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

被引：14

作者：

Cornwell, J. A. ^{[1
,2
]}

Li, J. ^{[3
]}

Mahadevan, S. ^{[4
]}

Draper, J. S. ^{[9
]}

Joun, G. L. ^{[5
]}

Zoellner, H. ^{[4
]}

Asli, N. S. ^{[5
,6
]}

Harvey, R. P. ^{[2
,7
,8
]}

Nordon, R. E. ^{[2
,3
]}

机构：

[1] NCI, Lab Canc Biol & Genet, Ctr Canc Res, Bethesda, MD 20892 USA

[2] Australian Res Council, Special Res Initiat Stem Cell Sci Stem Cells, Canberra, ACT, Australia

[3] Univ New South Wales, Grad Sch Biomed Engn, Sydney, NSW 2052, Australia

[4] Univ Sydney, Westmead Hosp, Cellular & Mol Pathol Res Unit, Oral Pathol & Oral Med,Fac Med & Hlth, Westmead, NSW 2145, Australia

[5] Univ Sydney, Westmead Hosp, Fac Med & Hlth, Dept Oral Biosci,Sch Dent, Westmead, NSW 2145, Australia

[6] Univ Sydney, Westmead Hosp, Fac Med & Hlth, Sydney Med Sch, Westmead, NSW 2145, Australia

[7] Victor Chang Cardiac Res Inst, Dev & Stem Cell Biol Div, Sydney, NSW 2010, Australia

[8] Univ New South Wales, Fac Med, St Vincents Clin Sch, Sydney, NSW 2052, Australia

[9] Michael G DeGroote Sch Med, McMaster Stem Cell & Canc Res Inst, Hamilton, ON, Canada

来源：

SOFTWAREX | 2020年 / 11卷

基金：

澳大利亚研究理事会; 澳大利亚国家健康与医学研究理事会;

关键词：

Computer-assisted image analysis; Cell lineage mapping; Template matching; DYNAMICS; TOOLS;

D O I：

10.1016/j.softx.2020.100440

中图分类号：

TP31 [计算机软件];

学科分类号：

081202 ; 0835 ;

摘要：

TrackPad is an open-source, biologist-friendly, graphical user interface for tracking and annotating single-cell lineage fates from time-lapse movies. The software applies cross-correlative, templatematching (CCTM) to track each cell using transmitted or fluorescent images. Machine tracking is supervised by the investigator, who can manually annotate cell fates such as division, death, or changes in cell phenotype. Search parameters that minimise user interventions and tracking time are selected by simulating tracking using verified tracking data as a ground truth. Investigators who use this software can produce high-quality annotated cell trajectories and division pedigrees to understand how intrinsic and extrinsic factors influence cell states and fates. (c) 2020 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

引用

页数：7

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