Professor Erik Meijering
Professor

Professor Erik Meijering

Engineering
Computer Science and Engineering

Erik Meijering is a Professor of Biomedical Image Computing in the School of Computer Science and Engineering. His research focuses on the development of innovative computer vision and machine learning (in particular deep learning) methods for automated quantitative analysis of biomedical imaging data.

He received the MSc degree in Electrical Engineering from Delft University of Technology (Delft, the Netherlands) in 1996 and the PhD degree in Medical Image Analysis from Utrecht University (Utrecht, the Netherlands) in 2000. Before coming to the University of New South Wales (UNSW, Sydney, Australia) in 2019, he was a Postdoctoral Fellow at the Swiss Federal Institute of Technology (Lausanne, Switzerland) from 2000-2002, an Assistant Professor at Erasmus University Medical Center (Rotterdam, the Netherlands) from 2002-2008, and an Associate Professor at the same institute from 2008-2019.

Since 2019 he is a Fellow of the Institute of Electrical and Electronics Engineers (IEEE). Within IEEE he is a member of the Signal Processing Society (SPS) and the Engineering in Medicine and Biology Society (EMBS), and served/serves on the SPS Technical Committee on Bio Imaging and Signal Processing (BISP) (2005-2010 and 2017-2020), the SPS Technical Directions Board (2018-2019), the EMBS Technical Committee on Biomedical Imaging and Image Processing (BIIP) (since 2007), and the cross-Society IEEE Life Sciences Technical Community (LSTC) (since 2018).

Over the years he was/is an Associate Editor for the IEEE Transactions on Medical Imaging (since 2004), the International Journal on Biomedical Imaging (2006-2009), the IEEE Transactions on Image Processing (2008-2011), has co-edited various journal special issues on topics related to biomedical imaging, and has co-organized various conferences in the field, notably the IEEE International Symposium on Biomedical Imaging (ISBI 2002, 2004, 2006, 2010, 2015, 2018). He also served/serves on a great variety of other international conference, advisory, and review boards.

Phone
+61 2 9065 2040
Location
Online or K17 Room 412D
  • Book Chapters | 2023
    2023, 'Neural Network Compression by Joint Sparsity Promotion and Redundancy Reduction', in Neural Information Processing, Springer International Publishing, pp. 612 - 623, http://dx.doi.org/10.1007/978-3-031-30105-6_51
    Book Chapters | 2022
    2022, 'Motion Tracking and Analysis', in Microscope Image Processing, Second Edition, Elsevier, pp. 393 - 430, http://dx.doi.org/10.1016/B978-0-12-821049-9.00013-7
    Book Chapters | 2021
    2021, 'Deep Representation Learning for Image-Based Cell Profiling', in Machine Learning in Medical Imaging, Springer International Publishing, pp. 487 - 497, http://dx.doi.org/10.1007/978-3-030-87589-3_50
    Book Chapters | 2021
    2021, 'Deformable Convolution and Semi-supervised Learning in Point Clouds for Aneurysm Classification and Segmentation', in Neural Information Processing, Springer International Publishing, pp. 283 - 290, http://dx.doi.org/10.1007/978-3-030-92310-5_33
    Book Chapters | 2017
    2017, 'Automated analysis of intracellular dynamic processes', in Methods in Molecular Biology, pp. 209 - 228, http://dx.doi.org/10.1007/978-1-4939-6810-7_14
    Book Chapters | 2012
    2012, 'Methods for cell and particle tracking', in Methods in Enzymology, pp. 183 - 200, http://dx.doi.org/10.1016/B978-0-12-391857-4.00009-4
    Book Chapters | 2008
    2008, 'Chapter 15 Time‐Lapse Imaging', in Microscope Image Processing, Elsevier, pp. 401 - 440, http://dx.doi.org/10.1016/b978-0-12-372578-3.00015-5
    Book Chapters | 2008
    2008, 'Time-Lapse Imaging', in Microscope Image Processing, pp. 401 - 440, http://dx.doi.org/10.1016/B978-0-12-372578-3.00015-5
  • Journal articles | 2023
    Manubens-Gil L; Zhou Z; Chen H; Ramanathan A; Liu X; Liu Y; Bria A; Gillette T; Ruan Z; Yang J; Radojević M; Zhao T; Cheng L; Qu L; Liu S; Bouchard KE; Gu L; Cai W; Ji S; Roysam B; Wang CW; Yu H; Sironi A; Iascone DM; Zhou J; Bas E; Conde-Sousa E; Aguiar P; Li X; Li Y; Nanda S; Wang Y; Muresan L; Fua P; Ye B; He HY; Staiger JF; Peter M; Cox DN; Simonneau M; Oberlaender M; Jefferis G; Ito K; Gonzalez-Bellido P; Kim J; Rubel E; Cline HT; Zeng H; Nern A; Chiang AS; Yao J; Roskams J; Livesey R; Stevens J; Liu T; Dang C; Guo Y; Zhong N; Tourassi G; Hill S; Hawrylycz M; Koch C; Meijering E; Ascoli GA; Peng H, 2023, 'BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets', Nature Methods, http://dx.doi.org/10.1038/s41592-023-01848-5
    Journal articles | 2023
    Mondol RK; Millar EKA; Graham PH; Browne L; Sowmya A; Meijering E, 2023, 'hist2RNA: An Efficient Deep Learning Architecture to Predict Gene Expression from Breast Cancer Histopathology Images.', Cancers (Basel), 15, pp. 2569 - 2569, http://dx.doi.org/10.3390/cancers15092569
    Journal articles | 2023
    Zhu Y; Wang M; Yin X; Zhang J; Meijering E; Hu J, 2023, 'Deep Learning in Diverse Intelligent Sensor Based Systems', Sensors, 23, pp. 62 - 62, http://dx.doi.org/10.3390/s23010062
    Journal articles | 2023
    2023, '3D Soma Detection in Large-Scale Whole Brain Images via a Two-Stage Neural Network', IEEE Transactions on Medical Imaging, 42, pp. 148 - 157, http://dx.doi.org/10.1109/TMI.2022.3206605
    Journal articles | 2023
    2023, 'A Compound Loss Function With Shape Aware Weight Map for Microscopy Cell Segmentation', IEEE Transactions on Medical Imaging, 42, pp. 1278 - 1288, http://dx.doi.org/10.1109/TMI.2022.3226226
    Journal articles | 2023
    2023, 'A comparison of manual and automated neural architecture search for white matter tract segmentation', Scientific Reports, 13, pp. 1617, http://dx.doi.org/10.1038/s41598-023-28210-1
