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Latest publications and patents



  1. ​"A radiological score for the assessment of tuberculosis progression: Validation in mouse models", Ortega-Gil, A., A. Munoz-Barrutia, J. J. Roca, L. Guijarro-Lopez, and J. J. Vaquero. 2020, Tuberculosis (Edinb), 121: 101918.

  2. "Optical Properties of Tissues in the Near Infrared: Their Relevance for Optical Bioimaging", Marcos-Vidal, Asier, Juan José Vaquero, and Jorge Ripoll. 2020. Near Infrared-Emitting Nanoparticles for Biomedical Applications (Springer, Cham).

  3. "Real-Time 3D PET Image with Pseudoinverse Reconstruction", López-Montes, Alejandro, Pablo Galve, José Manuel Udias, Jacobo Cal-González, Juan José Vaquero, Manuel Desco, and Joaquín L Herraiz. 2020.Applied Sciences, 10: 2829.

  4. "Simplified Statistical Image Reconstruction for X-ray CT With Beam-Hardening Artifact Compensation", Abella, M., C. Martinez, M. Desco, J. J. Vaquero, and J. A. Fessler. 2020. IEEE Trans Med Imaging, 39: 111-18.



  1. "SiPM-based PET detector module for a 4π span scanner", Perez-Benito, D, R Chil, JM Udias, M Desco, and JJ Vaquero. 2019. , Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 936: 18-21.

  2. "X-ray-based virtual slicing of TB-infected lungs", Ortega-Gil, A., J. J. Vaquero, M. Gonzalez-Arjona, J. Rullas, and A. Munoz-Barrutia. 2019. Sci Rep, 9: 19404.

  3. "Computed Tomography-Based Biomarker for Longitudinal Assessment of Disease Burden in Pulmonary Tuberculosis", Gordaliza, P. M., A. Munoz-Barrutia, L. E. Via, S. Sharpe, M. Desco, and J. J. Vaquero. 2019. , Mol Imaging Biol, 21: 19-24.

  4. "Applications of Light-Sheet Microscopy in Microdevices", Albert-Smet, I., A. Marcos-Vidal, J. J. Vaquero, M. Desco, A. Munoz-Barrutia, and J. Ripoll. 2019. Front Neuroanat, 13: 1.


  1. “Unsupervised CT Lung Image Segmentation of a Mycobacterium Tuberculosis Infection Model”, P. M. Gordaliza, A. Muñoz-Barrutia, M. Abella, M. Desco, S. Sharpe, and J. J. Vaquero, Sci. Rep., vol. 8, no. 1, p. 9802

  2. “Improving PET Quantification of Small Animal [68Ga]DOTA-Labeled PET/CT Studies by Using a CT-Based Positron Range Correction”, J. Cal-Gonzalez et al., Mol. Imaging Biol., vol. 20, no. 4, pp. 584–593  


  1. “Optimized CUBIC protocol for 3D imaging of chicken embryos at single-cell resolution,” Development, Apr. 2017, doi:10.1242/dev.145805.

  2. "Sub-surface laser engraving techniques for scintillator crystals: methods, applications and advantages", IEEE Transactions on Radiation and Plasma Medical Sciences, DOI 10.1109/TRPMS.2017.2714265  


  1. “Evaluation of PeneloPET Simulations of Biograph PET/CT Scanners,” IEEE Trans. Nucl. Sci., vol. 63, no. 3, pp. 1367–1374, Jun. 2016, DOI: 10.1109/TNS.2016.2527789.

  2. “Experimental validation of gallium production and isotope-dependent positron range correction in PET,” Nucl. Instruments Methods Phys. Res. Sect. A Accel. Spectrometers, Detect. Assoc. Equip., vol. 814, pp. 110–116, 2016, DOI: 10.1016/j.nima.2016.01.013.

