TrackPad: Software for semi-automated single-cell tracking and lineage annotation
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, template-matching (CCTM) to track each cell using transmitted or fluorescent images. Machine tracking is supe...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2020-01-01
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| Series: | SoftwareX |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352711019302390 |
| _version_ | 1818942289305665536 |
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| author | J.A. Cornwell J. Li S. Mahadevan J.S. Draper G.L. Joun H. Zoellner N.S. Asli R.P. Harvey R.E. Nordon |
| author_facet | J.A. Cornwell J. Li S. Mahadevan J.S. Draper G.L. Joun H. Zoellner N.S. Asli R.P. Harvey R.E. Nordon |
| author_sort | J.A. Cornwell |
| collection | DOAJ |
| description | 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, template-matching (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. |
| first_indexed | 2024-12-20T07:09:04Z |
| format | Article |
| id | doaj.art-861be22532614591a7e210f3d646de56 |
| institution | Directory Open Access Journal |
| issn | 2352-7110 |
| language | English |
| last_indexed | 2024-12-20T07:09:04Z |
| publishDate | 2020-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | SoftwareX |
| spelling | doaj.art-861be22532614591a7e210f3d646de562022-12-21T19:48:56ZengElsevierSoftwareX2352-71102020-01-0111TrackPad: Software for semi-automated single-cell tracking and lineage annotationJ.A. Cornwell0J. Li1S. Mahadevan2J.S. Draper3G.L. Joun4H. Zoellner5N.S. Asli6R.P. Harvey7R.E. Nordon8Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA; Australian Research Council Special Research Initiative in Stem Cell Science – Stem Cells, AustraliaGraduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, AustraliaThe 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, AustraliaMcMaster Stem Cell and Cancer Research Institute, Michael G DeGroote School of Medicine. Hamilton, Ontario, CanadaDepartment of Oral Biosciences, School of Dentistry, Faculty of Medicine and Health, University of Sydney, Westmead Hospital, Westmead NSW 2145, AustraliaThe 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, AustraliaDepartment of Oral Biosciences, School of Dentistry, Faculty of Medicine and Health, University of Sydney, Westmead Hospital, Westmead NSW 2145, Australia; Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Westmead Hospital, Westmead NSW 2145, AustraliaAustralian Research Council Special Research Initiative in Stem Cell Science – Stem Cells, Australia; Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, AustraliaAustralian Research Council Special Research Initiative in Stem Cell Science – Stem Cells, Australia; Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia; Corresponding author at: Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia.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, template-matching (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.http://www.sciencedirect.com/science/article/pii/S2352711019302390Computer-assisted image analysisCell lineage mappingTemplate matching |
| spellingShingle | J.A. Cornwell J. Li S. Mahadevan J.S. Draper G.L. Joun H. Zoellner N.S. Asli R.P. Harvey R.E. Nordon TrackPad: Software for semi-automated single-cell tracking and lineage annotation SoftwareX Computer-assisted image analysis Cell lineage mapping Template matching |
| title | TrackPad: Software for semi-automated single-cell tracking and lineage annotation |
| title_full | TrackPad: Software for semi-automated single-cell tracking and lineage annotation |
| title_fullStr | TrackPad: Software for semi-automated single-cell tracking and lineage annotation |
| title_full_unstemmed | TrackPad: Software for semi-automated single-cell tracking and lineage annotation |
| title_short | TrackPad: Software for semi-automated single-cell tracking and lineage annotation |
| title_sort | trackpad software for semi automated single cell tracking and lineage annotation |
| topic | Computer-assisted image analysis Cell lineage mapping Template matching |
| url | http://www.sciencedirect.com/science/article/pii/S2352711019302390 |
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