    Journal articles | 2023
    2023, 'Cancer Survival Prediction From Whole Slide Images With Self-Supervised Learning and Slide Consistency', IEEE Transactions on Medical Imaging, 42, pp. 1401 - 1412, http://dx.doi.org/10.1109/TMI.2022.3228275
    Journal articles | 2023
    2023, 'Imbalanced classification for protein subcellular localization with multilabel oversampling', Bioinformatics (Oxford, England), 39, http://dx.doi.org/10.1093/bioinformatics/btac841
    Journal articles | 2023
    2023, 'Simple and robust depth-wise cascaded network for polyp segmentation', Engineering Applications of Artificial Intelligence, 121, pp. 106023 - 106023, http://dx.doi.org/10.1016/j.engappai.2023.106023
    Journal articles | 2022
    Chen W; Liu M; Du H; Radojevic M; Wang Y; Meijering E, 2022, 'Deep-Learning-Based Automated Neuron Reconstruction From 3D Microscopy Images Using Synthetic Training Images', IEEE Transactions on Medical Imaging, 41, pp. 1031 - 1042, http://dx.doi.org/10.1109/TMI.2021.3130934
    Journal articles | 2022
    Jiang Y; Chen W; Liu M; Wang Y; Meijering E, 2022, 'DeepRayburst for Automatic Shape Analysis of Tree-Like Structures in Biomedical Images', IEEE Journal of Biomedical and Health Informatics, 26, pp. 2204 - 2215, http://dx.doi.org/10.1109/JBHI.2021.3124514
    Journal articles | 2022
    2022, 'A 3D Tubular Flux Model for Centerline Extraction in Neuron Volumetric Images', IEEE Transactions on Medical Imaging, 41, pp. 1069 - 1079, http://dx.doi.org/10.1109/TMI.2021.3130987
    Journal articles | 2022
    2022, 'Contraction pressure analysis using optical imaging in normal and MYBPC3-mutated hiPSC-derived cardiomyocytes grown on matrices with tunable stiffness', Biomaterials and Biosystems, 8, http://dx.doi.org/10.1016/j.bbiosy.2022.100068
    Journal articles | 2022
    2022, 'Data augmentation with improved regularisation and sampling for imbalanced blood cell image classification', Scientific Reports, 12, http://dx.doi.org/10.1038/s41598-022-22882-x
    Journal articles | 2022
    2022, 'Deep Learning in Biological Image and Signal Processing', IEEE Signal Processing Magazine, 39, pp. 24 - 26, http://dx.doi.org/10.1109/MSP.2021.3134525
    Journal articles | 2022
    2022, 'Fully Elman Neural Network: A Novel Deep Recurrent Neural Network Optimized by an Improved Harris Hawks Algorithm for Classification of Pulmonary Arterial Wedge Pressure', IEEE Transactions on Biomedical Engineering, 69, pp. 1733 - 1744, http://dx.doi.org/10.1109/TBME.2021.3129459
    Journal articles | 2022
    2022, 'Leveraging image complexity in macro-level neural network design for medical image segmentation', Scientific Reports, 12, http://dx.doi.org/10.1038/s41598-022-26482-7
    Journal articles | 2022
    2022, 'Structure-Guided Segmentation for 3D Neuron Reconstruction', IEEE Transactions on Medical Imaging, 41, pp. 903 - 914, http://dx.doi.org/10.1109/TMI.2021.3125777
    Journal articles | 2022
    2022, 'Survival prediction in triple negative breast cancer using multiple instance learning of histopathological images', Scientific Reports, 12, pp. 14527, http://dx.doi.org/10.1038/s41598-022-18647-1
    Journal articles | 2022
    2022, 'SwinPA-Net: Swin Transformer-Based Multiscale Feature Pyramid Aggregation Network for Medical Image Segmentation', IEEE Transactions on Neural Networks and Learning Systems, http://dx.doi.org/10.1109/TNNLS.2022.3204090
    Journal articles | 2021
    Chen W; Liu M; Zhan Q; Tan Y; Meijering E; Radojevic M; Wang Y, 2021, 'Spherical-Patches Extraction for Deep-Learning-Based Critical Points Detection in 3D Neuron Microscopy Images', IEEE Transactions on Medical Imaging, 40, pp. 527 - 538, http://dx.doi.org/10.1109/TMI.2020.3031289
    Journal articles | 2021
    Jiang Y; Chen W; Liu M; Wang Y; Meijering E, 2021, '3D Neuron Microscopy Image Segmentation via the Ray-Shooting Model and a DC-BLSTM Network', IEEE Transactions on Medical Imaging, 40, pp. 26 - 37, http://dx.doi.org/10.1109/TMI.2020.3021493
    Journal articles | 2021
    2021, 'Automatic improvement of deep learning-based cell segmentation in time-lapse microscopy by neural architecture search', Bioinformatics, 37, pp. 4844 - 4850, http://dx.doi.org/10.1093/bioinformatics/btab556
    Journal articles | 2021
    2021, 'Classifying retinal degeneration in histological sections using deep learning', Translational Vision Science and Technology, 10, pp. 9, http://dx.doi.org/10.1167/tvst.10.7.9
    Journal articles | 2021
    2021, 'Deep learning methods for automatic segmentation of lower leg muscles and bones from MRI scans of children with and without cerebral palsy', NMR in Biomedicine, 34, pp. e4609, http://dx.doi.org/10.1002/nbm.4609
    Journal articles | 2021
    2021, 'Efficient 3D Junction Detection in Biomedical Images Based on a Circular Sampling Model and Reverse Mapping', IEEE Journal of Biomedical and Health Informatics, 25, pp. 1612 - 1623, http://dx.doi.org/10.1109/JBHI.2020.3036743
    Journal articles | 2021
    2021, 'Estimation of three-dimensional chromatin morphology for nuclear classification and characterisation', Scientific Reports, 11, http://dx.doi.org/10.1038/s41598-021-82985-9
    Journal articles | 2021
    2021, 'Protein phosphatase 2b dual function facilitates synaptic integrity and motor learning', Journal of Neuroscience, 41, pp. 5579 - 5594, http://dx.doi.org/10.1523/JNEUROSCI.1741-20.2021
    Journal articles | 2020
    2020, 'A bird's-eye view of deep learning in bioimage analysis', Computational and Structural Biotechnology Journal, 18, pp. 2312 - 2325, http://dx.doi.org/10.1016/j.csbj.2020.08.003
    Journal articles | 2020
    2020, 'Concerted action of kinesins kif5b and kif13b promotes efficient secretory vesicle transport to microtubule plus ends', eLife, 9, pp. 1 - 37, http://dx.doi.org/10.7554/eLife.61302