  3. “Automatic Cardiac Self-Gating of Small-Animal PET Data,” Mol. Imaging Biol., vol. 18, no. 1, pp. 109–116, Feb. 2016, DOI: 10.1007/s11307-015-0868-y.

  4.  “Functional segmentation of dynamic PET studies: Open source implementation and validation of a leader-follower-based algorithm,” Comput. Biol. Med., vol. 69, pp. 181–188, Feb. 2016, DOI: 10.1016/j.compbiomed.2015.12.012.

  5. “3D imaging in CUBIC-cleared mouse heart tissue: going deeper,” Biomed. Opt. Express, vol. 7, no. 9, pp. 3716–3720, Sep. 2016, DOI: 10.1364/BOE.7.003716.

  6. “Design and Development of a Wireless Infrared EEG Recorder for chicken embryos,” 2016 IEEE Int. Symp. Med. Meas. Appl., pp. 487–492, 2016.

  7. “3D imaging of the cleared intact murine colon with light sheet microscopy,” SPIE BiOS, p. 97130Q, 2016, DOI: 10.1117/12.2212039.

  8. “Tissue-Dependent and Spatially-Variant Positron Range Correction in 3D PET,” IEEE Trans. Med. Imaging, vol. 35, no. 1, pp. 369–369, Jan. 2016, DOI: 10.1109/TMI.2015.2511958.


  1. “Positron Emission Tomography: Current Challenges and Opportunities for Technology Advances in Clinical and Pre-Clinical Imaging Systems”, Annual Review of Biomedical Engineering, Vol. 17, pp 385–414, December 2015

  2. “Tissue-Dependent and Spatially-Variant Positron Range Correction in 3D PET”, IEEE Transactions On Medical Imaging, vol. 34, no. 11, Nov 2015

  3. “Fluorescence multi-scale endoscopy and its applications in the study and diagnosis of gastro-intestinal diseases: set-up design and software implementation”, Proc. of SPIE Vol. 9531 953111-1

  4. “Automatic Cardiac Self-Gating of Small-Animal PET Data”, Mol Imaging Biol, DOI: 10.1007/s11307-015-0868-y, 2015

  5. “Recovery and normalization of triple coincidences in PET”, Medical Physics, vol. 42, no. 3, pp. 1398-1401, doi: 10.1118/1.4908226, 2015

  6. “Development and validation of an open source quantification tool for DSC-MRI studies”, Computers in Biology and Medicine, vol. 58, pp. 56–62, doi: 10.1016/j.compbiomed.2015.01.002, 2015



  1. “Application of the compressed sensing technique to self-gated cardiac cine sequences in small animals”, Magn Reson Med. Aug;72(2):369-80. doi: 10.1002/mrm.24936, 2014

  2. “Comparison of methods to reduce myocardial 18F-FDG uptake in mice: calcium channel blockers versus high-fat diets”, PLoS One. 2014 Sep 19;9(9):e107999. doi: 10.1371/journal.pone.0107999, 2014

  3. “Dual-exposure technique for extending the dynamic range of x-ray flat panel detectors”, Phys. Med. Biol., vol. 59, pp. 421–439, doi: 10.1088/0031-9155/59/2/421, 2014

  4. “Modification of the TASMIP x-ray spectral model for the simulation of microfocus x-ray sources”, Med. Phys., vol. 41, pp. 011902, doi: 10.1118/1.4837220, 2014



  1. ”jClustering, a n Open Framework for the Development of 4D Clustering Algorithms”, PLoS One, vol. 8, no. 8, doi: 10.1371/journal.pone.0070797, 2013

  2. “Automatic TAC extraction from dynamic cardiac PET imaging using iterative correlation from a population template” Computer Methods And Programs In Biomedicine, vol. 111, no. 2, pp.308-314, doi: 10.1016/j.cmpb.2013.04.010, 2013

