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Select Publications

Book Chapters

Khan TM; Naqvi SS; Robles-Kelly A; Meijering E, 2023, 'Neural Network Compression by Joint Sparsity Promotion and Redundancy Reduction', in , pp. 612 - 623, http://dx.doi.org/10.1007/978-3-031-30105-6_51

Zhu J; Bolsterlee B; Chow BVY; Song Y; Meijering E, 2023, 'Uncertainty and Shape-Aware Continual Test-Time Adaptation for Cross-Domain Segmentation of Medical Images', in , pp. 659 - 669, http://dx.doi.org/10.1007/978-3-031-43898-1_63

Meijering E; Smal I; Dzyubachyk O; Olivo-Marin JC, 2022, 'Motion Tracking and Analysis', in Microscope Image Processing, Second Edition, pp. 393 - 430, http://dx.doi.org/10.1016/B978-0-12-821049-9.00013-7

Wei W; Haidinger S; Lock J; Meijering E, 2021, 'Deep Representation Learning for Image-Based Cell Profiling', in Machine Learning in Medical Imaging, pp. 487 - 497, http://dx.doi.org/10.1007/978-3-030-87589-3_50

Hu Y; Meijering E; Xia Y; Song Y, 2021, 'Deformable Convolution and Semi-supervised Learning in Point Clouds for Aneurysm Classification and Segmentation', in Neural Information Processing, pp. 283 - 290, http://dx.doi.org/10.1007/978-3-030-92310-5_33

Yao Y; Smal I; Grigoriev I; Martin M; Akhmanova A; Meijering E, 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

Meijering E; Dzyubachyk O; Smal I, 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

Meijering E; Smal I; Dzyubachyk O; Olivo-Marin JC, 2008, 'Time-Lapse Imaging', in Microscope Image Processing, pp. 401 - 440, http://dx.doi.org/10.1016/B978-0-12-372578-3.00015-5

Meijering E; Smal I; Dzyubachyk O; Olivo‐Marin J, 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

Journal articles

Khan TM; Naqvi SS; Meijering E, 2024, 'ESDMR-Net: A lightweight network with expand-squeeze and dual multiscale residual connections for medical image segmentation', Engineering Applications of Artificial Intelligence, 133, http://dx.doi.org/10.1016/j.engappai.2024.107995

Maier-Hein L; Reinke A; Godau P; Tizabi MD; Buettner F; Christodoulou E; Glocker B; Isensee F; Kleesiek J; Kozubek M; Reyes M; Riegler MA; Wiesenfarth M; Kavur AE; Sudre CH; Baumgartner M; Eisenmann M; Heckmann-Nötzel D; Rädsch T; Acion L; Antonelli M; Arbel T; Bakas S; Benis A; Blaschko MB; Cardoso MJ; Cheplygina V; Cimini BA; Collins GS; Farahani K; Ferrer L; Galdran A; van Ginneken B; Haase R; Hashimoto DA; Hoffman MM; Huisman M; Jannin P; Kahn CE; Kainmueller D; Kainz B; Karargyris A; Karthikesalingam A; Kofler F; Kopp-Schneider A; Kreshuk A; Kurc T; Landman BA; Litjens G; Madani A; Maier-Hein K; Martel AL; Mattson P; Meijering E; Menze B; Moons KGM; Müller H; Nichyporuk B; Nickel F; Petersen J; Rajpoot N; Rieke N; Saez-Rodriguez J; Sánchez CI; Shetty S; van Smeden M; Summers RM; Taha AA; Tiulpin A; Tsaftaris SA; Van Calster B; Varoquaux G; Jäger PF, 2024, 'Metrics reloaded: recommendations for image analysis validation', Nature Methods, 21, pp. 195 - 212, http://dx.doi.org/10.1038/s41592-023-02151-z

