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Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data
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Cites
A Threshold Selection Method from Gray-Level Histograms
Otsu, N. (1979) · IEEE Transactions on Systems, Man, and Cybernetics · doi:10.1109/tsmc.1979.4310076 · Cited by 43,398
The Hungarian method for the assignment problem
Kuhn, H. W. (1955) · Naval Research Logistics Quarterly · doi:10.1002/nav.3800020109 · Cited by 13,120
Watersheds in digital spaces: an efficient algorithm based on immersion simulations
Vincent, L., & Soille, P. (1991) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/34.87344 · Cited by 5,649
Robust single-particle tracking in live-cell time-lapse sequences
Jaqaman, K., Loerke, D., Mettlen, M., Kuwata, H., Grinstein, S., Schmid, S. L., & Danuser, G. (2008) · Nature Methods · doi:10.1038/nmeth.1237 · Cited by 1,970
Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy
Keller, P. J., Schmidt, A. D., Wittbrodt, J., & Stelzer, E. H. K. (2008) · Science · doi:10.1126/science.1162493 · Cited by 1,560
Self-citationTomer, R., Khairy, K., Amat, F., & Keller, P. J. (2012) · Nature Methods · doi:10.1038/nmeth.2062 · Cited by 545
Self-citationDoe, C. Q. (1992) · Development · doi:10.1242/dev.116.4.855 · Cited by 416
CATMAID: collaborative annotation toolkit for massive amounts of image data
Saalfeld, S., Cardona, A., Hartenstein, V., & Tomančák, P. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp266 · Cited by 384
Mechanical Control of Morphogenesis by Fat/Dachsous/Four-Jointed Planar Cell Polarity Pathway
Bosveld, F., Bonnet, I., Guirao, B., Tlili, S., Wang, Z., Petitalot, A., Marchand, R., Bardet, P.-L., Marcq, P., Graner, F., et al. (2012) · Science · doi:10.1126/science.1221071 · Cited by 381
CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging
Held, M., Schmitz, M. H. A., Fischer, B., Walter, T., Neumann, B., Olma, M. H., Peter, M., Ellenberg, J., & Gerlich, D. W. (2010) · Nature Methods · doi:10.1038/nmeth.1486 · Cited by 378
Early neurogenesis in wild-typeDrosophila melanogaster
Hartenstein, V., & Campos-Ortega, J. A. (1984) · Wilhelm Roux's Archives of Developmental Biology · doi:10.1007/bf00848159 · Cited by 374
Cell Lineage Reconstruction of Early Zebrafish Embryos Using Label-Free Nonlinear Microscopy
Olivier, N., Luengo-Oroz, M. A., Duloquin, L., Faure, E., Savy, T., Veilleux, I., Solinas, X., Débarre, D., Bourgine, P., Santos, A., et al. (2010) · Science · doi:10.1126/science.1189428 · Cited by 370
Automated cell lineage tracing in Caenorhabditis elegans
Bao, Z., Murray, J. I., Boyle, T., Ooi, S. L., Sandel, M. J., & Waterston, R. H. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0511111103 · Cited by 364
Cell population tracking and lineage construction with spatiotemporal context
Li, K., Miller, E. D., Chen, M., Kanade, T., Weiss, L. E., & Campbell, P. G. (2008) · Medical Image Analysis · doi:10.1016/j.media.2008.06.001 · Cited by 346
The Drosophila NuMA Homolog Mud Regulates Spindle Orientation in Asymmetric Cell Division
Bowman, S. K., Neumüller, R. A., Novatchkova, M., Du, Q., & Knoblich, J. A. (2006) · Developmental Cell · doi:10.1016/j.devcel.2006.05.005 · Cited by 305
Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution
Fernandez, R., Das, P., Mirabet, V., Moscardi, E., Traas, J., Verdeil, J.-L., Malandain, G., & Godin, C. (2010) · Nature Methods · doi:10.1038/nmeth.1472 · Cited by 305
Megason, S. G., & Fraser, S. E. (2007) · Cell · doi:10.1016/j.cell.2007.08.031 · Cited by 254
Use of the viral 2A peptide for bicistronic expression in transgenic mice
Trichas, G., Begbie, J., & Srinivas, S. (2008) · BMC Biology · doi:10.1186/1741-7007-6-40 · Cited by 236
Broadus, J., Skeath, J. B., Spana, E. P., Bossing, T., Technau, G., & Doe, C. Q. (1995) · Mechanisms of Development · doi:10.1016/0925-4773(95)00454-8 · Cited by 213
Automated analysis of embryonic gene expression with cellular resolution in C. elegans
Murray, J. I., Bao, Z., Boyle, T. J., Boeck, M. E., Mericle, B. L., Nicholas, T. J., Zhao, Z., Sandel, M. J., & Waterston, R. H. (2008) · Nature Methods · doi:10.1038/nmeth.1228 · Cited by 201
Imaging Morphogenesis: Technological Advances and Biological Insights
Keller, P. J. (2013) · Science · doi:10.1126/science.1234168 · Cited by 189
Self-citationSpecified Neural Progenitors Sort to Form Sharp Domains after Noisy Shh Signaling
Xiong, F., Tentner, A. R., Huang, P., Gelas, A., Mosaliganti, K. R., Souhait, L., Rannou, N., Swinburne, I. A., Obholzer, N. D., Cowgill, P. D., et al. (2013) · Cell · doi:10.1016/j.cell.2013.03.023 · Cited by 174
Dynamic Analyses of Drosophila Gastrulation Provide Insights into Collective Cell Migration