  3. “MRI compatibility of position-sensitive photomultiplier depth-of-interaction PET detectors modules for in-line multimodality preclinical studies”, Nuclear Instruments and Methods in Physics Research A, vol. 702, pp. 83-87, 2013

  4. "Use of Split Bregman denoising for iterative reconstruction in fluorescence diffuse optical tomography". J Biomed Opt, 18(7): 076016 (8 pp), 2013

  5. "Positron range estimations with PeneloPET". Phys Med Biol, 58(15): 5127-5152, 2013

  6. "Monte Carlo study of the effects of system geometry and antiscatter grids on cone-beam CT scatter distributions". Med Phys, 40: 051915 (19pp), 2013

  7. "Improved dead-time correction for PET scanners: application to small-animal PET". Phys Med Biol, 58(7): 2059-2072, 2013

  8. "Massively parallelizable list-mode reconstruction using a Monte Carlo-based elliptical Gaussian model". Med Phys, 40(1): 012504 (11pp), 2013



  1. “A method for small-animal PET/CT alignment calibration”, Phys. Med. Biol. 57 N199-N207–7518, 2012

  2. “Misalignments calibration in small-animal PET scanners based on rotating planar detectors and parallel-beam geometry”, Phys. Med. Biol. 57 7493–7518, 2012

  3. “Approach to Assessing Myocardial Perfusion in Rats Using Static [13N]-Ammonia Images and a Small-Animal PET”, Molecular Imaging and Biology, vol. 14, pp. 541-545, 2012

  4. “Accuracy of CT-based attenuation correction in PET/CT bone imaging”, Phys. Med. Biol., vol. 57, pp. 2477–2490, 2012

  5. “NEMA NU 4-2008 Comparison of Preclinical PET Imaging Systems”, J Nuc Med, Vol. 53, no. 8, pp. 1300-1309, 2012

  6. “Waking-like brain function in embryos”, Current Biology, vol. 22, pp. 852-861, 2012

  7. “Software architecture for multi-bed FDK-based reconstruction in X-ray CT scanners”, Computer Methods and Programs in Biomedicine, vol. 107, pp. 218-232, 2012

  8. “A method for small-animal PET/CT alignment calibration”, Phys Med Biol, Vol. 57, pp. 199–207, 2012

  9. "Influence of absorption and scattering on the quantification of fluorescence diffuse optical tomography using normalized data", J Biomed Opt 17, 036013, DOI:10.1117/1.JBO.17.3.036013, 2012



  1. “GPU-Based Fast Iterative Reconstruction of Fully 3D PET Sinograms”, IEEE Transactions on Nuclear Science, vol. 58, no. 5, pp. 2257-2263, 2011

  2. “Fully 3D GPU PET reconstruction”, Nuclear Instruments and Methods in Physics Research A, vol. 648, pp. S169-S171, 2011

  3. “Study of CT-based positron range correction in high resolution 3D PET imaging”, Nuclear Instruments and Methods in Physics Research A, vol. 648, pp. S172-S175, 2011

  4. “Fluorescence diffuse optical tomography using the split Bregman method”, Med Phys 38, 6275-84, 2011

  5. "Split operator method for fluorescence diffuse optical tomography using anisotropic diffusion regularisation with prior anatomical information", Biomedical Optics Express 2(9), 2632–2648, 2011

  6. “Feasibility of U-curve method to select the regularization parameter for fluorescence diffuse optical tomography in phantom and small animal studies”, Optics Express, vol. 19, no. 12, pp. 11490-11506, 2011

  7. “Chronic Cannabinoid Administration to Periadolescent Rats Modulates the Metabolic Response to Acute Cocaine in the Adult Brain”, Molecular Imaging and Biology, vol. 13, no. 3, pp. 411-415, 2011

  8. “NEMA NU 4-2008 Performance Measurements of Two Commercial Small-Animal PET Scanners: ClearPET and rPET-1”, IEEE Transactions on Nuclear Science, vol. 58, no. 1, pp. 58-65, 2011