    Journal articles | 2020
    2020, 'Deep-learning method for data association in particle tracking', Bioinformatics, 36, pp. 4935 - 4941, http://dx.doi.org/10.1093/bioinformatics/btaa597
    Journal articles | 2020
    2020, 'Estimation of Three-Dimensional Chromatin Morphology for Nuclear Classification and Characterisation', , http://dx.doi.org/10.1101/2020.07.29.226498
    Journal articles | 2019
    2019, '3-D quantification of filopodia in motile cancer cells', IEEE Transactions on Medical Imaging, 38, pp. 862 - 872, http://dx.doi.org/10.1109/TMI.2018.2873842
    Journal articles | 2019
    2019, 'Automated Neuron Detection in High-Content Fluorescence Microscopy Images Using Machine Learning', Neuroinformatics, 17, pp. 253 - 269, http://dx.doi.org/10.1007/s12021-018-9399-4
    Journal articles | 2019
    2019, 'Automated Neuron Reconstruction from 3D Fluorescence Microscopy Images Using Sequential Monte Carlo Estimation', Neuroinformatics, 17, pp. 423 - 442, http://dx.doi.org/10.1007/s12021-018-9407-8
    Journal articles | 2019
    2019, 'Bayesian Polytrees with Learned Deep Features for Multi-Class Cell Segmentation', IEEE Transactions on Image Processing, 28, pp. 3246 - 3260, http://dx.doi.org/10.1109/TIP.2019.2895455
    Journal articles | 2019
    2019, 'Particle Mobility Analysis Using Deep Learning and the Moment Scaling Spectrum', Scientific Reports, 9, http://dx.doi.org/10.1038/s41598-019-53663-8
    Journal articles | 2019
    2019, 'Reverse genetic screen reveals that Il34 facilitates yolk sac macrophage distribution and seeding of the brain', DMM Disease Models and Mechanisms, 12, http://dx.doi.org/10.1242/dmm.037762
    Journal articles | 2018
    2018, 'Spotlight on Bioimaging and Signal Processing [In the Spotlight]', IEEE Signal Processing Magazine, 35, http://dx.doi.org/10.1109/MSP.2018.2864772
    Journal articles | 2017
    2017, 'An objective comparison of cell-tracking algorithms', Nature Methods, 14, pp. 1141 - 1152, http://dx.doi.org/10.1038/nmeth.4473
    Journal articles | 2017
    2017, 'Automated neuron tracing using probability hypothesis density filtering', Bioinformatics, 33, pp. 1073 - 1080, http://dx.doi.org/10.1093/bioinformatics/btw751
    Journal articles | 2017
    2017, 'Automatic tracing of ultra-volumes of neuronal images', Nature Methods, 14, pp. 332 - 333, http://dx.doi.org/10.1038/nmeth.4233
    Journal articles | 2017
    2017, 'EB1 and EB3 regulate microtubule minus end organization and Golgi morphology', Journal of Cell Biology, 216, pp. 3179 - 3198, http://dx.doi.org/10.1083/jcb.201701024
    Journal articles | 2016
    2016, 'Fuzzy-Logic Based Detection and Characterization of Junctions and Terminations in Fluorescence Microscopy Images of Neurons', Neuroinformatics, 14, pp. 201 - 219, http://dx.doi.org/10.1007/s12021-015-9287-0
    Journal articles | 2016
    2016, 'Imagining the future of bioimage analysis', Nature Biotechnology, 34, pp. 1250 - 1255, http://dx.doi.org/10.1038/nbt.3722
    Journal articles | 2015
    2015, 'BRCA2 diffuses as oligomeric clusters with RAD51 and changes mobility after DNA damage in live cells (vol 207, pg 599, 2014)', JOURNAL OF CELL BIOLOGY, 208, pp. 857 - 857, http://dx.doi.org/10.1083/jcb.20140501402182015c
    Journal articles | 2015
    2015, 'BigNeuron: Large-Scale 3D Neuron Reconstruction from Optical Microscopy Images', Neuron, 87, pp. 252 - 256, http://dx.doi.org/10.1016/j.neuron.2015.06.036
    Journal articles | 2015
    2015, 'Comprehensive single cell-resolution analysis of the role of chromatin regulators in early C. elegans embryogenesis', Developmental Biology, 398, pp. 153 - 162, http://dx.doi.org/10.1016/j.ydbio.2014.10.014
    Journal articles | 2015
    2015, 'Correction to: "BRCA2 diffuses as oligomeric clusters with RAD51 and changes mobility after DNA damage in live cells" [J. Cell Biol. Vol. 207 No. 5, December 8, 2014. Pages 599-613]', Journal of Cell Biology, 208, pp. 857 - 857, http://dx.doi.org/10.1083/jcb.20140501402182015c
    Journal articles | 2015
    2015, 'Erratum: Multiple sparse representations classification (PLoS ONE (2015) 10:7 (e0131968) (Doi:10.1371/journal.pone.0131968))', PLoS ONE, 10, http://dx.doi.org/10.1371/journal.pone.0136827
    Journal articles | 2015
    2015, 'From DIADEM to BigNeuron', Neuroinformatics, 13, pp. 259 - 260, http://dx.doi.org/10.1007/s12021-015-9270-9
    Journal articles | 2015
    2015, 'Multiple sparse representations classification', PLoS ONE, 10, http://dx.doi.org/10.1371/journal.pone.0131968
    Journal articles | 2015
    2015, 'Quantitative bioimaging: Signal processing in light microscopy', IEEE Signal Processing Magazine, 32, pp. 18 - 19, http://dx.doi.org/10.1109/MSP.2014.2359691
    Journal articles | 2015
    2015, 'Quantitative comparison of multiframe data association techniques for particle tracking in time-lapse fluorescence microscopy', Medical Image Analysis, 24, pp. 163 - 189, http://dx.doi.org/10.1016/j.media.2015.06.006
    Journal articles | 2015
    2015, 'Quantitative imaging of focal adhesion dynamics and their regulation by HGF and Rap1 signaling', Experimental Cell Research, 330, pp. 382 - 397, http://dx.doi.org/10.1016/j.yexcr.2014.10.012
    Journal articles | 2015
    2015, 'Toward a morphodynamic model of the cell: Signal processing for cell modeling', IEEE Signal Processing Magazine, 32, pp. 20 - 29, http://dx.doi.org/10.1109/MSP.2014.2358263
    Journal articles | 2014
    2014, 'A benchmark for comparison of cell tracking algorithms', Bioinformatics, 30, pp. 1609 - 1617, http://dx.doi.org/10.1093/bioinformatics/btu080
    Journal articles | 2014
