J. Franken and . Darcourt, Amplitude-based data selection for optimal retrospective reconstruction in micro-SPECT, Physics in Medicine and Biology, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00799381

M. Breuilly, G. Malandain, J. Guglielmi, R. Marsault, T. Pourcher et al., Amplitudebased data selection for optimal retrospective reconstruction in micro- SPECT, Physics in Medicine and Biology, vol.58, issue.8, p.26572674, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00799381

M. Breuilly, G. Malandain, N. Ayache, J. Darcourt, T. Pourcher et al., Simulated breath-hold reconstruction in micro-SPECT: Application to peritoneal metastases expressing NIS as reporter gene, Journal of Nuclear Medicine Meeting Abstracts, vol.53, issue.1, p.2381, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00759929

M. Breuilly, G. Malandain, N. Ayache, J. Guglielmi, T. Pourcher et al., Imagebased motion detection in 4D images and application to respiratory motion suppression, Proceedings of the 10th IEEE International Symposium on Biomedical Imaging 2013 (ISBI'13), 2013.
URL : https://hal.archives-ouvertes.fr/hal-00799368

M. Breuilly, A. Histace, C. Portefaix, B. Matuszewski, and F. Precioso, Segmentation des muscles oculomoteurs en irm cerebro-orbitaire pour l'aide au diagnostic de l'exophtalmie, 22eme Colloque GRETSI 2009, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00475242

M. Breuilly, G. Malandain, P. Franken, J. Darcourt, and T. Pourcher, Prise en compte du mouvement respiratoire du Miscellaneous petit animal pour la reconstruction 3D TEMP synchronisée: application aux métastases péritonéales

C. Portefaix, A. Histace, M. Breuilly, and B. Matuszewski, RECH-WS-10 Segmentation semi-automatique en IRM3T des muscles oculomoteurs dans le suivi de la maladie de Grave-Basedow, Actes des Journées Françaises de Radiologie (JFR), 2009.
DOI : 10.1016/S0221-0363(09)76311-5

M. Breuilly, Investigation of medical active contour image segmentation techniques, 2009.

M. Breuilly, G. Malandain, N. Ayache, P. Franken, J. Darcourt et al., Denition of motionless phases for monitoring gated reconstruction of SPECT images in alive mice, ICVSS, 2010.

M. Breuilly, G. Malandain, N. Ayache, P. Franken, J. Darcourt et al., Simulated breath-hold reconstruction in micro-SPECT: application to peritoneal metastases expressing NIS as reporter gene. 2ème colloque MIBO, 2012. 2.1 Presentation of pre-clinical imaging system eXplore speCZT CT 120
URL : https://hal.archives-ouvertes.fr/hal-00759929

4. Spect, Comparison between pressure signal and image-based measures computed on 4D, p.52

S. Forman and . Acton, Numerical methods that usually work. MAA, p.110, 1990.

R. Bellman and K. Åström, On structural identiability, Math. Biosci, vol.7, issue.92, pp.32939-171, 1970.

[. Bai, M. Brady, M. Bai, and . Brady, Regularized B-spline deformable registration for respiratory motion correction in PET images Motion correction and attenuation correction for respiratory gated PET images, Physics in Medicine and Biology IEEE Transactions on Medical Imaging, vol.54, issue.18, pp.271936-3635165, 2009.

I. Buvat, J. Darcourt, and P. Franken, Single Photon Emission Computed Tomography, Tomography, chapter 13, p.11, 2009.
DOI : 10.1002/9780470611784.ch13

URL : https://hal.archives-ouvertes.fr/in2p3-00012855

. Büther, . Dawood, . Stegger, M. Wubbeling, . Schäfers et al., List mode-driven cardiac and respiratory gating in PET Detection of respiratory tumour motion using intrinsic list mode-driven gating in positron emission tomography, BKS10] SH Bartling, J Kuntz, and W Semmler. Gating in small-animal cardio-thoracic CT. Methods, pp.67481-33231527, 2009.

. References, M. Laurel, . Burk, Z. Yueh, M. Lee et al., Non-contact respiration monitoring for invivo murine micro computed tomography: characterization and imaging applications, Phys Med Biol, vol.57, issue.41, pp.574963-57, 2012.