  1. “Effects of the super bialkali photocathode on the performance characteristics of a position-sensitive depth-of-interaction PET detector module”, IEEE Transactions on Nuclear Science, vol. 57, no. 5, pp. 2437-2441, 2010

  2. “A SPECT Scanner for Rodent Imaging Based on Small-Area Gamma Cameras”, IEEE Transactions on Nuclear Science, vol. 57, no. 5, pp. 2524-2531, 2010

  3. “Data acquisition electronics for gamma ray emission tomography using width-modulated leading-edge discriminators”, Phys Med Biol, 55(15): 4291-4308, 2010

  4. “Performance evaluation of SiPM photodetectors for PET imaging in the presence of magnetic fields”, Nuclear Instruments and Methods in Physics Research A, vol. 613, pp. 308–316, 2010



  1. M. Abella, J.J. Vaquero, M.L. Soto-Montenegro, E. Lage, M. Desco. “Sinogram bow-tie filtering in FBP PET reconstruction”, Med Phys, 36(5): 1663-1671, 2009

  2. “Design and performance evaluation of a coplanar multimodality scanner for rodent imaging”, Phys Med Biol, 54(18): 5427-5441, 2009

  3. “The chemokine receptor CXCR4 and the metalloproteinase MT1-MMP are mutually required during melanoma metastasis to lungs”, Am J Pathol, 174(2): 602-612, 2009

  4. “Automated Method for Small-Animal PET Image Registration with Intrinsic Validation”, Molecular Imaging and Biology, vol. 11, pp. 107-113, Mar 2009

  5. “Assessment of airway distribution of transnasal solutions in mice by PET/CT imaging”, Molecular Imaging and Biology, 11(4):263-268, 2009

  6. “PeneloPET, a Monte Carlo PET simulation tool based on PENELOPE: features and validation”, Phys Med Biol, 54: 1723-1742, 2009

  7. “Detection of Visual Activation in the Rat Brain Using 2-deoxy-2-[18F]fluoro-D-glucose and Statistical Parametric Mapping (SPM)”, Molecular Imaging and Biology, vol. 11, pp. 94-99, 2009

  8. “Automatic Quantification of Histological Studies in Allergic Asthma”, Cytom Part A, 75A(3): 271-277, 2009

  9. “Research at the Medical Imaging Laboratory, CIBERSAM CB07/09/0031”, Eur J Psychiat, 23(Supl.): 43-48, 2009



  1. “Real-time digital timing in positron emission tomography”, IEEE Trans Nucl Sci, vol. 55, no. 5, pp. 2531-2540, 2008

  2. “Assessment of a New High-Performance Small-Animal X-ray Tomograph”, IEEE Trans Nucl Sci, 55(3), pp. 898-905, 2008

  3. "Extraction of the respiratory signal from small-animal CT projections for a retrospective gating method". Phys Med Biol, 53, pp. 4683-4695, 2008

  4. “Augmented acquisition of cocaine self-administration and altered brain glucose metabolism in adult female but not male rats exposed to a cannabinoid agonist during adolescence”, Neuropsychopharmacol, 33(4):806-13, Mar, 2008

  5. “High resolution image in bone biology II. Review of the literature”, Med Oral Patol Oral Cir Bucal; Jan1;13(1):E31-5, 2008



  1. “High resolution image in bone biology I. Review of the literature”, Med Oral Patol Oral Cir Bucal;12(1):E454-8, 2007

  2. “Effects of MDMA on blood glucose levels and brain glucose metabolism”, Eur J Nucl Med Mol I, 34(6): 916-925, 2007

  3. “Noise and physical limits to maximum resolution of PET images”, Nucl Instrum Meth A, 580(2): 934-937, 2007



  1. “New embedded digital front-end for high resolution PET scanner”, IEEE T Nucl Sci; 53(3): 770-775, 2006

