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A 3D Digital Atlas of C. elegans and Its Application To Single-Cell Analyses

We have built a digital nuclear atlas of the newly hatched, first larval stage (L1) of the wild type hermaphrodite of C. elegans at single cell resolution from confocal image stacks of 15 individuals. The atlas quantifies the stereotypy of the locations and provides for other statistics on the spati...

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Detalles Bibliográficos
Autores principales: Long, Fuhui, Peng, Hanchuan, Liu, Xiao, Kim, Stuart K., Myers, Eugene
Formato: Texto
Lenguaje:English
Publicado: 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882208/
https://www.ncbi.nlm.nih.gov/pubmed/19684595
http://dx.doi.org/10.1038/nmeth.1366
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author Long, Fuhui
Peng, Hanchuan
Liu, Xiao
Kim, Stuart K.
Myers, Eugene
author_facet Long, Fuhui
Peng, Hanchuan
Liu, Xiao
Kim, Stuart K.
Myers, Eugene
author_sort Long, Fuhui
collection PubMed
description We have built a digital nuclear atlas of the newly hatched, first larval stage (L1) of the wild type hermaphrodite of C. elegans at single cell resolution from confocal image stacks of 15 individuals. The atlas quantifies the stereotypy of the locations and provides for other statistics on the spatial patterns of the 357 nuclei that could be faithfully segmented and annotated of the 558 present at this developmental stage. Given this atlas we then developed an automated approach to assign cell names to each nucleus in a 3D image of an L1 worm. We achieve 86% accuracy in identifying the 357 nuclei automatically. This computational method is essential for high-throughput single cell analyses of the worm at post-embryonic stages, such as determining the expression of every gene in every cell during development from the L1 onward, or ablating or stimulating cells under computer control in a high-throughput functional screen.
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spelling pubmed-28822082010-06-08 A 3D Digital Atlas of C. elegans and Its Application To Single-Cell Analyses Long, Fuhui Peng, Hanchuan Liu, Xiao Kim, Stuart K. Myers, Eugene Nat Methods Article We have built a digital nuclear atlas of the newly hatched, first larval stage (L1) of the wild type hermaphrodite of C. elegans at single cell resolution from confocal image stacks of 15 individuals. The atlas quantifies the stereotypy of the locations and provides for other statistics on the spatial patterns of the 357 nuclei that could be faithfully segmented and annotated of the 558 present at this developmental stage. Given this atlas we then developed an automated approach to assign cell names to each nucleus in a 3D image of an L1 worm. We achieve 86% accuracy in identifying the 357 nuclei automatically. This computational method is essential for high-throughput single cell analyses of the worm at post-embryonic stages, such as determining the expression of every gene in every cell during development from the L1 onward, or ablating or stimulating cells under computer control in a high-throughput functional screen. 2009-08-16 2009-09 /pmc/articles/PMC2882208/ /pubmed/19684595 http://dx.doi.org/10.1038/nmeth.1366 Text en http://www.nature.com/authors/editorial_policies/license.html#terms Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Long, Fuhui
Peng, Hanchuan
Liu, Xiao
Kim, Stuart K.
Myers, Eugene
A 3D Digital Atlas of C. elegans and Its Application To Single-Cell Analyses
title A 3D Digital Atlas of C. elegans and Its Application To Single-Cell Analyses
title_full A 3D Digital Atlas of C. elegans and Its Application To Single-Cell Analyses
title_fullStr A 3D Digital Atlas of C. elegans and Its Application To Single-Cell Analyses
title_full_unstemmed A 3D Digital Atlas of C. elegans and Its Application To Single-Cell Analyses
title_short A 3D Digital Atlas of C. elegans and Its Application To Single-Cell Analyses
title_sort 3d digital atlas of c. elegans and its application to single-cell analyses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882208/
https://www.ncbi.nlm.nih.gov/pubmed/19684595
http://dx.doi.org/10.1038/nmeth.1366
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