«Neuroimagerie en recherche préclinique : de l in vivo au post mortem»

Transcription

1 «Neuroimagerie en recherche préclinique : de l in vivo au post mortem» «Biomedical processing of images, computer science and engineering lab» URA CNRS-CEA 2210 Service MIRCen, I²BM, CEA Fontenay-aux-Roses, France 07/12/2012DSV/I²BM AERES EVALUATION - FEBRUARY 10-12, 2010 Thierry.Delzescaux@cea.fr

2 Commissariat à l Energie Atomique P O L E S Défense CEA O P E R A T I O N N E L S P O L E S F O N C T I O N N E L 07/12/2012DSV/I²BM S AERES EVALUATION - FEBRUARY 10-12, 2010 Nucléaire Recherche Technologique Recherche Fondamentale Maîtrise des risques Stratégie et Relations Extérieures Gestion et Systèmes d Information Ressources Humaines et Formation Direction Sciences du Vivant Direction Sciences de la Matière Institut d imagerie biomédicale I²BM Institut de radiobiologie cellulaire et moléculaire Institut des maladies émergentes et des thérapies innovantes Institut de biologie et biotechnologies de Saclay Institut de recherche en technologies et sciences pour le vivant Institut de biologie structurale Institut de biologie environnementale et de biotechnologie Institut de génomique SHFJ NeuroSpin MIRCen Ci-NapS SRHI

3 Organisation de la Direction des Sciences du Vivant Direction des Sciences du Vivant G. Bloch Institut de biologie et biotechnologies de Saclay (IBITEC-S) Institut de recherche en technologies et sciences pour le vivant (IRTSV) Institut des maladies émergentes et des thérapies innovantes (IMETI) Institut d Imagerie Biomédicale (I²BM) A. Flury-Hérard Institut de radiobiologie cellulaire et moléculaire (IRCM) Institut de biologie environnementale et de biotechnologie (IBEB) Institut de Biologie Structurale (IBS) Institut de Génomique 07/12/2012DSV/I²BM AERES EVALUATION - FEBRUARY 10-12, 2010

4 Les missions de l I²BM Mettre en œuvre des programmes de recherches destinés à : Comprendre le fonctionnement du cerveau humain Développer des outils de diagnostic & l'approche de thérapeutiques innovantes Renforcer les collaborations avec la recherche académique française et internationale Assurer le lien avec les industriels de l imagerie et du médicament 07/12/2012DSV/I²BM AERES EVALUATION - FEBRUARY 10-12, 2010

5 I²BM, au cœur des problèmes de santé publique Epilepsie SHFJ SHFJ (Orsay) 1958 Parkinson Alzheimer Cancer Autisme Sciences cognitives NeuroSpin MIRCen CI-NAPS SRHI MIRCen (Fontenayaux-Roses) Neurospin (Saclay) /12/2012DSV/I²BM AERES EVALUATION - FEBRUARY 10-12,

6 Les plateformes technologiques CI-NAPS Des services reconnus et complémentaires Une maîtrise de savoirs et savoir-faire allant de la molécule à l homme Un large et puissant ensemble d instruments : IRM, TEP (Positon Emission Tomography), SPECT (Single Photon Emission Computed Tomography), 07/12/2012DSV/I²BM AERES EVALUATION - FEBRUARY 10-12, 2010 Des équipes scientifiques pluridisciplinaires Cyclotron Labo. de biologie cellulaire Labo. de biologie moléculaire IRM 7T IRM 3T Caméra TEP MEG SRHI IRM 7T TEP Labo. de biologie cellulaire Labo. de biologie moléculaire IRM 3T IRM 7T IRM 11,7T homme IRM 17,65T MEG Cyclotron Labo. de production de radiopharmaceutique Labo. de contrôle qualité 3 caméras à positons 3 gamma caméras Micro TEP IRM 1,5T

7 Thierry DELZESCAUX «bio-picsel» group, URA CNRS-CEA 2210 Service MIRCen, I²BM, CEA Fontenay-aux-Roses, France T. Delzescaux A-S. Hérard N. Souedet D. Thenadey Collaboration avec le LNAO J-F. Mangin 07/12/2012 DELZESCAUX CMM, T.

