sample of publications

• articles 

  • Mechanical and Functional Responses in Astrocytes under Alternating Deformation Modes Using Magneto-Active Substrates.  ADVANCED MATERIALS.  36:1-15. 2024
  • JDLL: a library to run deep learning models on Java bioimage informatics platforms.  NATURE METHODS.  21:7-8. 2024
  • The Cell Tracking Challenge: 10 years of objective benchmarking.  NATURE METHODS.  20. 2023
  • From Nano to Macro: An overview of the IEEE Bio Image and Signal Processing Technical Committee.  IEEE SIGNAL PROCESSING MAGAZINE.  40. 2023
  • Integration of longitudinal deep-radiomics and clinical data improves the prediction of durable benefts to anti-PD-1/PD-L1 immunotherapy in advanced NSCLC patients.  Journal of Translational Medicine.  21:1-15. 2023
  • ABANICCO: A New Color Space for Multi-Label Pixel Classification and Color Analysis.  SENSORS.  23:1-23. 2023
  • Automatic determination of the handedness of single-particle maps of macromolecules solved by CryoEM.  JOURNAL OF STRUCTURAL BIOLOGY.  214:1-6. 2022
  • Single plane illumination microscopy for microfluidic device imaging.  Biosensors-Basel.  12:1-13. 2022
  • Correction: Image processing tools for the validation of CryoEM maps.  FARADAY DISCUSSIONS.  240:228-228. 2022
  • Image processing tools for the validation of CryoEM maps.  FARADAY DISCUSSIONS.  240:210-227. 2022
  • Deep learning based domain adaptation for mitochondria segmentation on EM volumes.  Computer Methods and Programs in Biomedicine.  222:1-11. 2022
  • Magneto-mechanical system to reproduce and quantify complex strain patterns in biological materials.  Applied Materials Today.  27:1-15. 2022
  • Stable deep neural network architectures for mitochondria segmentation on electron microscopy volumes.  NEUROINFORMATICS.  20:437-450. 2022
  • Reduction of motion effects in myocardial arterial spin labeling.  MAGNETIC RESONANCE IN MEDICINE.  87:1261-1275. 2022
  • Innovations in ex vivo Light Sheet Fluorescence Microscopy.  PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY.  168:37-51. 2022
  • The contribution of microfluidics to the fight against tuberculosis.  Nanotechnology Reviews.  11:40-54. 2022
  • Use of the p-values as a size-dependent function to address practical differences when analyzing large datasets.  Scientific Reports.  11:1-13. 2021
  • Tuning the cell and biological tissue environment through magneto-active materials.  Applied Sciences-Basel.  11:1-34. 2021
  • Predicting MHC I restricted T cell epitopes in mice with NAP-CNB, a novel online tool.  Scientific Reports.  11:1-10. 2021
  • DeepImageJ: A user-friendly environment to run deep learning models in ImageJ.  bioRxiv.  2021
  • Molecular imaging of pulmonary Tuberculosis in an Ex-Vivo Mouse Model Using Spectral Photon-Counting Computed Tomography and Micro-CT.  IEEE Access.  9:67201-67208. 2021
  • Association of visual and quantitative heterogeneity of 18F-FDG PET images with treatment response in locally advanced rectal cancer: A feasibility study..  PLoS One.  15:e0242597. 2020
  • Computational insights into the influence of substrate stiffness on collective cell migration.  Extreme Mechanics Letters.  40:1-9. 2020
  • Editorial: Introduction to the issue on domain enriched learning for medical imaging.  IEEE Journal of Selected Topics in Signal Processing.  14:1068 -1071. 2020
  • Nonlinear Image Registration and Pixel Classification Pipeline for the Study of Tumor Heterogeneity Maps.  Entropy.  22:1-19. 2020
