Select Publications

Book Chapters

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 J, 2008, 'Chapter 15 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 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

Journal articles

Rana P; Sowmya A; Meijering E; Song Y, 2021, 'Estimation of three-dimensional chromatin morphology for nuclear classification and characterisation', Scientific Reports, vol. 11, http://dx.doi.org/10.1038/s41598-021-82985-9

Zhu Y; Meijering E, 2021, 'Automatic Improvement of Deep Learning Based Cell Segmentation in Time-Lapse Microscopy by Neural Architecture Search.', Bioinformatics, http://dx.doi.org/10.1093/bioinformatics/btab556

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, vol. 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, vol. 10, pp. 9, 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 12, http://dx.doi.org/10.1242/dmm.037762

Meijering E; Munoz-Barrutia A, 2018, 'IN THE SPOTLIGHT', IEEE SIGNAL PROCESSING MAGAZINE, vol. 35, pp. 125 - +, http://gateway.webofknowledge.com/gateway/Gateway.cgi?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, vol. 35, 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 13, pp. 259 - 260, http://dx.doi.org/10.1007/s12021-015-9270-9

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

Reuter M; Zelensky A; Smal I; Meijering E; van Cappellen WA; de Gruiter HM; van Belle GJ; van Royen ME; Houtsmuller AB; Essers J; Kanaar R; Wyman C, 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, vol. 208, pp. 857 - 857, http://dx.doi.org/10.1083/jcb.20140501402182015c

Krüger AV; Jelier R; Dzyubachyk O; Zimmerman T; Meijering E; Lehner B, 2015, 'Comprehensive single cell-resolution analysis of the role of chromatin regulators in early C. elegans embryogenesis', Developmental Biology, vol. 398, pp. 153 - 162, http://dx.doi.org/10.1016/j.ydbio.2014.10.014

Spanjaard E; Smal I; Angelopoulos N; Verlaan I; Matov A; Meijering E; Wessels L; Bos H; de Rooij J, 2015, 'Quantitative imaging of focal adhesion dynamics and their regulation by HGF and Rap1 signaling', Experimental Cell Research, vol. 330, pp. 382 - 397, http://dx.doi.org/10.1016/j.yexcr.2014.10.012

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, vol. 87, pp. 252 - 256, http://dx.doi.org/10.1016/j.neuron.2015.06.036

Reuter M; Zelensky A; Smal I; Meijering E; van Cappellen WA; Martijn de Gruiter H; van Belle GJ; van Royen ME; Houtsmuller AB; Essers J; Kanaar R; Wyman C, 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, vol. 208, pp. 857 - 857, http://dx.doi.org/10.1083/jcb.20140501402182015c

Muñoz-Barrutia A; Kovačević J; Kozubek M; Meijering E; Parvin B, 2015, 'Quantitative bioimaging: Signal processing in light microscopy', IEEE Signal Processing Magazine, vol. 32, pp. 18 - 19, http://dx.doi.org/10.1109/MSP.2014.2359691

Ortiz-De-Solórzano C; Muñoz-Barrutia A; Meijering E; Kozubek M, 2015, 'Toward a morphodynamic model of the cell: Signal processing for cell modeling', IEEE Signal Processing Magazine, vol. 32, pp. 20 - 29, http://dx.doi.org/10.1109/MSP.2014.2358263

Ramnath NWM; Van De Luijtgaarden KM; Van Der Pluijm I; Van Nimwegen M; Van Heijningen PM; Swagemakers SMA; Van Thiel BS; Ridwan RY; Van Vliet N; Vermeij M; Hawinkels LJAC; De Munck A; Dzyubachyk O; Meijering E; Van Der Spek P; Rottier R; Yanagisawa H; Hendriks RW; Kanaar R; Rouwet EV; Kleinjan A; Essers J, 2014, 'Extracellular matrix defects in aneurysmal Fibulin-4 mice predispose to lung emphysema', PLoS ONE, vol. 9, http://dx.doi.org/10.1371/journal.pone.0106054

