TrackPad: Software for semi-automated single-cell tracking and lineage annotation

SoftwareX - Tập 11 - Trang 100440 - 2020
J.A. Cornwell1,2, J. Li3, S. Mahadevan4, J.S. Draper5, G.L. Joun6, H. Zoellner4, N.S. Asli6,7, R.P. Harvey2,8,9, R.E. Nordon2,3
1Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
2Australian Research Council Special Research Initiative in Stem Cell Science – Stem Cells, Australia
3Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
4The Cellular and Molecular Pathology Research Unit, Oral Pathology and Oral Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead Hospital, Westmead, NSW 2145, Australia
5McMaster Stem Cell and Cancer Research Institute, Michael G DeGroote School of Medicine. Hamilton, Ontario, Canada
6Department of Oral Biosciences, School of Dentistry, Faculty of Medicine and Health, University of Sydney, Westmead Hospital, Westmead NSW 2145, Australia
7Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Westmead Hospital, Westmead NSW 2145, Australia
8Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
9St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia

Tài liệu tham khảo

Woodworth, 2017, Building a lineage from single cells: genetic techniques for cell lineage tracking, Nat Rev Genet, 18, 230, 10.1038/nrg.2016.159 Lytle, 2018, Stem cell fate in cancer growth, progression and therapy resistance, Nat Rev Cancer, 18, 669, 10.1038/s41568-018-0056-x Balagopalan, 2011, Imaging techniques for assaying lymphocyte activation in action, Nat Rev Immunol, 11, 21, 10.1038/nri2903 Cooper, 2017, Accelerating live single-cell signalling studies, Trends Biotechnol, 35, 422, 10.1016/j.tibtech.2017.01.002 Hilsenbeck, 2016, Software tools for single-cell tracking and quantification of cellular and molecular properties, Nature Biotechnol, 34, 703, 10.1038/nbt.3626 Sebesta, 2016, HoloMonitor M4: holographic imaging cytometer for real-time kinetic label-free live-cell analysis of adherent cells Falck Miniotis, 2014, Digital holographic microscopy for non-invasive monitoring of cell cycle arrest in L929 cells, PLOS ONE, 9 Carpenter, 2006, CellProfiler: image analysis software for identifying and quantifying cell phenotypes, Genome Biol, 7, R100, 10.1186/gb-2006-7-10-r100 Tinevez, 2017, TrackMate: An open and extensible platform for single-particle tracking, Methods, 115, 80, 10.1016/j.ymeth.2016.09.016 Magnusson, 2015, Global linking of cell tracks using the viterbi algorithm, IEEE Trans Med Imaging, 34, 911, 10.1109/TMI.2014.2370951 Magnusson, 2019 Winter, 2016, LEVER: Software tools for segmentation, tracking and lineaging of proliferating cells, Bioinformatics, 32, 3530, 10.1093/bioinformatics/btw406 Bise, 2011, Reliable cell tracking by global data association Chalfoun, 2016, Lineage mapper: A versatile cell and particle tracker, Sci Rep, 6, 36984, 10.1038/srep36984 Magnusson, 2015, Global linking of cell tracks using the viterbi algorithm, IEEE Trans Med Imaging, 34, 911, 10.1109/TMI.2014.2370951 Nordon, 2019 Cornwell, 2016, Quantifying intrinsic and extrinsic control of single-cell fates in cancer and stem/progenitor cell pedigrees with competing risks analysis, Sci Rep, 6, 10.1038/srep27100 Cornwell, 2018, Analysis of cardiac stem cell self-renewal dynamics in serum-free medium by single cell lineage tracking, Stem Cell Res, 28, 115, 10.1016/j.scr.2018.02.004 Nordon, 2019 Nordon, 2019 Nordon, 2019 Nordon, 2019 Nordon, 2019 Nordon, 2019 Nordon, 2019 Nordon, 2019 Ulman, 2017, An objective comparison of cell-tracking algorithms, Nat Methods, 14, 1141, 10.1038/nmeth.4473 Carpenter, 2006, CellProfiler: image analysis software for identifying and quantifying cell phenotypes, Genome Biol, 7, 10.1186/gb-2006-7-10-r100 Challenge, 2019 Matula, 2015, Cell tracking accuracy measurement based on comparison of acyclic oriented graphs, Plos One, 10, 10.1371/journal.pone.0144959 Sakaue-Sawano, 2008, Visualizing spatiotemporal dynamics of multicellular cell-cycle progression, Cell, 132, 487, 10.1016/j.cell.2007.12.033 Hallett, 2015, Treatment-induced cell cycle kinetics dictate tumor response to chemotherapy, Oncotarget, 6, 7040, 10.18632/oncotarget.3140 Nordon, 2020 Hallett, 2015, Treatment-induced cell cycle kinetics dictate tumor response to chemotherapy, Oncotarget, 6, 7040, 10.18632/oncotarget.3140
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SoftwareX

Tập 11

100440

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