8 Cerebral imaging. MIRCen facilities In vivo imaging Post mortem imaging Function Anatomy Anatomy Function PET FDG, etc MRI 7T Blockface photographs Histology Cresyl, Nissl Autoradiography µ-pet 7T Varian Cryostat Dimension 3D 3D 3D/2D 2D 2D Images 07/12/2012DSV/I²BM T. AERES DELZESCAUX EVALUATION - FEBRUARY 10-12, CMM,

9 In vivo / Post mortem imaging techniques Advantages / Disadvantages In vivo imaging Post mortem imaging Before L After L Longitudinal studies 3D imaging Fast acquisition time Technical limitations Difficult to use Recent High cost 07/12/2012DSV/I²BM AERES EVALUATION - FEBRUARY 10-12, 2010 Complementary + High spatial resolution Easy to use Low cost Variety of stainings Single observation 2D imaging Tedious

10 Background: applications Merging of information acquired in vivo and post mortem: - at microscopic and macroscopic level, - anatomy and function. Quantitative validation of PET (instrumentation) Evaluation of PET abilities (follow-up) FDG, etc 1.5T, 3T Photographs Cresyl, Nissl, etc. Autoradiography PET MRI Photo PM anatomy PM function In vivo anatomo-functional co-registration (brain, whole body) 3D exploitation of the data Statistical analysis (intra and inter-subjects) 07/12/2012

11 Applications In vivo and post mortem co-registration FDG, etc 1.5T, 3T Photographies Cresyl, Nissl, etc. PET MRI Photo PM anatomy In vivo anatomofunctional registration 07/12/2012 DELZESCAUX CMM, T.

12 Applications In vivo and post mortem Co-registration FDG, etc 1.5T, 3T Photographies Cresyl, Nissl, etc. Autoradiographie PET MRI Photo PM anatomy PM function In vivo anatomofunctional registration 3D data analysis 07/12/2012 T. DELZESCAUX CMM,

13 ENVIRONNEMENT DE DÉVELOPPEMENT I2BM Développement algorithmiques (bibliothèques + commandes codées en C++) AIMS Diffusion des exécutables Anatomist Logiciel de visualisation des images (visualisation, fusion, segmentation) BrainVISA Interface graphique de scripting (organisation de base de données, traitement) Intégration de protocoles dédiés à l imagerie biologique dans BrainVISA Interface graphique de reconstruction 3-D 07/12/2012 Accès aux moyens de calcul du CEA (CCRT)

14 BrainRAT: Brain Reconstruction and Analysis Toolbox A freely available toolbox for the 3D reconstruction of anatomo-functional brain sections GOAL: BRAINRAT TOOLBOX IS A BRAINVISA ADD-ON PACKAGE PROVIDING ADDITIONAL PROCESSES AND FUNCTIONALITIES RELATING TO 3D RECONSTRUCTION AND ANALYSIS OF POST MORTEM BRAIN SECTIONS DOWNLOAD SITE: SUPPORT: brainrat@cea.fr Main contributions: Successful creationand free releaseof an automatedand generictoolbox for processing of post mortem brain sections in optimal conditions Intensively applied to Nissl stained and [ 14 C]-2DGautoradiographic sections and validated in rats and mice Successfully tested on other imaging modalities(immunohistochemistry, etc.) and species(primates) Could now be extended to various biological investigations(morphology, 07/12/2012DSV/I²BM lesion extension, development) AERES and domains EVALUATION of application(neurodegenerative - diseases, ischemia and FEBRUARY cancer) 10-12, 2010 PRÉSENTATION GÉNÉRALE I²BM

15 3-D post mortem reconstruction 07/12/2012DSV/I²BM T. AERES DELZESCAUX EVALUATION - FEBRUARY 10-12, CMM,