    2014, 'BRCA2 diffuses as oligomeric clusters with RAD51 and changes mobility after DNA damage in live cells', Journal of Cell Biology, 207, pp. 599 - 613, http://dx.doi.org/10.1083/jcb.201405014
    Journal articles | 2014
    2014, 'Extracellular matrix defects in aneurysmal Fibulin-4 mice predispose to lung emphysema', PLoS ONE, 9, http://dx.doi.org/10.1371/journal.pone.0106054
    Journal articles | 2014
    2014, 'Interactive local super-resolution reconstruction of whole-body MRI mouse data: A pilot study with applications to bone and kidney metastases', PLoS ONE, 9, http://dx.doi.org/10.1371/journal.pone.0108730
    Journal articles | 2014
    2014, 'Objective comparison of particle tracking methods', Nature Methods, 11, pp. 281 - 289, http://dx.doi.org/10.1038/nmeth.2808
    Journal articles | 2014
    2014, 'Three-dimensional inversion recovery manganese-enhanced MRI of mouse brain using super-resolution reconstruction to visualize nuclei involved in higher brain function', NMR in Biomedicine, 27, pp. 749 - 759, http://dx.doi.org/10.1002/nbm.3108
    Journal articles | 2013
    2013, 'End-binding proteins sensitize microtubules to the action of microtubule-targeting agents', Proceedings of the National Academy of Sciences of the United States of America, 110, pp. 8900 - 8905, http://dx.doi.org/10.1073/pnas.1300395110
    Journal articles | 2013
    2013, 'Super-resolution reconstruction using cross-scale self-similarity in multi-slice MRI', Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8151 LNCS, pp. 123 - 130, http://dx.doi.org/10.1007/978-3-642-40760-4_16
    Journal articles | 2012
    2012, 'Cell segmentation: 50 Years down the road [life Sciences]', IEEE Signal Processing Magazine, 29, pp. 140 - 145, http://dx.doi.org/10.1109/MSP.2012.2204190
    Journal articles | 2012
    2012, 'Reversible jump MCMC methods for fully automatic motion analysis in tagged MRI', Medical Image Analysis, 16, pp. 301 - 324, http://dx.doi.org/10.1016/j.media.2011.08.006
    Journal articles | 2012
    2012, 'Super-resolution methods in MRI: Can they improve the trade-off between resolution, signal-to-noise ratio, and acquisition time?', Magnetic Resonance in Medicine, 68, pp. 1983 - 1993, http://dx.doi.org/10.1002/mrm.24187
    Journal articles | 2011
    2011, 'ATP-dependent and independent functions of Rad54 in genome maintenance', Journal of Cell Biology, 192, pp. 735 - 750, http://dx.doi.org/10.1083/jcb.201011025
    Journal articles | 2011
    2011, 'Insights into EB1 structure and the role of its c-terminal domain for discriminating microtubule tips from the lattice', Molecular Biology of the Cell, 22, pp. 2912 - 2923, http://dx.doi.org/10.1091/mbc.E11-01-0017
    Journal articles | 2011
    2011, 'Rab6, Rab8, and MICAL3 cooperate in controlling docking and fusion of exocytotic carriers', Current Biology, 21, pp. 967 - 974, http://dx.doi.org/10.1016/j.cub.2011.04.030
    Journal articles | 2010
    2010, 'Advanced level-set-based cell tracking in time-lapse fluorescence microscopy', IEEE Transactions on Medical Imaging, 29, pp. 852 - 867, http://dx.doi.org/10.1109/TMI.2009.2038693
    Journal articles | 2010
    2010, 'Automated analysis of time-lapse fluorescence microscopy images: From live cell images to intracellular foci', Bioinformatics, 26, pp. 2424 - 2430, http://dx.doi.org/10.1093/bioinformatics/btq434
    Journal articles | 2010
    2010, 'Correction to “An Inverse Problem Approach for Elasticity Imaging through Vibroacoustics” [Apr 10 1012-1021', IEEE Transactions on Medical Imaging, 29, pp. 1331 - 1331, http://dx.doi.org/10.1109/tmi.2010.2051071
    Journal articles | 2010
    2010, 'Erratum: Advanced level-set-based cell tracking in time-lapse fluorescence microscopy (IEEE Transactions on Medical Imaging (2010) 29:3 (852-867))', IEEE Transactions on Medical Imaging, 29, pp. 1331, http://dx.doi.org/10.1109/TMI.2010.2049183
    Journal articles | 2010
    2010, 'History-dependent catastrophes regulate axonal microtubule behavior', Current Biology, 20, pp. 1023 - 1028, http://dx.doi.org/10.1016/j.cub.2010.04.024
    Journal articles | 2010
    2010, 'In vitro reconstitution of the functional interplay between MCAK and EB3 at microtubule plus ends', Current Biology, 20, pp. 1717 - 1722, http://dx.doi.org/10.1016/j.cub.2010.08.020
    Journal articles | 2010
    2010, 'Microtubule dynamics analysis using kymographs and variable-rate particle filters', IEEE Transactions on Image Processing, 19, pp. 1861 - 1876, http://dx.doi.org/10.1109/TIP.2010.2045031
    Journal articles | 2010
    2010, 'Neuron tracing in perspective', Cytometry Part A, 77, pp. 693 - 704, http://dx.doi.org/10.1002/cyto.a.20895
    Journal articles | 2010
    2010, 'Quantitative comparison of spot detection methods in fluorescence microscopy', IEEE Transactions on Medical Imaging, 29, pp. 282 - 301, http://dx.doi.org/10.1109/TMI.2009.2025127
    Journal articles | 2009
    2009, 'Intracranial internal carotid artery calcifications: Association with vascular risk factors and ischemic cerebrovascular disease', American Journal of Neuroradiology, 30, pp. 177 - 184, http://dx.doi.org/10.3174/ajnr.A1301
    Journal articles | 2009
    2009, 'Tracking in cell and developmental biology', Seminars in Cell and Developmental Biology, 20, pp. 894 - 902, http://dx.doi.org/10.1016/j.semcdb.2009.07.004
    Journal articles | 2008
    2008, 'Assessment of atherosclerotic carotid plaque volume with multidetector computed tomography angiography', International Journal of Cardiovascular Imaging, 24, pp. 751 - 759, http://dx.doi.org/10.1007/s10554-008-9309-1
    Journal articles | 2008
    2008, 'Multiple object tracking in molecular bioimaging by Rao-Blackwellized marginal particle filtering', Medical Image Analysis, 12, pp. 764 - 777, http://dx.doi.org/10.1016/j.media.2008.03.004
