Taking Aim at Moving Targets in Computational Cell Migration

Aman, 2010, Cell migration during morphogenesis, Dev. Biol., 341, 20, 10.1016/j.ydbio.2009.11.014 Vicente-Manzanares, 2011, Cell migration: an overview, Methods Mol. Biol., 769, 1, 10.1007/978-1-61779-207-6_1 Theveneau, 2012, Neural crest delamination and migration: from epithelium-to-mesenchyme transition to collective cell migration, Dev. Biol., 366, 34, 10.1016/j.ydbio.2011.12.041 Friedl, 2012, Classifying collective cancer cell invasion, Nat. Cell Biol., 14, 777, 10.1038/ncb2548 Li, 2013, Collective cell migration: implications for wound healing and cancer invasion, Burns Trauma, 1, 21, 10.4103/2321-3868.113331 Cooper, 2013, Cell biology in neuroscience: mechanisms of cell migration in the nervous system, J. Cell Biol., 202, 725, 10.1083/jcb.201305021 Teijeira, 2014, Taking the lymphatic route: dendritic cell migration to draining lymph nodes, Semin. Immunopathol., 36, 261, 10.1007/s00281-013-0410-8 Reig, 2014, Cell migration: from tissue culture to embryos, Development, 141, 1999, 10.1242/dev.101451 Sanz-Moreno, 2010, The plasticity of cytoskeletal dynamics underlying neoplastic cell migration, Curr. Opin. Cell Biol., 22, 690, 10.1016/j.ceb.2010.08.020 Wells, 2013, Targeting tumor cell motility as a strategy against invasion and metastasis, Trends Pharmacol. Sci., 34, 283, 10.1016/j.tips.2013.03.001 Biro, 2014, Targeting Rho-GTPases in immune cell migration and inflammation, Br. J. Pharmacol., 171, 5491, 10.1111/bph.12658 Cockle, 2015, Cell migration in paediatric glioma; characterisation and potential therapeutic targeting, Br. J. Cancer, 112, 693, 10.1038/bjc.2015.16 Ashby, 2012, Established and novel methods of interrogating two-dimensional cell migration, Integr. Biol., 4, 1338, 10.1039/c2ib20154b Kramer, 2013, In vitro cell migration and invasion assays, Mutat. Res., 752, 10, 10.1016/j.mrrev.2012.08.001 Friedl, 2012, New dimensions in cell migration, Nat. Rev. Mol. Cell Biol., 13, 743, 10.1038/nrm3459 Doyle, 2013, Dimensions in cell migration, Curr. Opin. Cell Biol., 25, 642, 10.1016/j.ceb.2013.06.004 Yarrow, 2005, Screening for cell migration inhibitors via automated microscopy reveals a Rho-kinase inhibitor, Chem. Biol., 12, 385, 10.1016/j.chembiol.2005.01.015 Hulkower, 2011, Cell migration and invasion assays as tools for drug discovery, Pharmaceutics, 3, 107, 10.3390/pharmaceutics3010107 Zhou, 2011, Tumor-stroma: In vivo assays and intravital imaging to study cell migration and metastasis, Drug Discov. Today Dis. Models, 8, 95, 10.1016/j.ddmod.2011.07.003 Leong, 2012, Assessing cancer cell migration and metastatic growth in vivo in the chick embryo using fluorescence intravital imaging, Methods Mol. Biol., 872, 1, 10.1007/978-1-61779-797-2_1 Patsialou, 2013, Intravital multiphoton imaging reveals multicellular streaming as a crucial component of in vivo cell migration in human breast tumors, Intravital, 2, e25294, 10.4161/intv.25294 Benechet, 2014, Visualizing T cell migration in situ, Front. Immunol., 5, 363, 10.3389/fimmu.2014.00363 Munoz, 2014, T cell migration in intact lymph nodes in vivo, Curr. Opin. Cell Biol., 30, 17, 10.1016/j.ceb.2014.05.002 Masuzzo, 2015, An open data ecosystem for cell migration research, Trends Cell Biol., 25, 55, 10.1016/j.tcb.2014.11.005 Danuser, 2013, Mathematical modeling of eukaryotic cell migration: insights beyond experiments, Annu. Rev. Cell Dev. Biol., 29, 501, 10.1146/annurev-cellbio-101512-122308 Kam, 2012, Cellular modeling of cancer invasion: integration of in silico and in vitro approaches, J. Cell. Physiol., 227, 431, 10.1002/jcp.22766 Debeir, 2008, Models of cancer cell migration and cellular imaging and analysis, 123 Eils, 2003, Computational imaging in cell