  • Development of an Inverted Epifluorescence Microscope for Long-Term Monitoring of Bacteria in Multiplexed Microfluidic Devices.  SENSORS.  20:1-14. 2020
  • Guest editorial: Special issue on imaging-based diagnosis of COVID-19.  IEEE TRANSACTIONS ON MEDICAL IMAGING.  39:2569-2571. 2020
  • A radiological score for the assessment of tuberculosis progression: Validation in mouse models.  Tuberculosis.  121. 2020
  • X-ray-based virtual slicing of TB-infected lungs.  Scientific Reports.  9:19404. 2019
  • The role of versican in the skin ECM and its interaction with hyaluronic acid / The role of hyaluronic acid and versican in the skin extracellular matrix.  Biomecánica: Órgano de la Sociedad Ibérica de Biomecánica y Biomateriales.  27:35-49. 2019
  • Deep-learning-based segmentation of small extracellular vesicles in transmission electron microscopy images.  Scientific Reports.  9:1-10. 2019
  • Automated detection of neutropenia using noninvasive video microscopy of superficial capillaries.  AMERICAN JOURNAL OF HEMATOLOGY.  94:E219-E222. 2019
  • Dynamic Atlas-Based Segmentation and Quantification of Neuromelanin-Rich Brainstem Structures in Parkinson Disease.  IEEE TRANSACTIONS ON MEDICAL IMAGING.  38:813-823. 2019
  • Computed tomography-based biomarker for longitudinal assessment of disease Burden in pulmonary tuberculosis.  MOLECULAR IMAGING AND BIOLOGY.  21:19-24. 2019
  • Applications of light-sheet microscopy in microdevices.  Frontiers in Neuroanatomy.  13:1-15. 2019
  • Spotlight on Bioimaging and Signal Processing [In the Spotlight].  IEEE SIGNAL PROCESSING MAGAZINE.  35. 2018
  • Unsupervised CT lung image segmentation of a mycobacterium tuberculosis infection model.  Scientific Reports.  8 (9802):1-10. 2018
  • An objective comparison of cell-tracking algorithms.  NATURE METHODS.  14:1141-1152. 2017
  • Full L-1-regularized Traction Force Microscopy over whole cells.  BMC BIOINFORMATICS.  18:1-14. 2017
  • Characterization of three-dimensional cancer cell migration in mixed collagen-Matrigel scaffolds using microfluidics and image analysis.  PLoS One.  12:1-24. 2017
  • Free Form Deformation-Based Image Registration Improves Accuracy of Traction Force Microscopy.  PLoS One.  10:1-22. 2015
  • Quantitative Assessment of Emphysema Severity in Histological Lung Analysis.  ANNALS OF BIOMEDICAL ENGINEERING.  43:2515-2529. 2015
  • Automated Neuromelanin Imaging as a Diagnostic Biomarker for Parkinson's Disease.  MOVEMENT DISORDERS.  30:945-952. 2015
  • Quantitative Bioimaging: Signal Processing in Light Microscopy.  IEEE SIGNAL PROCESSING MAGAZINE.  32:18-19. 2015
  • Toward a morphodynamic model of the cell: Signal processing for cell modeling.  IEEE SIGNAL PROCESSING MAGAZINE.  32:20-29. 2015
  • Validation tool for traction force microscopy.  COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING.  18:1377-1385. 2015
  • Comparing algorithms for automated vessel segmentation in computed tomography scans of the lung: The VESSEL12 study.  MEDICAL IMAGE ANALYSIS.  18:1217-1232. 2014
  • A novel automated microscopy platform for multiresolution multispectral early detection of lung cancer cells in bronchoalveolar lavage samples.  IEEE Systems Journal.  8:985-994. 2014
  • Interactive lung segmentation in abnormal human and animal chest CT scans.  MEDICAL PHYSICS.  41:1-14. 2014
  • A benchmark for comparison of cell tracking algorithms.  BIOINFORMATICS.  30:1609-1617. 2014