Reinke A; Tizabi MD; Baumgartner M; Eisenmann M; Heckmann-Nötzel D; Kavur AE; Rädsch T; Sudre CH; Acion L; Antonelli M; Arbel T; Bakas S; Benis A; Buettner F; Cardoso MJ; Cheplygina V; Chen J; Christodoulou E; Cimini BA; Farahani K; Ferrer L; Galdran A; van Ginneken B; Glocker B; Godau P; Hashimoto DA; Hoffman MM; Huisman M; Isensee F; Jannin P; Kahn CE; Kainmueller D; Kainz B; Karargyris A; Kleesiek J; Kofler F; Kooi T; Kopp-Schneider A; Kozubek M; Kreshuk A; Kurc T; Landman BA; Litjens G; Madani A; Maier-Hein K; Martel AL; Meijering E; Menze B; Moons KGM; Müller H; Nichyporuk B; Nickel F; Petersen J; Rafelski SM; Rajpoot N; Reyes M; Riegler MA; Rieke N; Saez-Rodriguez J; Sánchez CI; Shetty S; Summers RM; Taha AA; Tiulpin A; Tsaftaris SA; Van Calster B; Varoquaux G; Yaniv ZR; Jäger PF; Maier-Hein L, 2024, 'Understanding metric-related pitfalls in image analysis validation', Nature Methods, 21, pp. 182 - 194, http://dx.doi.org/10.1038/s41592-023-02150-0

Hasan MM; Phu J; Sowmya A; Meijering E; Kalloniatis M, 2024, 'Artificial intelligence in the diagnosis of glaucoma and neurodegenerative diseases', Clinical and Experimental Optometry, 107, pp. 130 - 146, http://dx.doi.org/10.1080/08164622.2023.2235346

Liu M; Wu S; Chen R; Lin Z; Wang Y; Meijering E, 2024, 'Brain Image Segmentation for Ultrascale Neuron Reconstruction via an Adaptive Dual-Task Learning Network', IEEE Transactions on Medical Imaging, http://dx.doi.org/10.1109/TMI.2024.3367384

Tchetchenian A; Zhu Y; Zhang F; O’Donnell LJ; Song Y; Meijering E, 2023, 'A comparison of manual and automated neural architecture search for white matter tract segmentation', Scientific Reports, 13, http://dx.doi.org/10.1038/s41598-023-28210-1

Rahaman MM; Millar EKA; Meijering E, 2023, 'Breast cancer histopathology image-based gene expression prediction using spatial transcriptomics data and deep learning', Scientific Reports, 13, pp. 13604, http://dx.doi.org/10.1038/s41598-023-40219-0

Chen R; Liu M; Chen W; Wang Y; Meijering E, 2023, 'Deep learning in mesoscale brain image analysis: A review', Computers in Biology and Medicine, 167, http://dx.doi.org/10.1016/j.compbiomed.2023.107617

Shen W; Wang Y; Liu M; Wang J; Ding R; Zhang Z; Meijering E, 2023, 'Branch Aggregation Attention Network for Robotic Surgical Instrument Segmentation', IEEE Transactions on Medical Imaging, 42, pp. 3408 - 3419, http://dx.doi.org/10.1109/TMI.2023.3288127

Gunawan I; Vafaee F; Meijering E; Lock JG, 2023, 'An introduction to representation learning for single-cell data analysis', Cell Reports Methods, 3, http://dx.doi.org/10.1016/j.crmeth.2023.100547

Maška M; Ulman V; Delgado-Rodriguez P; Gómez-de-Mariscal E; Nečasová T; Guerrero Peña FA; Ren TI; Meyerowitz EM; Scherr T; Löffler K; Mikut R; Guo T; Wang Y; Allebach JP; Bao R; Al-Shakarji NM; Rahmon G; Toubal IE; Palaniappan K; Lux F; Matula P; Sugawara K; Magnusson KEG; Aho L; Cohen AR; Arbelle A; Ben-Haim T; Raviv TR; Isensee F; Jäger PF; Maier-Hein KH; Zhu Y; Ederra C; Urbiola A; Meijering E; Cunha A; Muñoz-Barrutia A; Kozubek M; Ortiz-de-Solórzano C, 2023, 'The Cell Tracking Challenge: 10 years of objective benchmarking', Nature Methods, 20, pp. 1010 - 1020, http://dx.doi.org/10.1038/s41592-023-01879-y