    Journal articles | 2008
    2008, 'Particle filtering for multiple object tracking in dynamic fluorescence microscopy images: Application to microtubule growth analysis', IEEE Transactions on Medical Imaging, 27, pp. 789 - 804, http://dx.doi.org/10.1109/TMI.2008.916964
    Journal articles | 2007
    2007, 'Evaluation of an improved technique for lumen path definition and lumen segmentation of atherosclerotic vessels in CT angiography', European Radiology, 17, pp. 1738 - 1745, http://dx.doi.org/10.1007/s00330-006-0469-x
    Journal articles | 2006
    2006, 'Evaluation of an improved technique for automated center lumen line definition in cardiovascular image data', European Radiology, 16, pp. 391 - 398, http://dx.doi.org/10.1007/s00330-005-2854-2
    Journal articles | 2006
    2006, 'In vivo characterization and quantification of atherosclerotic carotid plaque components with multidetector computed tomography and histopathological correlation', Arteriosclerosis, Thrombosis, and Vascular Biology, 26, pp. 2366 - 2372, http://dx.doi.org/10.1161/01.ATV.0000240518.90124.57
    Journal articles | 2006
    2006, 'Tracking in molecular bioimaging', IEEE Signal Processing Magazine, 23, pp. 46 - 53, http://dx.doi.org/10.1109/MSP.2006.1628877
    Journal articles | 2005
    2005, 'Guest editorial', IEEE Transactions on Image Processing, 14, pp. 1233 - 1236, http://dx.doi.org/10.1109/TIP.2005.855701
    Journal articles | 2004
    2004, 'Design and Validation of a Tool for Neurite Tracing and Analysis in Fluorescence Microscopy Images', Cytometry Part A, 58, pp. 167 - 176, http://dx.doi.org/10.1002/cyto.a.20022
    Journal articles | 2003
    2003, 'A note on cubic convolution interpolation', IEEE Transactions on Image Processing, 12, pp. 477 - 479, http://dx.doi.org/10.1109/TIP.2003.811493
    Journal articles | 2002
    2002, 'A chronology of interpolation: From ancient astronomy to modern signal and image processing', Proceedings of the IEEE, 90, pp. 317 - 318, http://dx.doi.org/10.1109/JPROC.2002.993399
    Journal articles | 2002
    2002, 'A chronology of interpolation: From ancient astronomy to modern signal and image processing', Proceedings of the IEEE, 90, pp. 319 - 342, http://dx.doi.org/10.1109/5.993400
    Journal articles | 2001
    2001, 'Quantitative evaluation of convolution-based methods for medical image interpolation', Medical Image Analysis, 5, pp. 111 - 126, http://dx.doi.org/10.1016/S1361-8415(00)00040-2
    Journal articles | 2001
    2001, 'Reduction of patient motion artifacts in digital subtraction angiography: Evaluation of a fast and fully automatic technique', Radiology, 219, pp. 288 - 293, http://dx.doi.org/10.1148/radiology.219.1.r01ap19288
    Journal articles | 1999
    1999, 'Image reconstruction by convolution with symmetrical piecewise nth-order polynomial kernels', IEEE Transactions on Image Processing, 8, pp. 192 - 201, http://dx.doi.org/10.1109/83.743854
    Journal articles | 1999
    1999, 'Image registration for digital subtraction angiography', International Journal of Computer Vision, 31, pp. 227 - 246, http://dx.doi.org/10.1023/a:1008074100927
    Journal articles | 1999
    1999, 'Retrospective motion correction in digital subtraction angiography: A review', IEEE Transactions on Medical Imaging, 18, pp. 2 - 21, http://dx.doi.org/10.1109/42.750248
  • Conference Papers | 2022
    Hu Y; Pan Y; Song Y; Meijering E; Cui Z; Zhao Y; Ding Z; Zhu M; Shen D, 2022, 'Parallel Sinogram and Image Framework With Co-Training Strategy for Metal Artifact Reduction in Tooth Ct Images', in Proceedings - International Symposium on Biomedical Imaging, http://dx.doi.org/10.1109/ISBI52829.2022.9761653
    Conference Papers | 2022
    2022, 'Fast FF-to-FFPE Whole Slide Image Translation via Laplacian Pyramid and Contrastive Learning', in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Nature Switzerland, pp. 409 - 419, http://dx.doi.org/10.1007/978-3-031-16434-7_40
    Conference Papers | 2022
    2022, 'Hybrid Attentive Unet for Segmentation of Lower Leg Muscles and Bones From MRI Scans For Musculoskeletal Research', in Proceedings - International Symposium on Biomedical Imaging, http://dx.doi.org/10.1109/ISBI52829.2022.9761501
    Conference Papers | 2022
    2022, 'Imbalanced Cell-Cycle Classification Using Wgan-Div and Mixup', in Proceedings - International Symposium on Biomedical Imaging, http://dx.doi.org/10.1109/ISBI52829.2022.9761488
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    2022, 'MKIS-Net: A Light-Weight Multi-Kernel Network for Medical Image Segmentation', in 2022 International Conference on Digital Image Computing: Techniques and Applications (DICTA), IEEE, presented at 2022 International Conference on Digital Image Computing: Techniques and Applications (DICTA), 30 November 2022 - 02 December 2022, http://dx.doi.org/10.1109/dicta56598.2022.10034573
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    2022, BigNeuron: A resource to benchmark and predict best-performing algorithms for automated reconstruction of neuronal morphology, , http://dx.doi.org/10.1101/2022.05.10.491406
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    2022, Data augmentation for imbalanced blood cell image classification, , http://dx.doi.org/10.1101/2022.08.30.505762
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    2022, Data augmentation for imbalanced blood cell image classification, , http://dx.doi.org/10.21203/rs.3.rs-1645828/v1
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    2022, From Nano to Macro: Overview of the IEEE Bio Image and Signal Processing Technical Committee, , http://dx.doi.org/10.48550/arxiv.2210.17346