biology, J. Cell Biol., 161, 477, 10.1083/jcb.200302097 Dormann, 2006, Imaging of cell migration, EMBO J., 25, 3480, 10.1038/sj.emboj.7601227 Combs, 2001, Fluorescence microscopy: a concise guide to current imaging methods, Curr. Protoc. Neurosci., 50 Boutet de Monvel, 2001, Image restoration for confocal microscopy: improving the limits of deconvolution, with application to the visualization of the mammalian hearing organ, Biophys. J., 80, 2455, 10.1016/S0006-3495(01)76214-5 Gerlich, 2003, Quantitative motion analysis and visualization of cellular structures, Methods, 29, 3, 10.1016/S1046-2023(02)00287-6 Biggs, 2010, A practical guide to deconvolution of fluorescence microscope imagery, Microsc. Today, 18, 10, 10.1017/S1551929510991311 Sekko, 1999, A deconvolution technique using optimal Wiener filtering and regularization, Signal Process., 72, 23, 10.1016/S0165-1684(98)00161-3 Ramani, 2008, Deconvolution of 3D fluorescence micrographs with automatic risk minimization, 732 Sarder, 2006, Deconvolution methods for 3-D fluorescence microscopy images, IEEE Signal Process. Mag., 23, 32, 10.1109/MSP.2006.1628876 Soulez, 2012, Blind deconvolution of 3D data in wide field fluorescence microscopy, 1735 Agard, 1984, Optical sectioning microscopy: cellular architecture in three dimensions, Annu. Rev. Biophys. Bioeng., 13, 191, 10.1146/annurev.bb.13.060184.001203 Keuper, 2012, Blind deconvolution with PSF regularization for wide-field microscopy, 1292 Vonesch, 2009, A fast multilevel algorithm for wavelet-regularized image restoration, IEEE Trans. Image Process., 18, 509, 10.1109/TIP.2008.2008073 Dupe, 2008, Deconvolution of confocal microscopy images using proximal iteration and sparse representations, 736 Ben Hadj, 2012, Modeling and removing depth variant blur in 3D fluorescence microscopy, 689 Trepat, 2012, Cell migration, Compr. Physiol., 2, 2369, 10.1002/cphy.c110012 Ilina, 2009, Mechanisms of collective cell migration at a glance, J. Cell Sci., 122, 3203, 10.1242/jcs.036525 Theveneau, 2013, Collective cell migration of epithelial and mesenchymal cells, Cell. Mol. Life Sci., 70, 3481, 10.1007/s00018-012-1251-7 Huth, 2010, Significantly improved precision of cell migration analysis in time-lapse video microscopy through use of a fully automated tracking system, BMC Cell Biol., 11, 24, 10.1186/1471-2121-11-24 Zaritsky, 2013, Benchmark for multi-cellular segmentation of bright field microscopy images, BMC Bioinformatics, 14, 319, 10.1186/1471-2105-14-319 Maška, 2014, A benchmark for comparison of cell tracking algorithms, Bioinformatics, 30, 1609, 10.1093/bioinformatics/btu080 Wu, 2010 Sankur, 2004, Survey over image thresholding techniques and quantitative performance evaluation, J. Electron. Imaging, 13, 146, 10.1117/1.1631315 Gonzalez, 2008 Wählby, 2004, Combining intensity, edge and shape information for 2D and 3D segmentation of cell nuclei in tissue sections, J. Microsc., 215, 67, 10.1111/j.0022-2720.2004.01338.x Yang, 2006, Nuclei segmentation using marker-controlled watershed, tracking using mean-shift, and Kalman Filter in time-lapse microscopy, IEEE Trans. Circ. Syst. I: Regul. Papers, 53, 2405, 10.1109/TCSI.2006.884469 Lin, 2007, A multi-model approach to simultaneous segmentation and classification of heterogeneous populations of cell nuclei in 3D confocal microscope images, Cytometry A, 71, 724, 10.1002/cyto.a.20430 Ali, 2008, Advanced phase-based segmentation of multiple cells from brightfield microscopy images, 181 Zordan, 2011, A high throughput, interactive imaging, bright-field wound healing assay, Cytometry A, 79, 227, 10.1002/cyto.a.21029 Yin, 2010, Cell segmentation in microscopy imagery using a bag of local Bayesian classifiers, 125 Zaritsky, 2011, Cell motility dynamics: a