16 3-D PHOTOGRAPHIC MODALITY Cryostat Cutting process Histological staining Banana effect First prototype developed 07/12/2012DSV/I²BM T. AERES DELZESCAUX EVALUATION - FEBRUARY 10-12, CMM,

17 3-D PHOTOGRAPHIC MODALITY 3-D photographic volume Coronal view + Axial view R V B Sagittal view 3D 07/12/2012DSV/I²BM AERES EVALUATION - FEBRUARY 10-12, 2010

18 TISSUE SECTION DIGITIZATION Optimized acquisition of the data Histological staining Flatbed scanner Column acquisition Several dozens of sections can be digitized at once Automated extraction and stacking of the sections 07/12/2012DSV/I²BM T. AERES DELZESCAUX EVALUATION - FEBRUARY 10-12, CMM,

19 3-D POST MORTEM VOLUME / MOUSE ALZHEIMER S MODEL P H O T O C R E S Y L APP/PS1de9 A U T O R A D I O B A M /12/2012DSV/I²BM T. AERES DELZESCAUX EVALUATION - FEBRUARY 10-12, CMM,

20 Applications in Alzheimer s disease 1) Metabolism changes 2) Amyloid load assessment 3) In vivo / post mortem co-registration 07/12/2012DSV/I²BM T. AERES DELZESCAUX EVALUATION - FEBRUARY 10-12, CMM,

21 1) Metabolism changes T. 07/12/2012 DELZESCAUX CMM,

22 1) Metabolism changes in Alzheimer s disease Material: - APP-PS1 (n=3), - PS1 control (n=4). Hemibrain studied Photographic volume Reconstruction strategy: - Use of reference volume, Histological volume - Multimodality 3-D consistency, - Photography : reconstruction + spatial normalisation. 07/12/2012DSV/I²BM T. AERES DELZESCAUX EVALUATION - FEBRUARY 10-12, CMM, Autoradiographical volume

23 1) Voxel-wise metabolism analysis [1/2] Synthesis of glucose changes detected: - : cortex Cg, hippocampus Rad and Mol, thalamus Th, - : hippocampus CA1, CA3, Pir cortex, Limitations: - Huge amount of data, - Reconstruction step, - A single measurement. Interests: - Without anatomical a priori, - Possibility to perform exploratory studies (identification of structures / sub-structures involved), - Anatomo-functional data, high resolution (~20-40 µm). 07/12/2012DSV/I²BM T. AERES DELZESCAUX EVALUATION - FEBRUARY 10-12, CMM,

24 1) Voxel-wise metabolism analysis [2/2] Surface rendering Improve our understanding of pathophysiological processes Possibility to quantitatively evaluate drug efficacy / new therapeutic strategies Possibility to apply this methodology to other species (mouse, rat, microcebe, etc.) 3-D Hippocampus 07/12/2012DSV/I²BM T. AERES DELZESCAUX EVALUATION - FEBRUARY 10-12, CMM, Dubois et al, Neuroimage, 2010

25 APPLICATION OF THE NUMERIC ATLAS Use of the atlas to supervise automated data segmentation (histology, autoradiography, MRI, micropet) (Jessica Lebenberg; thesis) Right hippocampus Left hippocampus 3D volume rendering of the atlas 07/12/2012

26 CONSTRUCTION OF A DIGITAL ATLAS OF MOUSE BRAIN Pre-processing applied to the downloaded files Coronal view Axial view Sagittal view MRI volume Labeled volume Downloaded volumes Processed volumes 07/12/2012DSV/I²BM AERES EVALUATION - FEBRUARY 10-12, 2010

27 ANALYSIS OF AN ANATOMO-FUNCTIONAL POST MORTEM DATASET USING A 3D DIGITAL ATLAS 2 3 Section-to-section registration Section-to-section registration Lebenberg et al., ISMRM and ISBI conferences nci/g 1 Stacking 0 2 3D-reconstructed histological data 1 Block-face volume Lebenberg et al., Neuroimage D-reconstructed autoradiographic data MRI volume Atlas volume A- Registration strategy[a,b,c]: Estimation of linear and non-linear parameters to register the MRI to 3D-reconstructed data Warping of the atlas using estimated deformation parameters T. 07/12/2012 DELZESCAUX CMM, CEA-MIRCen T. Delzescaux, Master «Biologie intégrative et physiologie»,