  • Individual nodule tracking in micro-CT images of a longitudinal lung cancer mouse model.  MEDICAL IMAGE ANALYSIS.  17:1095-1105. 2013
  • Efficient Blind Spectral Unmixing of FluorescentlyLabeled Samples Using Multi-Layer Non-Negative MatrixFactorization.  PLoS One.  8:1-11. 2013
  • Segmentation and shape tracking of whole fluorescent cells based on the Chan-Vese model.  IEEE TRANSACTIONS ON MEDICAL IMAGING.  32:995-1006. 2013
  • Smokers with CT Detected Emphysema and No Airway Obstruction Have Decreased Plasma Levels of EGF, IL-15, IL-8 and IL-1ra.  PLoS One.  8:1-6. 2013
  • Multiscale in situ analysis of the role of dyskerin in lung cancer cells.  Integrative Biology (United Kingdom).  5:402-413. 2013
  • Numerical estimation of 3D mechanical forces exerted by cells on non-linear materials.  JOURNAL OF BIOMECHANICS.  46:50-55. 2013
  • Adiposoft: Automated software for the analysis of white adipose tissue cellularity in histological sections.  JOURNAL OF LIPID RESEARCH.  53:2791-2796. 2012
  • Quantification of Lung Damage in an Elastase-Induced Mouse Model of Emphysema.  International Journal of Biomedical Imaging.  2012:1-11. 2012
  • Wavelet-based detection of transcriptional activity on a novel Staphylococcus aureus tiling microarray.  BMC BIOINFORMATICS.  13:1-16. 2012
  • New Strategies for Echocardiographic Evaluation of Left Ventricular Function in a Mouse Model of Long-Term Myocardial Infarction.  PLoS One.  7:1-9. 2012
  • Robust, Standardized Quantification of Pulmonary Emphysema in Low Dose CT Exams.  ACADEMIC RADIOLOGY.  18:1382-1390. 2011
  • Evaluation of micro-CT for emphysema assessment in mice: comparison with non-radiological techniques.  EUROPEAN RADIOLOGY.  21:954-962. 2011
  • Longitudinal study of a mouse model of chronic pulmonary inflammation using breath hold gated micro-CT.  EUROPEAN RADIOLOGY.  20:2600-2608. 2010
  • 3D Reconstruction of Histological Sections: Applicationto Mammary Gland Tissue.  MICROSCOPY RESEARCH AND TECHNIQUE.  73:1019-1029. 2010
  • Non-rigid consistent registration of 2D image sequences.  PHYSICS IN MEDICINE AND BIOLOGY.  55:6215-6242. 2010
  • Fast Space-Variant Elliptical Filtering Using Box Splines.  IEEE TRANSACTIONS ON IMAGE PROCESSING.  19:2290-2306. 2010
  • Spatially variant convolution with scaled B-splines.  IEEE TRANSACTIONS ON IMAGE PROCESSING.  19:11-24. 2010
  • Airway segmentation and analysis for the study of mouse models of lung disease using micro-CT.  PHYSICS IN MEDICINE AND BIOLOGY.  54:7009-7024. 2009
  • Combination Strategies in Multi-Atlas Image Segmentation: Application to Brain MR Data.  IEEE TRANSACTIONS ON MEDICAL IMAGING.  28:1266-1277. 2009
  • Halton sampling for autofocus.  Journal of Microscopy.  235:50-58. 2009

• book chapters 

  • Building a bioimage analysis workflow using deep learning. In: Bioimage data analysis workflows ¿ Advanced components and methods.  Springer Berlin / Heidelberg. 61-87. 2022
  • Emerging technologies and outlook. In: ImagingModalitiesforBiological andPreclinicalResearch: ACompendium,Volume2 Parts II&-IV: In vivo preclinical imaging, multimodality imaging and outlook.  IOP PUBLISHING LTD. V.1-1-IV.1-14. 2021
  • Acquisition and Automated Analysis of Normal and Pathological Lungs in Small Animals Using Microcomputed Tomography. In: Lung Imaging and Computer Aided Diagnosis.  CRC PRESS. 137-150. 2016

• conference contributions 

  • NANOTECH START'22 2022