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, 20, pp. 824 - 835, http://dx.doi.org/10.1038/s41592-023-01848-5

Aviyente S; Frangi AF; Meijering E; Munoz-Barrutia A; Liebling M; Van De Ville D; Olivo-Marin JC; Kovacevic J; Unser M, 2023, 'From Nano to Macro: An overview of the IEEE Bio Image and Signal Processing Technical Committee', IEEE Signal Processing Magazine, 40, pp. 61 - 71, http://dx.doi.org/10.1109/MSP.2023.3242833

Zhu Y; Yin X; Meijering E, 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

Fan L; Sowmya A; Meijering E; Song Y, 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

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, 15, pp. 2569, http://dx.doi.org/10.3390/cancers15092569

Khan TM; Arsalan M; Razzak I; Meijering E, 2023, 'Simple and robust depth-wise cascaded network for polyp segmentation', Engineering Applications of Artificial Intelligence, 121, http://dx.doi.org/10.1016/j.engappai.2023.106023

Wei X; Liu Q; Liu M; Wang Y; Meijering E, 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

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, http://dx.doi.org/10.3390/s23010062

Rana P; Sowmya A; Meijering E; Song Y, 2023, 'Imbalanced classification for protein subcellular localization with multilabel oversampling', Bioinformatics, 39, http://dx.doi.org/10.1093/bioinformatics/btac841

Liu M; Han Y; Wang J; Wang C; Wang Y; Meijering E, 2023, 'LSKANet: Long Strip Kernel Attention Network for Robotic Surgical Scene Segmentation', IEEE Transactions on Medical Imaging, http://dx.doi.org/10.1109/TMI.2023.3335406

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', Biomaterials and Biosystems, 8, http://dx.doi.org/10.1016/j.bbiosy.2022.100068

Rana P; Sowmya A; Meijering E; Song Y, 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

Khan TM; Naqvi SS; Meijering E, 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

Sandarenu P; Millar EKA; Song Y; Browne L; Beretov J; Lynch J; Graham PH; Jonnagaddala J; Hawkins N; Huang J; Meijering E, 2022, 'Survival prediction in triple negative breast cancer using multiple instance learning of histopathological images', Scientific Reports, 12, http://dx.doi.org/10.1038/s41598-022-18647-1

Wang X; Liu M; Wang Y; Fan J; Meijering E, 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

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

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

Fetanat M; Stevens M; Jain P; Hayward C; Meijering E; Lovell NH, 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

Yang B; Liu M; Wang Y; Zhang K; Meijering E, 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

Meijering E; Calhoun VD; Menegaz G; Miller DJ; Ye JC, 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

Du H; Wang J; Liu M; Wang Y; Meijering E, 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

Zhu Y; Meijering E, 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

Zhu J; Bolsterlee B; Chow BVY; Cai C; Herbert RD; Song Y; Meijering E, 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, http://dx.doi.org/10.1002/nbm.4609

Rana P; Sowmya A; Meijering E; Song Y, 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

Lin Z; Wu B; Paul MW; Li KW; Yao Y; Smal I; Onori MP; Hasanbegovic H; Bezstarosti K; Demmers J; Houtsmuller AB; Meijering E; Hoebeek FE; Schonewille M; Smit AB; Gao Z; de Zeeuw CI, 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

Mouiee DA; Meijering E; Kalloniatis M; Nivison-Smith L; Williams RA; Nayagam DAX; Spencer TC; Luu CD; McGowan C; Epp SB; Shivdasani MN, 2021, 'Classifying retinal degeneration in histological sections using deep learning', Translational Vision Science and Technology, 10, http://dx.doi.org/10.1167/tvst.10.7.9

Shen L; Liu M; Wang C; Guo C; Meijering E; Wang Y, 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

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

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

Serra-Marques A; Martin M; Katrukha EA; Grigoriev I; Peeters CAE; Liu Q; Hooikaas PJ; Yao Y; Solianova V; Smal I; Pedersen LB; Meijering E; Kapitein LC; Akhmanova A, 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


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