28 COMBINATION OF ATLAS-BASED AND VOXEL-WISE APPROACHES Identification of clusters computed with a voxel-wise approach 1) Use of registered atlas to localize clusters Areas of lower levels of glucose uptake in APP/PS1 than in PS1 mice SPM results* Atlas-based Segmentation results Cingular cortex Rest of cortex Hippocampus Thalamus Striatum 2) Use of registered atlas to analyze clusters Distribution of clusters (in %) in different ROIs of the atlas Lebenberg et al., EMBC conf /12/2012DSV/I²BM AERES EVALUATION - FEBRUARY 10-12, 2010 T. DELZESCAUX CMM, Lebenberg et al., Neuroimage 2011

29 DETECTION OF METABOLIC CHANGES IN AD MOUSE MODEL Lebenberg et al, Neuroimage, 2010 Dubois et al, Neuroimage, D digital atlas Photographical volume Combined approaches Histological volume Statistical Parametric Mapping analysis (SPM) without anatomical a priori Lebenberg et al, Neuroimage, 2011 Autoradiographical volume 07/12/2012 3D post mortem reconstruction Automated detection of regions presenting metabolic changes Automated labelling of these regions based on the use of digital atlas

30 2) Amyloid load assessment T. 07/12/2012 DELZESCAUX CMM,

31 2) AMYLOID LOAD ASSESSMENT Perspectives - Amyloid plaques, - Tangles. 3-D Digital atlas 2% 1000 AP ~10 parameters biomarker 07/12/2012

32 2) Amyloid plaques segmentation Congo Red staining: (frontal cortex, hippocampus) Congo Red Pre-processing Segmentation Amyloid plaques Téboul et al., EMBC, 2007 Féki et al., MICCAI, 2007 Analysis 07/12/2012DSV/I²BM T. AERES DELZESCAUX EVALUATION - FEBRUARY 10-12, CMM,

33 2) Amyloid plaques segmentation T. 07/12/2012 DELZESCAUX CMM,

34 2) Amyloid plaques segmentation APP-PS1 BAM10 staining 4800 dpi in plane resolution 07/12/2012DSV/I²BM AERES EVALUATION FEBRUARY 10-12, 2010 T. Delzescaux, CEA-MIRCen Master «Biologie intégrative et physiologie»,

35 Virtual microscopy Tests on image scanner Leica SCN400 Thionine 6E10 CD68 Autoloader device 07/12/2012 Confidential CEA / DSV / I2BM / MIRCen

36 3) In vivo / post mortem co-registration T. 07/12/2012 DELZESCAUX CMM,

37 3) In vivo / post mortem co-registration 6 mois 9 mois 14 mois 20 mois M. Dhenain team (post mortem MRI) 07/12/2012

38 3) In vivo / post mortem co-registration PET-anat MRI Photograph H&E Glioma IV / PM Dubois et al., ESMI, 2010 (Poster award) Dubois, Dauguet and Delzescaux, «Ex Vivo and In Vitro Cross Calibration Methods, Small Animal Imaging (book chapter, 2011) PBR IV / PM Vimentine GFAP 07/12/2012 Photograph Axial incidence Lavisse et al., J. Neuroscience, 2012 MRI / PET

39 Collaborators A-S. Hérard N. Souedet J. Dauguet D. Thenadey M. Vandenberghe M. Sadouni 07/12/2012 A. Dubois (IMNC, Orsay) CEA-MIRCen URA 2210: P. Hantraye F. Condé G. Bonvento M. Dhenain C. Jan F. Petit E. Diguet E. Brouillet V. Lebon C. Escartin M. Guillermet LNAO: J.-F. Mangin D. Rivière Y. Cointepas D. Geffroy V. Frouin ACADEMIC: ANSTO, Australia Ecole Centrale Paris IMNC, Orsay U678, Paris