Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing

Mark Winter, Eric Wait, Badrinath Roysam, Susan K. Goderie, Rania Ahmed Naguib Ali, Erzsebet K Cearley, Sally Temple, Andrew R. Cohen

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

This protocol and the accompanying software program called LEVER (lineage editing and validation) enable quantitative automated analysis of phase-contrast time-lapse images of cultured neural stem cells. Images are captured at 5-min intervals over a period of 5-15 d as the cells proliferate and differentiate. LEVER automatically segments, tracks and generates lineage trees of the stem cells from the image sequence. In addition to generating lineage trees capturing the population dynamics of clonal development, LEVER extracts quantitative phenotypic measurements of cell location, shape, movement and size. When available, the system can include biomolecular markers imaged using fluorescence. It then displays the results to the user for highly efficient inspection and editing to correct any errors in the segmentation, tracking or lineaging. To enable high-throughput inspection, LEVER incorporates features for rapid identification of errors and for learning from user-supplied corrections to automatically identify and correct related errors.

Original languageEnglish (US)
Pages (from-to)1942-1952
Number of pages11
JournalNature Protocols
Volume6
Issue number12
DOIs
StatePublished - Dec 2011
Externally publishedYes

Fingerprint

Cell Tracking
Neural Stem Cells
Cell Shape
Population Dynamics
Stem cells
Cell Size
Vertebrates
Stem Cells
Software
Fluorescence
Learning
Inspection
Population dynamics
Error correction
Throughput

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Winter, M., Wait, E., Roysam, B., Goderie, S. K., Ali, R. A. N., Cearley, E. K., ... Cohen, A. R. (2011). Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing. Nature Protocols, 6(12), 1942-1952. https://doi.org/10.1038/nprot.2011.422

Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing. / Winter, Mark; Wait, Eric; Roysam, Badrinath; Goderie, Susan K.; Ali, Rania Ahmed Naguib; Cearley, Erzsebet K; Temple, Sally; Cohen, Andrew R.

In: Nature Protocols, Vol. 6, No. 12, 12.2011, p. 1942-1952.

Research output: Contribution to journalArticle

Winter, M, Wait, E, Roysam, B, Goderie, SK, Ali, RAN, Cearley, EK, Temple, S & Cohen, AR 2011, 'Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing', Nature Protocols, vol. 6, no. 12, pp. 1942-1952. https://doi.org/10.1038/nprot.2011.422
Winter, Mark ; Wait, Eric ; Roysam, Badrinath ; Goderie, Susan K. ; Ali, Rania Ahmed Naguib ; Cearley, Erzsebet K ; Temple, Sally ; Cohen, Andrew R. / Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing. In: Nature Protocols. 2011 ; Vol. 6, No. 12. pp. 1942-1952.
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