  2. “FIRST: Fast Iterative Reconstruction Software for (PET) Tomography”. Phys Med Biol; 51(18): 4547-4565, 2006

  3. “Modeling the acquisition front-end in high resolution gamma-ray imaging”, IEEE T Nucl Sci; 53(3): 1150-1155, 2006

  4. “Performance Evaluation of the GE Healthcare eXplore VISTA Dual-Ring Small-Animal PET Scanner”, J Nucl Med; 47: 1891-1900, 2006



  1. “ROC evaluation of statistical wavelet-based analysis of brain activation in [15O]-H2O PET scans”, Neuroimage, 24(3): 763-770, 2005



  1. “Experiment assessment of mass effects in the rat: implications for small animal PET imaging”, Nuclear Medicine and Biology 31(6): 771-779, 2004

  2. “Automatic Tuning and Matching of a Small Multifrequency Saddle Coil at 4.7 T”, Magnet Reson Med, 51: 869-873, 2004

  3. “Method for Bias Field Correction of Brain T1-Weighted Magnetic Resonance Images Minimizing Segmentation Error”, Hum Brain Mapp, 22: 133-144, 2004

  4. “Resolution recovery in Turbo Spin Echo using segmented Half Fourier acquisition”, Magn Reson Imaging, 22: 369-378, 2004



Book chapters​

  1. A Sisniega, M Desco, JJ Vaquero. “Design and assessment principles of semiconductor Flat-Panel detector based X-Ray micro-CT systems for small animal imaging”. Book chapter in “Integrated Microsystems and Nanotechnology: MEMs, Photonic and Biological Interfaces”, CRC Press, pp. 309-335, ISBN: 978-1-4398-3620-0, 2012

  2. J Lafuente, JJ Vaquero, J Sánchez. Secuencias en resonancia magnética. In: “Aprendiendo los fundamentos de la Resonancia Magnética”, E Oleaga, J Lafuente, Editorial Médica Panamericana, 2006, pp 33-43. ISBN 84-9835-121-9

  3. JJ Vaquero. “Medicina nuclear e Imagen Molecular”, in Ingeniería Biomédica e Imágenes Médicas, Ediciones de la Universidad Castilla-La Mancha, 2006, pp145-158, ISBN 84-8427-426-8

  4. JJ Vaquero. Imagen Molecular. In: Cáncer. P García-Barreno, D Espinós-Pérez and M Cascales-Angosto, Eds. Madrid: Instituto de España, 2003; pp 283-310. ISBN 84-85559-57-6


Patents in exploitation

  1. Planning System for Intraoperative Radiation Therapy and Method for Carrying out Said Planning, US 2011/0052036 A1, 03/03/2011

  2. Procedimiento y dispositivo para la detección y discriminación de eventos válidos en detectores de radiación gamma, PCT/ES2009/070456, 26/10/2009

  3. Incubadora para imagen con radiación no ionizante, WO 2009/077626 A1, 25/06/2009

  4. Multi-Modality Tomography Apparatus, US 2009/0213983 A1, 27/08/2009

  5. Sistema de planificación para radioterapia intraoperatoria y procedimiento para llevar a cabo dicha planificación, PCT/ES2008/000240, 14/04/2008, WO 2009/127747 A1, 22/10/2009

  6. Incubator for non-ionizing radiation imaging, US2011/0125010A1, 19/12/2007

  7. Incubadora para imagen con radiación no ionizante, PCT/ES2007/070214, 19/12/2007

  8. Multi-Modality Tomography Apparatus, PCT/ES2006/070150, 26/10/2006

  9. Tomography scanner with axially discontinuous detector array, PCT/US2004/030656, 20/09/2004

  10. Compact modular, configurable base for position sensitive photomultipliers, US 6,642,493 B1, 04/11/2003

  11. A multi-slice PET scanner from side-looking phoswich scintillators, PCT/US98/22875, WO 99/24848, 20/05/1999

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