novel segmentation algorithm to quantify multi-cellular bright field microscopy images, PLoS ONE, 6, e27593, 10.1371/journal.pone.0027593 Gebäck, 2009, TScratch: a novel and simple software tool for automated analysis of monolayer wound healing assays, Biotechniques, 46, 265, 10.2144/000113083 Topman, 2012, A standardized objective method for continuously measuring the kinematics of cultures covering a mechanically damaged site, Med. Eng. Phys., 34, 225, 10.1016/j.medengphy.2011.07.014 Kass, 1988, Snakes: active contour models, Int. J. Comput. Vis., 1988, 321, 10.1007/BF00133570 Cohen, 1991, On active contour models and balloons, CVGIP: Image Underst., 53, 211, 10.1016/1049-9660(91)90028-N Ray, 2002, Active contours for cell tracking, 274 Li, 2008, Cell population tracking and lineage construction with spatiotemporal context, Med. Image Anal., 12, 546, 10.1016/j.media.2008.06.001 Yang, 2005, Cell segmentation, tracking, and mitosis detection using temporal context, Med. Image Comput. Comput. Assist. Interv., 8, 302 Dufour, 2005, Segmenting and tracking fluorescent cells in dynamic 3-D microscopy with coupled active surfaces, IEEE Trans. Image Process., 14, 1396, 10.1109/TIP.2005.852790 Dzyubachyk, 2010, Advanced level-set-based cell tracking in time-lapse fluorescence microscopy, IEEE Trans. Med. Imaging, 29, 852, 10.1109/TMI.2009.2038693 Cheng, 1995, Mean shift, mode seeking, and clustering, IEEE Trans. Pattern Anal. Mach. Intell., 17, 790, 10.1109/34.400568 Liu, 2008 Smal, 2008, Particle filtering for multiple object tracking in dynamic fluorescence microscopy images: application to microtubule growth analysis, IEEE Trans. Med. Imaging, 27, 789, 10.1109/TMI.2008.916964 Rapoport, 2011, A novel validation algorithm allows for automated cell tracking and the extraction of biologically meaningful parameters, PLoS ONE, 6, e27315, 10.1371/journal.pone.0027315 Kanade, 2011, Cell image analysis: Algorithms, system and applications, 374 Huh, 2011, Automated mitosis detection of stem cell populations in phase-contrast microscopy images, IEEE Trans. Med. Imaging, 30, 586, 10.1109/TMI.2010.2089384 Amat, 2013, 3D Haar-like elliptical features for object classification in microscopy, 1194 Friedl, 2009, Collective cell migration in morphogenesis, regeneration and cancer, Nat. Rev. Mol. Cell Biol., 10, 445, 10.1038/nrm2720 Rørth, 2009, Collective cell migration, Annu. Rev. Cell Dev. Biol., 25, 407, 10.1146/annurev.cellbio.042308.113231 Rørth, 2012, Fellow travellers: emergent properties of collective cell migration, EMBO Rep., 13, 984, 10.1038/embor.2012.149 Riahi, 2012, Advances in wound-healing assays for probing collective cell migration, J. Lab. Autom., 17, 59, 10.1177/2211068211426550 Anon, 2012, Cell crawling mediates collective cell migration to close undamaged epithelial gaps, Proc. Natl. Acad. Sci. U.S.A., 109, 10891, 10.1073/pnas.1117814109 Meyvantsson, 2008, Cell culture models in microfluidic systems, Annu. Rev. Anal. Chem., 1, 423, 10.1146/annurev.anchem.1.031207.113042 Liang, 2007, In vitro scratch assay: a convenient and inexpensive method for analysis of cell migration in vitro, Nat. Protoc., 2, 329, 10.1038/nprot.2007.30 Ranzato, 2011, Wound healing properties of jojoba liquid wax: an in vitro study, J. Ethnopharmacol., 134, 443, 10.1016/j.jep.2010.12.042 Walter, 2010, Mesenchymal stem cell-conditioned medium accelerates skin wound healing: an in vitro study of fibroblast and keratinocyte scratch assays, Exp. Cell Res., 316, 1271, 10.1016/j.yexcr.2010.02.026 Büth, 2007, Cathepsin B is essential for regeneration of scratch-wounded normal human epidermal keratinocytes, Eur. J. Cell Biol., 86, 747, 10.1016/j.ejcb.2007.03.009 Simpson, 2008, Identification of genes that regulate epithelial