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    2022, Imbalanced classification for protein subcellular localisation with multilabel oversampling, , http://dx.doi.org/10.1101/2022.09.12.507675
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    2022, Leveraging Image Complexity in Macro-Level Neural Network Design for Medical Image Segmentation, , http://dx.doi.org/10.21203/rs.3.rs-1833303/v1
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    2022, MKIS-Net: A Light-Weight Multi-Kernel Network for Medical Image Segmentation, , http://dx.doi.org/10.48550/arxiv.2210.08168
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    2022, Neural Network Compression by Joint Sparsity Promotion and Redundancy Reduction, , http://dx.doi.org/10.48550/arxiv.2210.07451
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    Snelders M; Koedijk IH; Schirmer J; Mulleners O; van Leeuwen J; de Wagenaar NP; Bartulos O; Voskamp P; Braam S; Guttenberg Z; Danser AHJ; Majoor-Krakauer D; Meijering E; van der Pluijm I; Essers J, 2022, 'Contraction pressure analysis using optical imaging in normal and MYBPC3-mutated hiPSC-derived cardiomyocytes grown on matrices with tunable stiffness', in Biomaterials and Biosystems, LIPPINCOTT WILLIAMS & WILKINS, http://dx.doi.org/10.1016/j.bbiosy.2022.100068
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    2021, 'Learning Visual Features by Colorization for Slide-Consistent Survival Prediction from Whole Slide Images', in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer International Publishing, pp. 592 - 601, http://dx.doi.org/10.1007/978-3-030-87237-3_57
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    2021, 'Multi-label classification based on subcellular region-guided feature description for protein localisation', in Proceedings - International Symposium on Biomedical Imaging, IEEE, pp. 1929 - 1933, presented at 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), 13 April 2021 - 16 April 2021, http://dx.doi.org/10.1109/ISBI48211.2021.9434145
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    2020, 'Automated Quantitative Analysis of Microglia in Bright-Field Images of Zebrafish', in Proceedings - International Symposium on Biomedical Imaging, pp. 522 - 525, http://dx.doi.org/10.1109/ISBI45749.2020.9098339
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    2020, 'Neural Architecture Search for Microscopy Cell Segmentation', Lima, Peru, presented at Neural Architecture Search for Microscopy Cell Segmentation, Lima, Peru, 04 October 2020
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    2020, Concerted action of kinesins KIF5B and KIF13B promotes efficient secretory vesicle transport to microtubule plus ends, , http://dx.doi.org/10.1101/2020.04.06.027862
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    2019, 'Facilitating data association in particle tracking using autoencoding and score matching', in Proceedings - International Symposium on Biomedical Imaging, pp. 1523 - 1526, http://dx.doi.org/10.1109/ISBI.2019.8759418
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    2019, 'Nerve fiber segmentation in bright-field microscopy images of skin biopsies using deep learning', in Proceedings - International Symposium on Biomedical Imaging, pp. 232 - 235, http://dx.doi.org/10.1109/ISBI.2019.8759504
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    2018, 'Accurate estimation of intracellular dynamics and underlying spatial structures using hierarchical trajectory smoothing', in Proceedings - International Symposium on Biomedical Imaging, pp. 973 - 976, http://dx.doi.org/10.1109/ISBI.2018.8363733
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    2018, 'Deep neural networks for data association in particle tracking', in Proceedings - International Symposium on Biomedical Imaging, pp. 458 - 461, http://dx.doi.org/10.1109/ISBI.2018.8363615
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    2018, 'Segmentation of actin-stained 3D fluorescent cells with filopodial protrusions using convolutional neural networks', in Proceedings - International Symposium on Biomedical Imaging, pp. 413 - 417, http://dx.doi.org/10.1109/ISBI.2018.8363605
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    2018, Reverse genetic screen reveals that Il34 facilitates yolk sac macrophage distribution and seeding of the brain, , http://dx.doi.org/10.1101/406553
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    2017, 'Gaussian processes for trajectory analysis in microtubule tracking applications', in Proceedings - International Symposium on Biomedical Imaging, pp. 206 - 209, http://dx.doi.org/10.1109/ISBI.2017.7950502
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    2017, 'Neuron reconstruction from fluorescence microscopy images using sequential Monte Carlo estimation', in Proceedings - International Symposium on Biomedical Imaging, pp. 36 - 39, http://dx.doi.org/10.1109/ISBI.2017.7950462
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    2016, 'Automatic detection of neurons in high-content microscope images using machine learning approaches', in Proceedings - International Symposium on Biomedical Imaging, pp. 330 - 333, http://dx.doi.org/10.1109/ISBI.2016.7493276
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    2016, 'Poisson point processes for solving stochastic inverse problems in fluorescence microscopy', in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 326 - 338, http://dx.doi.org/10.1007/978-3-319-46604-0_24
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    2016, Automatic Tracing of Ultra-Volume of Neuronal Images, , http://dx.doi.org/10.1101/087726
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    2015, 'Automated neuron morphology reconstruction using fuzzy-logic detection and Bayesian tracing algorithms', in Proceedings - International Symposium on Biomedical Imaging, pp. 885 - 888, http://dx.doi.org/10.1109/ISBI.2015.7164012