  • Search for temporal cell segmentation robustness in phase-contrast microscopy videos.  1-3. 2022
  • Delta-radiomics signature for prediction of survival in advanced nsclc patients treated with immunotherapy.  886-890. 2021
  • Tuberculosis Lesions in CT Images Inferred using 3D-CNN and Multi-Task Learning.  294-297. 2019
  • Automatic Segmentation of Cell Protrusions in Low Magnification Phase Contrast Microscopy Videos 2018
  • BENCHMARKING OF IMAGE REGISTRATION METHODS FOR DIFFERENTLY STAINED HISTOLOGICAL SLIDES.  3368-3372. 2018
  • Deep Learning Applications to BioImage Analysis.  108-108. 2018
  • Fully Automatic Segmentation of Exosomes in Transmission Electron Microscopy 2018
  • PDMS Microfluidic Chip for Multiplexed Testing of Antibiotics against Tuberculosis.  279-282. 2018
  • Radiomics for the Discrimination of Tuberculosis Lesions 2018
  • Spectral photon-counting CT of lungs of mice infected with Mycobacterium Tuberculosis: potential for locating Tuberculosis involvement 2018
  • TOWARDS AN INFORMATIONAL MODEL FOR TUBERCULOSIS LESIONDISCRIMINATION ON X-RAY CT IMAGES.  265-268. 2018
  • Tuberculosis Histopathology on X Ray CT.  169-179. 2018
  • What Have We Learned from the Cell Tracking Challenge.  103-103. 2018
  • Accurate Lung Segmentation of Thorax CT Images on a Tuberculosis Infection Model.  251-254. 2017
  • Automated Analysis of Collagen Networks via Microscopy.  2659-2663. 2017
  • PET Texture Analysis: Does it Have Clinical Significance in Locally Advanced Rectal Cancer?.  403-406. 2017
  • Semi-Automatic Processing of Infrared Thermography to Characterize Emotional Stress: A Pilot Study 2017
  • Super-Resolved
    Traction Foce Microscopy Over Whole Cells 2017
  • Super-resolved Traction Force Microscopy over whole cells.  40-43. 2017
  • Characterization of 3D network geometry in collagen hydrogels 2016
  • L1-REGULARIZED RECONSTRUCTION FOR TRACTION FORCE MICROSCOPY.  140-144. 2016
  • Atlas-based segmentation of brainstem regions in neuromelanin-sensitive magnetic resonance images 2015
  • Characterization of the Role of Collagen Network Structure and Composition in Cancer Cell Migration.  8139-8142. 2015
  • QUANTIFICATION OF THE 3D COLLAGEN NETWORK GEOMETRY IN CONFOCAL REFLECTION MICROSCOPY.  1791-1794. 2015
  • Quantification of pulmonary vessel diameter in low-dose CT images.  118. 2015
  • A probabilistic model of emphysema based on granulometry analysis.  1-14. 2013
  • Automatic quantification of filopodia-based cell migration.  668-671. 2013
  • Modeling airway probability.  378-381. 2013
  • Registration of multiple stained histological sections.  1034-1037. 2013
  • Characterization of emphysema in low dose computed tomography images using maximum likelihood estimation of the scale exponent.  1447-1450. 2012
  • Detecting airway remodeling in COPD and emphysema using low-dose CT imaging 2012
  • Fast tracking of fluorescent cells based on the Chan-Vese model.  1316-1319. 2012
  • Individual nodule tracking in micro-CT images of a mouse model of lung cancer.  362-365. 2012
  • Automatic leakage detection and recovery for airway tree extraction in chest CT images.  568-571. 2010
  • Fast detection of cells using a continuously scalable Mexican-hat-like template.  1277-1280. 2010
  • A Two-Phase Segmentation of Cell NucleiUsing Fast Level Set-Like Algorithms.  390-399. 2009
  • Segmentation of Touching Cell NucleiUsing a Two-Stage Graph Cut Model.  410-419. 2009