cell migration using an siRNA screening approach, Nat. Cell Biol., 10, 1027, 10.1038/ncb1762 Supatto, 2005, In vivo modulation of morphogenetic movements in Drosophila embryos with femtosecond laser pulses, Proc. Natl. Acad. Sci. U.S.A., 102, 1047, 10.1073/pnas.0405316102 Raffel, 2007 Petitjean, 2010, Velocity fields in a collectively migrating epithelium, Biophys. J., 98, 1790, 10.1016/j.bpj.2010.01.030 Milde, 2012, Cell Image Velocimetry (CIV): boosting the automated quantification of cell migration in wound healing assays, Integr. Biol., 4, 1437, 10.1039/c2ib20113e Friedl, 2010, Plasticity of cell migration: a multiscale tuning model, J. Exp. Med., 207, 11, 10.1084/JEM2071OIA4 Huttenlocher, 2011, Integrins in cell migration, Cold Spring Harb. Perspect. Biol., 3, a005074, 10.1101/cshperspect.a005074 Maheshwari, 1998, Deconstructing (and reconstructing) cell migration, Microsc. Res. Tech., 43, 358, 10.1002/(SICI)1097-0029(19981201)43:5<358::AID-JEMT2>3.0.CO;2-D Mokhtari, 2013, Automated characterization and parameter-free classification of cell tracks based on local migration behavior, PLoS ONE, 8, e80808, 10.1371/journal.pone.0080808 Gorelik, 2014, Quantitative and unbiased analysis of directional persistence in cell migration, Nat. Protoc., 9, 1931, 10.1038/nprot.2014.131 Beltman, 2009, Analysing immune cell migration, Nat. Rev. Immunol., 9, 789, 10.1038/nri2638 Pincus, 2007, Comparison of quantitative methods for cell-shape analysis, J. Microsc., 227, 140, 10.1111/j.1365-2818.2007.01799.x Murray, 2006, The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree, Nat. Protoc., 1, 1468, 10.1038/nprot.2006.222 Abràmoff, 2004, Image processing with Image, J. Biophotonics Int., 11, 36 Schindelin, 2012, Fiji: an open-source platform for biological-image analysis, Nat. Methods, 9, 676, 10.1038/nmeth.2019 Carpenter, 2006, CellProfiler: image analysis software for identifying and quantifying cell phenotypes, Genome Biol., 7, R100, 10.1186/gb-2006-7-10-r100 De Chaumont, 2012, Icy: an open bioimage informatics platform for extended reproducible research, Nat. Methods, 9, 690, 10.1038/nmeth.2075 Deforet, 2012, Automated velocity mapping of migrating cell populations (AVeMap), Nat. Methods, 9, 1081, 10.1038/nmeth.2209 Taylor, 2010, Long-duration time-resolved PIV to study unsteady aerodynamics, IEEE Trans. Instrum. Meas., 59, 3262, 10.1109/TIM.2010.2047149 Chapnick, 2013, The development of a novel high throughput computational tool for studying individual and collective cellular migration, PLoS ONE, 8, e82444, 10.1371/journal.pone.0082444 Culjak, 2013, A brief introduction to OpenCV, 2142 Sacan, 2008, CellTrack: an open-source software for cell tracking and motility analysis, Bioinformatics, 24, 1647, 10.1093/bioinformatics/btn247 Van der Walt, 2014, scikit-image: image processing in Python, PeerJ, 2, e453, 10.7717/peerj.453 Goldberg, 2005, The open microscopy environment (OME) data model and XML file: open tools for informatics and quantitative analysis in biological imaging, Genome Biol., 6, R47, 10.1186/gb-2005-6-5-r47 Held, 2010, CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging, Nat. Methods, 7, 747, 10.1038/nmeth.1486 Sommer, 2013, CellH5: a format for data exchange in high-content screening, Bioinformatics, 29, 1580, 10.1093/bioinformatics/btt175 Lock, 2010, Systems microscopy: an emerging strategy for the life sciences, Exp. Cell Res., 316, 1438, 10.1016/j.yexcr.2010.04.001 Le Dévédec, 2010, Systems microscopy approaches to understand cancer cell migration and metastasis, Cell. Mol. Life Sci., 67, 3219, 10.1007/s00018-010-0419-2 Eddy, 2015, Fostering synergy between cell biology and systems biology, Trends Cell Biol., 25, 440, 10.1016/j.tcb.2015.04.005 Rosello, 2004, Model