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    2014, 'An adaptive distributed resampling algorithm with non-proportional allocation', in ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings, pp. 1635 - 1639, http://dx.doi.org/10.1109/ICASSP.2014.6853875
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    2014, 'Fuzzy logic based detection of neuron bifurcations in microscopy images', in 2014 IEEE 11th International Symposium on Biomedical Imaging, ISBI 2014, pp. 1307 - 1310, http://dx.doi.org/10.1109/isbi.2014.6868117
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    2014, 'PPF - A parallel particle filtering library', in IET Conference Publications, http://dx.doi.org/10.1049/cp.2014.0529
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    2014, 'Piecewise constant sequential importance sampling for fast particle filtering', in IET Conference Publications, http://dx.doi.org/10.1049/cp.2014.0528
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    2013, 'Super-resolution reconstruction using cross-scale self-similarity in multi-slice MRI', in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 123 - 130, http://dx.doi.org/10.1007/978-3-642-40760-4_16
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    2013, Adaptive Distributed Resampling Algorithm with Non-Proportional Allocation, , http://dx.doi.org/10.48550/arxiv.1310.4624
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    2013, PPF - A Parallel Particle Filtering Library, , http://dx.doi.org/10.48550/arxiv.1310.5045
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    2013, Piecewise Constant Sequential Importance Sampling for Fast Particle Filtering, , http://dx.doi.org/10.48550/arxiv.1310.5541
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    2012, 'RECONSTRUCTION AND QUANTIFICATION OF NEURONAL MORPHOLOGY', in 2012 9TH IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING (ISBI), IEEE, SPAIN, Barcelona, pp. 1787 - 1787, presented at 9th IEEE International Symposium on Biomedical Imaging (ISBI) - From Nano to Macro, SPAIN, Barcelona, 02 May 2012 - 05 May 2012, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000312384100460&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
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    2012, 'Super-resolution reconstruction in MRI: Better images faster?', in Progress in Biomedical Optics and Imaging - Proceedings of SPIE, http://dx.doi.org/10.1117/12.911235
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    2012, 'Super-resolution reconstruction of whole-body MRI mouse data: An interactive approach', in Proceedings - International Symposium on Biomedical Imaging, pp. 1723 - 1726, http://dx.doi.org/10.1109/ISBI.2012.6235912
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    2011, 'Automated lineage tree reconstruction from Caenorhabditis elegans image data using particle filtering based cell tracking', in Proceedings - International Symposium on Biomedical Imaging, pp. 1921 - 1924, http://dx.doi.org/10.1109/ISBI.2011.5872785
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    2011, 'Quantitative comparison of tracking methods for motion analysis in tagged MRI', in Proceedings - International Symposium on Biomedical Imaging, pp. 345 - 348, http://dx.doi.org/10.1109/ISBI.2011.5872420
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    2011, 'Trans-dimensional MCMC methods for fully automatic motion analysis in tagged MRI', in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 573 - 580, http://dx.doi.org/10.1007/978-3-642-23623-5_72
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    2011, 'Trans-dimensional MCMC methods for fully automatic motion analysis in tagged MRI', in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 573 - 580, http://dx.doi.org/10.1007/978-3-642-23623-5_72
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    2010, '2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings: Welcome', in 2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings, http://dx.doi.org/10.1109/ISBI.2010.5490277
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    2010, 'Particle filtering methods for motion analysis in tagged MRI', in 2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings, pp. 488 - 491, http://dx.doi.org/10.1109/ISBI.2010.5490302
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    2009, 'Accurate estimation of microtubule dynamics using kymographs and variable-rate particle filters', in Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009, pp. 1012 - 1015, http://dx.doi.org/10.1109/IEMBS.2009.5333350
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    2009, 'Energy minimization methods for cell motion correction and intracellular analysis in live-cell fluorescence microscopy', in Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009, pp. 1127 - 1130, http://dx.doi.org/10.1109/ISBI.2009.5193255
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    2009, 'Model-based approach for tracking embryogenesis in Caenorhabditis elegans fluorescence microscopy data', in Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009, pp. 5356 - 5359, http://dx.doi.org/10.1109/IEMBS.2009.5334046
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    2009, 'Quantitative comparison of spot detection methods in live-cell fluorescence microscopy imaging', in Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009, pp. 1178 - 1181, http://dx.doi.org/10.1109/ISBI.2009.5193268
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    2008, 'A new detection scheme for multiple object tracking in fluorescence microscopy by joint probabilistic data association filtering', in 2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Proceedings, ISBI, pp. 264 - 267, http://dx.doi.org/10.1109/ISBI.2008.4540983