M. Breuilly, G. Malandain, J. Guglielmi, R. Marsault, T. Pourcher et al., Amplitude-based data selection for optimal retrospective reconstruction in micro-SPECT, Physics in Medicine and Biology, vol.58, issue.8, pp.265774-187, 2013.
DOI : 10.1088/0031-9155/58/8/2657

URL : https://hal.archives-ouvertes.fr/hal-00799381

A. Bundschuh, M. Martinez-moller, . Essler, S. Sg-nekolla, M. Ziegler et al., Local motion correction for lung tumours in PET/CT???first results, Bor86] Gunilla Borgefors. Distance transformations in digital images. Computer Vision, Graphics, and Image Processing, pp.58344-71, 1986.
DOI : 10.1007/s00259-008-0868-0

. Bettinardi, D. Picchio, . Muzio, . Gianolli, C. Mc-gilardi et al., Detection and compensation of organ/lesion motion using 4D-PET/CT respiratory gated acquisition techniques Respiratory motion detection and correction in ECG-gated SPECT: a new approach, Radiother Oncol Korean Journal of Radiology, vol.96, issue.17, pp.3116-414907, 2008.

[. Bettinardi, M. Rapisarda, E. Berman, M. F. Shahn, C. Weiss et al., Number of partitions (gates) needed to obtain motion-free images in a respiratory gated 4D-PET/CT study as a function of the lesion size and motion displacement The routine tting of kinetic data to models: A mathematical formalism for digital computers, Medical Physics Biophysical Journal Phys Med Biol, vol.36554758, issue.2311, pp.27587-175, 1962.

G. Chang, . Chang, . Pan, O. Clark, and . Mawlawi, Implementation of an Automated Respiratory Amplitude Gating Technique for PET/CT: Clinical Evaluation, Journal of Nuclear Medicine, vol.51, issue.1, pp.1624-1665, 2010.
DOI : 10.2967/jnumed.109.068759

. Cavanaugh, . Johnson, . Price, . Kurie, D. Travis et al., In Vivo Respiratory-Gated Micro-CT Imaging in Small-Animal Oncology Models, Molecular Imaging, vol.3, issue.1, pp.5562-5593, 2004.
DOI : 10.1162/153535004773861723

E. Clarkson and M. Kupinski, Global Compartmental Pharmacokinetic Models for Spatiotemporal SPECT and PET Imaging, SIAM Journal on Imaging Sciences, vol.2, issue.1, pp.203225-175, 2009.
DOI : 10.1137/080715226

J. Margaret and . Cook, The anatomy of the laboratory mouse, p.71, 1965.

. Soto, P. Montenegro, . García-mohammad-dawood, X. Buther, K. P. Jiang et al., Extraction of the respiratory signal from small-animal CT projections for a retrospective gating method Respiratory motion correction in 3-D PET data with advanced optical ow algorithms, Physics in Medicine and Biology IEEE Transactions on Medical Imaging, vol.53, issue.178, pp.468395-2711641175, 2008.

. Nm-de-clerck, H. Meurrens, . Weiler, . Van-dyck, . Van-houtte et al., High-resolution Xray microtomography for the detection of lung tumors in living mice, Neoplasia, vol.6, issue.16, pp.3749-3777, 2004.

A. Orsolya-dohan, V. De-la-vieja, C. Paroder, M. Riedel, M. Artani et al., The sodium/iodide Symporter (NIS): characterization , regulation, and medical signicance, Endocr Rev, vol.24, issue.1, pp.4877-70, 2003.

R. Daouk, . Fin, M. Bailly, and . Meyer, Respiratory-gated positron emission tomography and breathhold computed tomography coupling to reduce the inuence of respiratory motion: methodology and feasibility, Acta radiologica, vol.50, issue.18, pp.14455-14484, 1987.

M. Dawood, T. Kösters, M. Fieseler, F. Büther, X. Jiang et al., Motion correction in respiratory gated cardiac PET/CT using multi-scale optical ow Lung motion correction on respiratory gated 3-D PET/CT images Small-animal SPECT and SPECT/CT: important tools for preclinical investigation, Medical Image Computing and Computer-Assisted Intervention IEEE Trans Med Imaging J Nucl Med, vol.11, issue.1137, pp.15562-15597, 1989.

R. Philippe, J. Franken, C. Guglielmi, M. Vanhove, M. Koulibaly et al., Distribution and Dynamics of 99m Tc-Pertechnetate Uptake in the Thyroid and Other Organs Assessed by Single- Photon Emission Computed Tomography in Living Mice A note on Foss's method of obtaining initial estimates for exponential curve tting by numerical integration A method of exponential curve tting by numerical integration Optimization of a retrospective technique for respiratory-gated high speed micro-CT of free-breathing rodents, Thyroid Biometrics Biometrics Physics in Medicine and Biology, vol.20, issue.100 11, pp.51926-175821827815821, 1970.

