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 Kokovay; Sally Temple; Andrew R. Cohen

doi:10.1038/nprot.2011.422

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 Kokovay, Sally Temple, Andrew R. Cohen

Research output: Contribution to journal › Article › peer-review

48 Scopus citations

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 language	English (US)
Pages (from-to)	1942-1952
Number of pages	11
Journal	Nature Protocols
Volume	6
Issue number	12
DOIs	https://doi.org/10.1038/nprot.2011.422
State	Published - Dec 2011
Externally published	Yes

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology

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10.1038/nprot.2011.422

Cite this

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

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.",

author = "Mark Winter and Eric Wait and Badrinath Roysam and Goderie, {Susan K.} and Ali, {Rania Ahmed Naguib} and Erzsebet Kokovay and Sally Temple and Cohen, {Andrew R.}",

note = "Funding Information: acknoWleDGMents This project was supported by the University of Wisconsin-Milwaukee, and by grant number NS033529 from the US National Institutes of Health (NIH) and by New York State Department of Health (NYSDOH) Contract C024352 from the Empire State Stem Cell Fund and the Regenerative Research Foundation. This project was also supported by NIH grant number R01EB005157 and by grant no. R01NS076709 from the National Institute of Neurological Disorders and Stroke. The authors would like to thank S. Shahmohammadi, R. Ference, A. DiRisio, S. Hardwick, S.M. Goderie, E. McAuley, R. Futia and C. Davenport for their help with cell culture and lineage validation.",

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AU - Kokovay, Erzsebet

AU - Temple, Sally

AU - Cohen, Andrew R.

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

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