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    2008, 'Advanced level-set based multiple-cell segmentation and tracking in time-lapse fluorescence microscopy images', in 2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Proceedings, ISBI, pp. 185 - 188, http://dx.doi.org/10.1109/ISBI.2008.4540963
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    2007, 'A variational model for level-set based cell tracking in time-lapse fluorescence microscopy images', in 2007 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings, pp. 97 - 100, http://dx.doi.org/10.1109/ISBI.2007.356797
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    2007, 'Advanced particle filtering for multiple object tracking in dynamic fluorescence microscopy images', in 2007 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings, pp. 1048 - 1051, http://dx.doi.org/10.1109/ISBI.2007.357035
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    2007, 'Rao-blackwellized marginal particle filtering for multiple object tracking in molecular bioimaging', in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 110 - 121, http://dx.doi.org/10.1007/978-3-540-73273-0_10
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    2006, '2006 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings: Welcome', in 2006 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings
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    2006, 'Bayesian tracking for fluorescence microscopic imaging', in 2006 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings, pp. 550 - 553
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    2006, 'Particle filtering for multiple object tracking in molecular cell biology', in NSSPW - Nonlinear Statistical Signal Processing Workshop 2006, http://dx.doi.org/10.1109/NSSPW.2006.4378836
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    2004, 'Neurite tracing in fluorescence microscopy images using ridge filtering and graph searching: Principles and validation', in 2004 2nd IEEE International Symposium on Biomedical Imaging: Macro to Nano, pp. 1219 - 1222
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    2004, 'VAMPIRE: Improved method for automated center lumen line definition in atherosclerotic carotid arteries in CTA data', in Lecture Notes in Computer Science, pp. 525 - 532
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    2003, 'A novel approach to neurite tracing in fluorescence microscopy images', in Proceedings of the IASTED International Conference on Signal and Image Processing, pp. 491 - 495
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    2002, 'Diffusion-enhanced visualization and quantification of vascular anomalies in three-dimensional rotational angiography: Results of an in-vitro evaluation', in Medical Image Analysis, pp. 215 - 233, http://dx.doi.org/10.1016/S1361-8415(02)00081-6
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    2001, 'Evaluation of diffusion techniques for improved vessel visualization and quantification in three-dimensional rotational angiography', in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 177 - 185, http://dx.doi.org/10.1007/3-540-45468-3_22
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    2000, 'Guide wire tracking during endovascular interventions', in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 727 - 734, http://dx.doi.org/10.1007/978-3-540-40899-4_75
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    2000, 'Guide wire tracking in interventional radiology', in Lemke HU; Vannier MW; Inamura K; Farman AG; Doi K (eds.), CARS 2000: COMPUTER ASSISTED RADIOLOGY AND SURGERY, ELSEVIER SCIENCE BV, CA, SAN FRANCISCO, pp. 537 - 542, presented at 14th International Congress and Exhibition on Computer Assisted Radiology and Surgery (CARS 2000), CA, SAN FRANCISCO, 28 June 2000 - 01 July 2000, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000165685600090&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
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    2000, 'Spline interpolation in medical imaging: Comparison with other convolution-based approaches', in European Signal Processing Conference
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    1999, 'Fast image registration technique for motion artifact reduction in DSA', in IEEE International Conference on Image Processing, pp. 435 - 439
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    1999, 'Piecewise polynomial kernels for image interpolation: A generalization of cubic convolution', in IEEE International Conference on Image Processing, pp. 647 - 651
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    1999, 'Quantitative comparison of sinc-approximating kernels for medical image interpolation', in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 210 - 218, http://dx.doi.org/10.1007/10704282_23
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    1999, 'Sinc-approximating kernels of classical polynomial interpolation', in IEEE International Conference on Image Processing, pp. 652 - 656
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    1998, 'A fast technique for motion correction in DAS using a feature-based, irregular grid', in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 590 - 597, http://dx.doi.org/10.1007/bfb0056244
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    1998, 'General multimodal elastic registration based on mutual information', in Proceedings of SPIE - The International Society for Optical Engineering, pp. 144 - 154, http://dx.doi.org/10.1117/12.310845
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