K. Godfrey, Compartmental models and their application, p.169, 1983.

. Grotus, . Reader, J. Stute, . Rosenwald, I. Giraud et al., Fully 4D list-mode reconstruction applied to respiratory-gated PET scans, Physics in Medicine and Biology, vol.54, issue.6, pp.170521-170562, 2009.
DOI : 10.1088/0031-9155/54/6/020

T. Grant, . Gullberg, W. Bryan, A. Reutter, . Sitek et al., Dynamic single photon emission computed tomography-basic principles and cardiac applications Kinetics of the human thyroid trap: a compartmental model, Physics in Medicine and Biology Journal of Nuclear Medicine, vol.55, issue.96, pp.17578995-175, 1978.

A. Hwang, . Bl-franc, B. Gullberg, and . Hasegawa, Assessment of the sources of error aecting the quantitative accuracy of SPECT imaging in small animals, Phys Med Biol, vol.53, issue.40, pp.223352-185, 2005.

[. Hudson, S. Richard, and . Larkin, Ordered Subsets of Projection Data, pp.601609-601652, 1994.

M. Hatt, A. Le-maitre, D. Wallach, H. Fayad, and D. Hofmeyr, Comparison of dierent methods of incorporating respiratory motion for lung cancer tumor volume delineation on PET images: a simulation study Stomach scanning after intravenous 99mTc administration . A preliminary report. South African medical journal/Suid-Afrikaanse tydskrif vir geneeskunde, Physics in Medicine and Biology, vol.57, issue.3623, pp.740930-41572, 1967.

R. Huesman, G. Reutter, G. Zeng, and . Gullberg, Kinetic parameter estimation from SPECT cone-beam projection measurements, Physics in Medicine and Biology, vol.43, issue.4, pp.97382-175, 1998.
DOI : 10.1088/0031-9155/43/4/024

V. Joseph, N. Hajnal, A. Saeed, E. J. Oatridge, . Williams et al., Detection of subtle brain changes using subvoxel registration and subtraction of serial mr images, Journal of Computer Assisted Tomography, vol.19, issue.5, pp.677691-677728, 1995.

Y. Hori, . Takasuka, . Mutoh, . Kitahashi, . Kojima et al., Periodic analysis of urethaneinduced pulmonary tumors in living A/J mice by respirationgated X-ray microcomputed tomography, Cancer science, vol.99, issue.9, pp.17747-17779, 2008.

J. A. Jacquez, Compartmental analysis in biology and medicine

J. Jiao, . Ge-searle, C. Tziortzi, . Salinas, J. Gunn et al., Spatial-temporal pharmacokinetic model based registration of 4d brain pet data Spatiotemporal Image Analysis for Longitudinal and Time-Series Image Data Comparison of the gastrointestinal anatomy, physiology , and biochemistry of humans and commonly used laboratory animals Molecular-genetic imaging based on reporter gene expression, Lecture Notes in Computer Science Biopharmaceutics & Drug Disposition J Nucl Med, vol.7570, issue.49 2, pp.10012-176351, 1995.

J. Kuntz, . Dinkel, . Zwick, . Bauerle, . Grasruck et al., Fully automated intrinsic respiratory and cardiac gating for small animal CT 4D maximum a posteriori reconstruction in dynamic SPECT using a compartmental modelbased prior, Phys Med Biol Physics in Medicine and Biology, vol.55, issue.92, pp.206985-4115531574, 2001.

G. Kovalski, . Israel, . Keidar, . Frenkel, H. Sachs et al., Correction of Heart Motion Due to Respiration in Clinical Myocardial Perfusion SPECT Scans Using Respiratory Gating Dynamic modeling of lung tumor motion during respiration, J Nucl Med Phys Med Biol, vol.48, issue.18KM1110, pp.630636-630677, 1941.

[. Konukoglu, X. Pennec, O. Clatz, and N. Ayache, Tumor Growth Modeling in Oncological Image Analysis
DOI : 10.1016/B978-012373904-9.50027-1

URL : https://hal.archives-ouvertes.fr/inria-00616081

S. Krueger, A. Roessner, and D. Kuester, Murine models of H. pylori-induced gastritis and gastric adenocarcinoma . Pathology, research and practice, pp.599607-197, 2011.