driven quantification of individual and collective cell migration, Acta Biotheor., 52, 343, 10.1023/B:ACBI.0000046602.58202.5e Safferling, 2013, Wound healing revised: a novel reepithelialization mechanism revealed by in vitro and in silico models, J. Cell Biol., 203, 691, 10.1083/jcb.201212020 Sanga, 2007, Predictive oncology: a review of multidisciplinary, multiscale in silico modeling linking phenotype, morphology and growth, Neuroimage, 37, S120, 10.1016/j.neuroimage.2007.05.043 Anderson, 2008, Integrative mathematical oncology, Nat. Rev. Cancer, 8, 227, 10.1038/nrc2329 Lock, 2014, Plasticity in the macromolecular-scale causal networks of cell migration, PLoS ONE, 9, e90593, 10.1371/journal.pone.0090593 Bergert, 2015, Force transmission during adhesion-independent migration, Nat. Cell Biol., 17, 524, 10.1038/ncb3134 Liu, 2015, Confinement and low adhesion induce fast amoeboid migration of slow mesenchymal cells, Cell, 160, 659, 10.1016/j.cell.2015.01.007 Hinow, 2009, A spatial model of tumor-host interaction: application of chemotherapy, Math. Biosci. Eng., 6, 521, 10.3934/mbe.2009.6.521 Lowengrub, 2010, Nonlinear modelling of cancer: bridging the gap between cells and tumours, Nonlinearity, 23, R1, 10.1088/0951-7715/23/1/R01 Painter, 2010, The impact of adhesion on cellular invasion processes in cancer and development, J. Theor. Biol., 264, 1057, 10.1016/j.jtbi.2010.03.033 Tozluoğlu, 2013, Matrix geometry determines optimal cancer cell migration strategy and modulates response to interventions, Nat. Cell Biol., 15, 751, 10.1038/ncb2775 Tozluoglu, 2015, Cost–benefit analysis of the mechanisms that enable migrating cells to sustain motility upon changes in matrix environments, J. R. Soc. Interface, 12, 20141355, 10.1098/rsif.2014.1355 Alber, 2003, On cellular automaton approaches to modeling biological cells, 1 Quaranta, 2008, Invasion emerges from cancer cell adaptation to competitive microenvironments: quantitative predictions from multiscale mathematical models, Semin. Cancer Biol., 18, 338, 10.1016/j.semcancer.2008.03.018 2007 Szabó, 2013, Cellular Potts modeling of tumor growth, tumor invasion, and tumor evolution, Front. Oncol., 3, 87, 10.3389/fonc.2013.00087 Scianna, 2013, A cellular Potts model simulating cell migration on and in matrix environments, Math. Biosci. Eng., 10, 235, 10.3934/mbe.2013.10.235 Rubenstein, 2008, The role of extracellular matrix in glioma invasion: a cellular Potts model approach, Biophys. J., 95, 5661, 10.1529/biophysj.108.140624 Voss-Böhme, 2012, Multi-scale modeling in morphogenesis: a critical analysis of the cellular Potts model, PLoS ONE, 7, e42852, 10.1371/journal.pone.0042852 Vroomans, 2012, Chemotactic migration of T cells towards dendritic cells promotes the detection of rare antigens, PLoS Comput. Biol., 8, e1002763, 10.1371/journal.pcbi.1002763 Setty, 2011, How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex, BMC Syst. Biol., 5, 154, 10.1186/1752-0509-5-154 Jiao, 2011, Emergent behaviors from a cellular automaton model for invasive tumor growth in heterogeneous microenvironments, PLoS Comput. Biol., 7, e1002314, 10.1371/journal.pcbi.1002314 Borau, 2014, Probabilistic Voxel-FE model for single cell motility in 3D, In Silico Cell Tissue Sci., 1, 2, 10.1186/2196-050X-1-2 Sepúlveda, 2013, Collective cell motion in an epithelial sheet can be quantitatively described by a stochastic interacting particle model, PLoS Comput. Biol., 9, e1002944, 10.1371/journal.pcbi.1002944 Mirschel, 2009, ProMoT: modular modeling for systems biology, Bioinformatics, 25, 687, 10.1093/bioinformatics/btp029 Kootsey, 1986, SCoP: an interactive simulation control program for micro- and minicomputers, Bull. Math. Biol., 48, 427, 10.1007/BF02459691 Slepchenko, 