McMahon, A., Supatto, W., Fraser, S. E., & Stathopoulos, A. (2008) · Science · doi:10.1126/science.1167094 · Cited by 148
A Two-round Variant of EM for Gaussian MixturesPreprint
Dasgupta, S., & Schulman, L. J. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1301.3850 · Cited by 141
Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans
Liu, X., Long, F., Peng, H., Aerni, S. J., Jiang, M., Sánchez-Blanco, A., Murray, J. I., Preston, E. A., Mericle, B., Batzoglou, S., et al. (2009) · Cell · doi:10.1016/j.cell.2009.08.044 · Cited by 141
Self-citationTrichas, G., Smith, A. M., White, N., Wilkins, V., Watanabe, T., Moore, A., Joyce, B. W., Sugnaseelan, J., Rodríguez, T. A., Kay, D., et al. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001256 · Cited by 131
Technau, G. M., Berger, C., & Urbach, R. (2005) · Developmental Dynamics · doi:10.1002/dvdy.20566 · Cited by 130
Extrinsic cues orient the cell division axis inDrosophilaembryonic neuroblasts
Siegrist, S. E., & Doe, C. Q. (2006) · Development · doi:10.1242/dev.02211 · Cited by 122
Persistence-based segmentation of deformable shapes
Škraba, P., Ovsjanikov, M., Chazal, F., & Guibas, L. J. (2010) · 2009 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops · doi:10.1109/cvprw.2010.5543285 · Cited by 115
Challenges of Ground Truth Evaluation of Multi-target Tracking
Milan, A., Konrad Schindler, B., & Roth, S. (2013) · IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW) · doi:10.1109/cvprw.2013.111 · Cited by 98
Multiple object tracking in molecular bioimaging by Rao-Blackwellized marginal particle filtering
Smal, I., Meijering, E. H. W., Draegestein, K., Galjart, N., Grigoriev, I., Akhmanova, A. S., van Royen, M. E., Houtsmuller, A. B., & Niessen, W. J. (2008) · Medical Image Analysis · doi:10.1016/j.media.2008.03.004 · Cited by 87
Reconstructing embryonic development
Khairy, K. A., & Keller, P. (2010) · genesis · doi:10.1002/dvg.20698 · Cited by 86
Self-citation4D retrospective lineage tracing using SPIM for zebrafish organogenesis studies
Swoger, J., Muzzopappa, M., López‐Schier, H., & Sharpe, J. A. (2010) · Journal of Biophotonics · doi:10.1002/jbio.201000087 · Cited by 57
Fast and robust optical flow for time-lapse microscopy using super-voxels
Amat, F., Myers, E. W., & Keller, P. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts706 · Cited by 56
Self-citationWang, F., Dumstrei, K., Haag, T. A., & Hartenstein, V. (2004) · Developmental Biology · doi:10.1016/j.ydbio.2004.03.002 · Cited by 45
A Discrete Chain Graph Model for 3d+t Cell Tracking with High Misdetection Robustness
Kausler, B. X., Schiegg, M., Andres, B., Lindner, M., Köthe, U., Leitte, H., Wittbrodt, J., Hufnagel, L., & Hamprecht, F. A. (2012) · Lecture notes in computer science · doi:10.1007/978-3-642-33712-3_11 · Cited by 40
Towards comprehensive cell lineage reconstructions in complex organisms using light‐sheet microscopy
Amat, F., & Keller, P. (2013) · Development Growth & Differentiation · doi:10.1111/dgd.12063 · Cited by 31
Self-citationLive imaging of nervous system development and function using light‐sheet microscopy
Lemon, W. C., & Keller, P. (2013) · Molecular Reproduction and Development · doi:10.1002/mrd.22258 · Cited by 12
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Schmidt, U., Weigert, M., Broaddus, C., & Myers, G. (2018) · Lecture Notes in Computer Science · doi:10.1007/978-3-030-00934-2_30 · Cited by 1,826
Deep learning for cellular image analysis
Moen, E., Bannon, D., Kudo, T., Graf, W., Covert, M., & Van Valen, D. (2019) · Nature Methods · doi:10.1038/s41592-019-0403-1 · Cited by 1,225
In toto imaging and reconstruction of post-implantation mouse development at the single-cell level
McDole, K., Guignard, L., Amat, F., Berger, A., Malandain, G., Royer, L. A., Turaga, S. C., Branson, K., & Keller, P. J. (2018) · Cell · doi:10.1016/j.cell.2018.09.031 · Cited by 522
Self-citationBigDataViewer: visualization and processing for large image data sets
Pietzsch, T., Saalfeld, S., Preibisch, S., & Tomancak, P. (2015) · Nature Methods · doi:10.1038/nmeth.3392 · Cited by 290
Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data
Ocone, A., Haghverdi, L., Mueller, N. S., & Theis, F. J. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv257 · Cited by 155
Metadata
- Authors
- Amat, F., Lemon, W., Mossing, D. P., McDole, K., Wan, Y., Branson, K., Myers, E. W., & Keller, P. J.
- Venue
- Nature Methods
- Published
- 2014-07-20
- Volume
- 11
- Issue
- 9
- Pages
- 951-958
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2030233281
- Cited by
- 290
- References
- 38
- FWCI
- 20.86
- Type
- journal article
- Language
- en
- Open access
- closed
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