Dzyubachyk O; Khmelinskii A; Plenge E; Kok P; Snoeks TJA; Poot DHJ; Lowik CWGM; Botha CP; Niessen WJ; Van Der Weerd L; Meijering E; Lelieveldt BPF, 2014, 'Interactive local super-resolution reconstruction of whole-body MRI mouse data: A pilot study with applications to bone and kidney metastases', PLoS ONE, vol. 9, http://dx.doi.org/10.1371/journal.pone.0108730

Maška M; Ulman V; Svoboda D; Matula P; Matula P; Ederra C; Urbiola A; España T; Venkatesan S; Balak DMW; Karas P; Bolcková T; Štreitová M; Carthel C; Coraluppi S; Harder N; Rohr K; Magnusson KEG; Jaldén J; Blau HM; Dzyubachyk O; Křížek P; Hagen GM; Pastor-Escuredo D; Jimenez-Carretero D; Ledesma-Carbayo MJ; Muñoz-Barrutia A; Meijering E; Kozubek M; Ortiz-De-Solorzano C, 2014, 'A benchmark for comparison of cell tracking algorithms', Bioinformatics, vol. 30, pp. 1609 - 1617, http://dx.doi.org/10.1093/bioinformatics/btu080

Chenouard N; Smal I; De Chaumont F; Maška M; Sbalzarini IF; Gong Y; Cardinale J; Carthel C; Coraluppi S; Winter M; Cohen AR; Godinez WJ; Rohr K; Kalaidzidis Y; Liang L; Duncan J; Shen H; Xu Y; Magnusson KEG; Jaldén J; Blau HM; Paul-Gilloteaux P; Roudot P; Kervrann C; Waharte F; Tinevez JY; Shorte SL; Willemse J; Celler K; Van Wezel GP; Dan HW; Tsai YS; De Solórzano CO; Olivo-Marin JC; Meijering E, 2014, 'Objective comparison of particle tracking methods', Nature Methods, vol. 11, pp. 281 - 289, http://dx.doi.org/10.1038/nmeth.2808

Reuter M; Zelensky A; Smal I; Meijering E; van Cappellen WA; de Gruiter HM; van Belle GJ; van Royen ME; Houtsmuller AB; Essers J; Kanaar R; Wyman C, 2014, 'BRCA2 diffuses as oligomeric clusters with RAD51 and changes mobility after DNA damage in live cells', Journal of Cell Biology, vol. 207, pp. 599 - 613, http://dx.doi.org/10.1083/jcb.201405014

Poole DS; Plenge E; Poot DHJ; Lakke EAJF; Niessen WJ; Meijering E; van der Weerd L, 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, vol. 27, pp. 749 - 759, http://dx.doi.org/10.1002/nbm.3108

Plenge E; Poot DHJ; Niessen WJ; Meijering E, 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), vol. 8151 LNCS, pp. 123 - 130, http://dx.doi.org/10.1007/978-3-642-40760-4_16

Mohan R; Katrukha EA; Doodhi H; Smal I; Meijering E; Kapitein LC; Steinmetz MO; Akhmanova A, 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, vol. 110, pp. 8900 - 8905, http://dx.doi.org/10.1073/pnas.1300395110

Meijering E, 2012, 'Cell segmentation: 50 Years down the road [life Sciences]', IEEE Signal Processing Magazine, vol. 29, pp. 140 - 145, http://dx.doi.org/10.1109/MSP.2012.2204190

Smal I; Carranza-Herrezuelo N; Klein S; Wielopolski P; Moelker A; Springeling T; Bernsen M; Niessen W; Meijering E, 2012, 'Reversible jump MCMC methods for fully automatic motion analysis in tagged MRI', Medical Image Analysis, vol. 16, pp. 301 - 324, http://dx.doi.org/10.1016/j.media.2011.08.006

Plenge E; Poot DHJ; Bernsen M; Kotek G; Houston G; Wielopolski P; Van Der Weerd L; Niessen WJ; Meijering E, 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, vol. 68, pp. 1983 - 1993, http://dx.doi.org/10.1002/mrm.24187


Back to profile page