2003, Quantitative cell biology with the virtual cell, Trends Cell Biol., 13, 570, 10.1016/j.tcb.2003.09.002 Moraru, 2008, Virtual Cell modelling and simulation software environment, IET Syst. Biol., 2, 352, 10.1049/iet-syb:20080102 Bairoch, 1996, The SWISS-PROT protein sequence data bank and its new supplement TREMBL, Nucleic Acids Res., 24, 21, 10.1093/nar/24.1.21 Kanehisa, 2000, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Res., 28, 27, 10.1093/nar/28.1.27 Swat, 2012, Multi-scale modeling of tissues using CompuCell3D, Methods Cell Biol., 110, 325, 10.1016/B978-0-12-388403-9.00013-8 Sanford, 2006, Cell++ – simulating biochemical pathways, Bioinformatics, 22, 2918, 10.1093/bioinformatics/btl497 Miller, 2010, An overview of the CellML API and its implementation, BMC Bioinformatics, 11, 178, 10.1186/1471-2105-11-178 Machné, 2006, The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks, Bioinformatics, 22, 1406, 10.1093/bioinformatics/btl086 Shapiro, 2004, MathSBML: a package for manipulating SBML-based biological models, Bioinformatics, 20, 2829, 10.1093/bioinformatics/bth271 Keating, 2006, SBMLToolbox: an SBML toolbox for MATLAB users, Bioinformatics, 22, 1275, 10.1093/bioinformatics/btl111 Wellock, 2005, The SBW–MATLAB interface, Bioinformatics, 21, 823, 10.1093/bioinformatics/bti110 Gillespie, 2006, Tools for the SBML Community, Bioinformatics, 22, 628, 10.1093/bioinformatics/btk042 Masuzzo, 2013, CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays, Bioinformatics, 29, 2661, 10.1093/bioinformatics/btt437 Maiuri, 2012, The first World Cell Race, Curr. Biol., 22, R673, 10.1016/j.cub.2012.07.052 Maiuri, 2015, Actin flows mediate a universal coupling between cell speed and cell persistence, Cell, 161, 374, 10.1016/j.cell.2015.01.056 Hossain, 2011, An active particle-based tracking framework for 2D and 3D time-lapse microscopy images, Conf. Proc. IEEE Eng. Med. Biol. Soc., 2011, 6613 Tokunaga, 2014, Automated detection and tracking of many cells by using 4D live-cell imaging data, Bioinformatics, 30, i43, 10.1093/bioinformatics/btu271 Schiegg, 2015, Graphical model for joint segmentation and tracking of multiple dividing cells, Bioinformatics, 31, 948, 10.1093/bioinformatics/btu764 Adanja, 2011, A new method to address unmet needs for extracting individual cell migration features from a large number of cells embedded in 3D volumes, PLoS ONE, 6, e22263, 10.1371/journal.pone.0022263 Pimentel, 2012, A segmentation algorithm for automated tracking of fast swimming unlabelled cells in three dimensions, J. Microsc., 245, 72, 10.1111/j.1365-2818.2011.03545.x Barry, 2015, Open source software for quantification of cell migration, protrusions, and fluorescence intensities, J. Cell Biol., 209, 163, 10.1083/jcb.201501081 Shen, 2006, Automatic tracking of biological cells and compartments using particle filters and active contours, Chemometr. Intell. Lab. Syst., 82, 276, 10.1016/j.chemolab.2005.07.007 Cordelières, 2013, Automated cell tracking and analysis in phase-contrast videos (iTrack4U): development of Java software based on combined mean-shift processes, PLoS ONE, 8, e81266, 10.1371/journal.pone.0081266 Downey, 2011, Extracting fluorescent reporter time courses of cell lineages from high-throughput microscopy at low temporal resolution, PLoS ONE, 6, e27886, 10.1371/journal.pone.0027886 Meijering, 2012, Methods for cell and particle tracking, Methods Enzymol., 504, 183, 10.1016/B978-0-12-391857-4.00009-4 Chenouard, 2013, Multiple hypothesis tracking for cluttered biological image sequences, IEEE Trans. Pattern Anal. Mach. Intell., 35, 2736, 10.1109/TPAMI.2013.97 Jaqaman, 2008, Robust single-particle tracking in live-cell time-lapse sequences, Nat. Methods, 5, 695, 10.1038/nmeth.1237