. Lamare, . Cresson, C. Savean, . Cheze-le-rest, D. Aj-reader et al., Respiratory motion correction for PET oncology applications using ane transformation of list mode data AMIDE: a free software tool for multimodality medical image analysis, Biologic behavior of 99m Tc from 99m Tc-pertechnetate ion. Progress in nuclear medicine, pp.121401317145-93, 0198.

. Lamare, . Mj-ledesma-carbayo, . Cresson, . Kontaxakis, C. Santos et al., Listmode-based reconstruction for respiratory motion correction in PET using non-rigid body transformations, Phys Med Biol, vol.34, issue.17, pp.525187204-525187245, 2007.

. Livieratos, . Rajappan, . Stegger, . Schäfers, P. Bailey et al., Respiratory gating of cardiac PET data in listmode acquisition, Eur J Nucl Med Mol Imaging, vol.33, issue.29, pp.5848-5889, 2006.

R. Lagarias, J. Reeds, P. Wright, and . Lucignani, Convergence Properties of the NelderMead Simplex Method in Low Dimensions Respiratory and cardiac motion correction with 4D PET imaging: shooting at moving targets, SIAM Journal on Optimization Eur J Nucl Med Mol Imaging, vol.9, issue.362, pp.1121473159-1121473200, 1998.

[. Menke, K. Atkins, and . Buckley, Compensation methods for head motion detected during PET imaging, Nuclear Science Symposium and Medical Imaging Conference, pp.1638-1642, 1994.
DOI : 10.1109/23.485971

R. Maroy, C. Boisgard, . Comtat, Y. Jego, . Fontyn et al., Quantitative organ time activity curve extraction from rodent PET images without anatomical prior, Medical Physics, vol.6, issue.4, pp.150717-190, 2010.
DOI : 10.1118/1.3327454

P. Mancosu, . Danna, . Bettinardi, . Ma-aquilina, . Lobefalo et al., Semiautomatic method to identify the best phase for gated RT in lung region by 4D-PET/CT acquisitions, Medical Physics, vol.47, issue.1, pp.35462-35493, 2011.
DOI : 10.1080/02841860802256442

[. Moody, A. Mark, S. Zoccola, and . Mantero, Derivation of respiratory signals from multi-lead ECGs, Computers in cardiology, pp.19-37, 1985.

. Martiniova, . Schimel, . Lai, . Limpuangthip, K. Kvetnansky et al., In vivo micro-CT imaging of liver lesions in small animal models, Methods, vol.50, issue.1, pp.205-246, 2010.
DOI : 10.1016/j.ymeth.2009.05.016

[. Nehmeh and Y. Erdi, Respiratory Motion in Positron Emission Tomography/Computed Tomography: A Review, Seminars in Nuclear Medicine, vol.38, issue.3, pp.16776-16817, 2008.
DOI : 10.1053/j.semnuclmed.2008.01.002

Y. Sa-nehmeh, . Erdi, . Ke-rosenzweig, . Schoder, . Sm-larson et al., Reduction of respiratory motion artifacts in PET imaging of lung cancer by respiratory correlated dynamic PET: methodology and comparison with respiratory gated PET, Journal of Nuclear Medicine, vol.27, issue.10, pp.4416448-4416479, 2003.

N. , J. A. Nelder, and R. Mead, A novel respiratory tracking system for smart-gated PET acquisition A Simplex Method for Function Minimization, Med Phys The Computer Journal, vol.38, issue.108, pp.5318-41308313, 1965.

C. Nioche, M. Soret, E. Gontier, M. Lahutte, G. Dutertre et al., Evaluation of quantitative criteria for glioma grading with static and dynamic Comparison study of temporal regularization methods for fully 5D reconstruction of cardiac gated dynamic SPECT Block Matching: A General Framework to Improve Robustness of Rigid Registration of Medical Images, NYK12] Xiaofeng Niu, Yongyi Yang, and Michael a King Third International Conference on Medical Robotics, pp.817-176552342, 1935.

R. Penrose, A generalized inverse for matrices, Proc. Cambridge Philos. Soc, p.51406413, 1955.
DOI : 10.1093/qmath/2.1.189

[. Pysz, J. Gambhir, and . Willmann, Molecular imaging: current status and emerging strategies, Clinical Radiology, vol.65, issue.7, pp.500-516, 2010.
DOI : 10.1016/j.crad.2010.03.011

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150531

Y. Dmitri, . Riabkov, V. Edward, and . Bella, Blind identication of the kinetic parameters in three-compartment models, Physics in Medicine and Biology, vol.49, issue.5, pp.63964-175, 2004.

