By Professor Erik Meijering

Journal articles

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

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

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

Yao Y; Smal I; Grigoriev I; Akhmanova A; Meijering E, 2020, 'Deep-learning method for data association in particle tracking', Bioinformatics, 36, pp. 4935 - 4941, http://dx.doi.org/10.1093/bioinformatics/btaa597

Meijering E, 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

Arts M; Smal I; Paul MW; Wyman C; Meijering E, 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

Radojević M; Meijering E, 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

Fehri H; Gooya A; Lu Y; Meijering E; Johnston SA; Frangi AF, 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

Mata G; Radojević M; Fernandez-Lozano C; Smal I; Werij N; Morales M; Meijering E; Rubio J, 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

Castilla C; Maska M; Sorokin DV; Meijering E; Ortiz-De-Solorzano C, 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

Kuil LE; Oosterhof N; Geurts SN; Van Der Linde HC; Meijering E; Van Ham TJ, 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

Meijering E; Munoz-Barrutia A, 2018, 'IN THE SPOTLIGHT', IEEE SIGNAL PROCESSING MAGAZINE, 35, pp. 125 - +, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000450235600013&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Meijering E; Munoz-Barrutia A, 2018, 'Spotlight on Bioimaging and Signal Processing [In the Spotlight]', IEEE Signal Processing Magazine, 35, pp. 125 - 128, http://dx.doi.org/10.1109/MSP.2018.2864772

Ulman V; Maška M; Magnusson KEG; Ronneberger O; Haubold C; Harder N; Matula P; Matula P; Svoboda D; Radojevic M; Smal I; Rohr K; Jaldén J; Blau HM; Dzyubachyk O; Lelieveldt B; Xiao P; Li Y; Cho SY; Dufour AC; Olivo-Marin JC; Reyes-Aldasoro CC; Solis-Lemus JA; Bensch R; Brox T; Stegmaier J; Mikut R; Wolf S; Hamprecht FA; Esteves T; Quelhas P; Demirel Ö; Malmström L; Jug F; Tomancak P; Meijering E; Muñoz-Barrutia A; Kozubek M; Ortiz-De-Solorzano C, 2017, 'An objective comparison of cell-tracking algorithms', Nature Methods, 14, pp. 1141 - 1152, http://dx.doi.org/10.1038/nmeth.4473

Yang C; Wu J; de Heus C; Grigoriev I; Liv N; Yao Y; Smal I; Meijering E; Klumperman J; Qi RZ; Akhmanova A, 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

Radojević M; Meijering E, 2017, 'Automated neuron tracing using probability hypothesis density filtering', Bioinformatics, 33, pp. 1073 - 1080, http://dx.doi.org/10.1093/bioinformatics/btw751

Peng H; Zhou Z; Meijering E; Zhao T; Ascoli GA; Hawrylycz M, 2017, 'Automatic tracing of ultra-volumes of neuronal images', Nature Methods, 14, pp. 332 - 333, http://dx.doi.org/10.1038/nmeth.4233

Meijering E; Carpenter AE; Peng H; Hamprecht FA; Olivo-Marin JC, 2016, 'Imagining the future of bioimage analysis', Nature Biotechnology, 34, pp. 1250 - 1255, http://dx.doi.org/10.1038/nbt.3722

Radojević M; Smal I; Meijering E, 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

Plenge E; Klein S; Niessen WJ; Meijering E, 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

Smal I; Meijering E, 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

Peng H; Meijering E; Ascoli GA, 2015, 'From DIADEM to BigNeuron', Neuroinformatics, 13, pp. 259 - 260, http://dx.doi.org/10.1007/s12021-015-9270-9

Peng H; Hawrylycz M; Roskams J; Hill S; Spruston N; Meijering E; Ascoli GA, 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

Plenge E; Klein SS; Niessen WJ; Meijering E, 2015, 'Multiple sparse representations classification', Plos One, 10, http://dx.doi.org/10.1371/journal.pone.0131968

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