sample of publications
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articles
- Mechanical and Functional Responses in Astrocytes under Alternating Deformation Modes Using Magneto-Active Substrates. ADVANCED MATERIALS. 36:2312497-1-2312497-15. 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
- 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
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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
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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
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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