M. Reutter, G. Gullberg, and R. Huesman, Respiratory Motion Compensation in Emission Tomography Kinetic parameter estimation from attenuated SPECT projection measurements, IEEE Transactions on Nuclear Science, vol.45, issue.92, pp.343007-3013, 1998.

[. Reutter, G. Gullberg, R. Reutter, R. Gullberg, and . Huesman, Direct least-squares estimation of spatiotemporal distributions from dynamic SPECT projections using a spatial segmentation and temporal B-splines Eects of temporal modelling on the statistical uncertainty of spatiotemporal distributions estimated directly from dynamic SPECT projections, Physics in Medicine and Biology, vol.19, issue.92, pp.43450-175, 2000.

M. Reyes, P. Malandain, M. Koulibaly, J. Gonzalez-ballester, and . Darcourt, Model-based respiratory motion compensation for emission tomography image reconstruction, Physics in Medicine and Biology, vol.52, issue.12, pp.3579600-3579641, 2007.
DOI : 10.1088/0031-9155/52/12/016

URL : https://hal.archives-ouvertes.fr/inria-00616030

[. Ritt, . Vija, T. Hornegger, and . Kuwert, Absolute quantication in SPECT, Eur J Nucl Med Mol Imaging, vol.38, issue.1, p.6977, 1940.

[. Rubinow and A. Winzer, Compartment analysis: An inverse problem, Mathematical Biosciences, vol.11, issue.3-4, pp.203247-175, 1971.
DOI : 10.1016/0025-5564(71)90085-X

P. J. Slomka, D. Dey, C. Przetak, U. E. Aladl, and R. P. Baum, Automated 3-Dimensional Registration of Stand-Alone 18F-FDG Whole-Body PET with CT, Journal of Nuclear Medicine, vol.44, issue.7, pp.115667-115687, 2003.

J. Paul, . Schleyer, J. Michael, . Doherty, F. Sally et al., Retrospective data-driven respiratory gating for PET/CT, Phys Med Biol, vol.54, issue.41SOM11, p.58, 2009.

. Srk-+-06-]-nikolas-sakellios, N. Rubio, . Karakatsanis, . Kontaxakis, . Loudos et al., GATE simulations for small animal SPECT/PET using voxelized phantoms and rotating-head detectors, Nuclear Science Symposium Conference Record, pp.20002003-60, 2006.

W. Segars, . Tsui, . Frey, S. Johnson, C. Berr et al., Development of a 4-D digital mouse phantom for molecular imaging research Mechanical ventilation of mice, Mol Imaging Basic research in cardiology, vol.6, issue.1306, pp.14959-192, 2000.

[. Travaglini, C. Lamberti, M. Debie, and . Ferri, Respiratory signal derived from eight-lead ECG, Computers in Cardiology 1998. Vol. 25 (Cat. No.98CH36292), pp.6568-6586, 1998.
DOI : 10.1109/CIC.1998.731718

K. Umeda, K. Tani, M. Tsuda, M. Kobayashi, S. Ogata et al., High resolution SPECT imaging for visualization of intratumoral heterogeneity using a SPECT/CT scanner dedicated for small animal imaging Optimal gating compared to 3D and 4D PET reconstruction for characterization of lung tumours, Annals of Nuclear Medicine Eur J Nucl Med Mol Imaging, vol.26, issue.385, pp.6776-19384355, 2011.

D. Visvikis, . Lamare, . Bruyant, Y. Turzo, C. Bizais et al., Correction de mouvement respiratoire en References TEP/TDM, 9è Conférence Internationale de l'ACOMEN : L'instrumentation en, p.153159, 2007.
DOI : 10.1016/j.mednuc.2007.02.002

D. Welti, . Gerig, . Ew-radü, G. Kappos, and . Székely, Spatio- Temporal Segmentation of Active Multiple Sclerosis Lesions in Serial MRI Data, Information Processing in Medical Imaging, pp.43845-193, 2001.

H. Watabe, Y. Ikoma, Y. Kimura, M. Naganawa, M. Shidahara et al., PET kinetic analysis-compartmental model Super:resolution in respiratory synchronized positron emission tomography Respiratory motion blur identication and reduction in ungated thoracic PET imaging, XYY11] Quansheng Xu, Kehong Yuan, and Datian Ye Physics in medicine and biology, pp.5838-5874, 2006.

L. Gengsheng, . Zeng, T. Grant, D. J. Gullberg, and . Kadrmas, Closed-form kinetic parameter estimation solution to the truncated data problem, Physics in Medicine and Biology, vol.55, issue.92, pp.745368-175, 2010.