detection of activated cortical areas © Charly Caredda, Laurent Mahieu Williame, Raphaël Sablong, Michaël Sdika, Jacques Guyotat and Bruno Montcel
    CREATIS_team-MAGICS_illus1
  • CREATIS_team-MAGICS_illus2
    Ex vivo tractography of a rat brain obtained with mrtrix3, when setting up a multiparametric MRI protocol on the new 11.7T system, for monitoring a demyelinisation/remyelination rat model © Denis Grenier, Fabien Chauveau (CRNL-BioRan), Sophie Gaillard, Olivier Beuf, Françoise Durand Dubief, Hélène Ratiney
    CREATIS_team-MAGICS_illus2
    Ex vivo tractography of a rat brain obtained with mrtrix3, when setting up a multiparametric MRI protocol on the new 11.7T system, for monitoring a demyelinisation/remyelination rat model (axial view, pulsed-gradient spin echo, 12 b-values, 3 hours acquisition time, 0.125x0.125 mm2 in plane pixel size, 25 slices with a thickness of 0.45 mm) resonance and optICS: from measure to biomarker]
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PUBLICATIONS
  • Alston L., Mahieu-Williame L., Hébert M., Kantapareddy P., Meyronet D., Rousseau D., Guyotat J., Montcel B. (2019). « Spectral complexity of 5-ALA induced PpIX fluorescence in guided surgery: a clinical study towards the discrimination of healthy tissue and margin boundaries in high and low grade gliomas ». Biomedical optics express, 10(5):2478
  • Viallon M., Leporq B., Drinda S., Wilhelmi De Toledo F., Galusca B., Ratiney H., Croisille P. (2019). « Chemical-Shift-Encoded Magnetic Resonance Imaging and Spectroscopy to Reveal Immediate and Long-Term Multi-Organs Composition Changes of a 14-Days Periodic Fasting Intervention: A Technological and Case Report ». Frontiers in nutrition, 6 :5.
  • Sdika M., Alston L., Rousseau D., Guyotat J., Mahieu-Williame L., Montcel B. (2019). « Repetitive Motion Compensation for Real Time Intraoperative Video Processing ». Medical Image Analysis, 53:1-10
  • Nemeth A., Segrestin B., Leporq B., Seyssel K., Faraz K., Sauvinet V., Disse E., Valette P.-J., Laville M., Ratiney H., Beuf O. (2018). « 3D Chemical Shift-Encoded MRI for Volume and Composition Quantification of Abdominal Adipose Tissue During an Overfeeding Protocol in Healthy Volunteers ». Journal of Magnetic Resonance Imaging, selected for Young Investigator Award at ISMRM 2019.
  • Pilar Sango Solanas, Kevin Tse Ve Koon, Hélène Ratiney, Fabien Millioz, Cyrielle Caussy, Olivier Beuf « Harmonic wideband simultaneous dual‐frequency MR Elastography”. NMR in Biomedicine, Wiley, 2021, 34 (2), pp.e4442. ⟨10.1002/nbm.4442⟩