Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing <Emphasis Type="Italic">C. elegans</Emphasis> embryo |
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Authors: | Zafer Aydin John I Murray Robert H Waterston William S Noble |
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Institution: | (1) Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA;(2) Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA |
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Abstract: | Background Image analysis is an essential component in many biological experiments that study gene expression, cell cycle progression,
and protein localization. A protocol for tracking the expression of individual C. elegans genes was developed that collects image samples of a developing embryo by 3-D time lapse microscopy. In this protocol, a
program called StarryNite performs the automatic recognition of fluorescently labeled cells and traces their lineage. However,
due to the amount of noise present in the data and due to the challenges introduced by increasing number of cells in later
stages of development, this program is not error free. In the current version, the error correction (i.e., editing) is performed manually using a graphical interface tool named AceTree, which is specifically developed for this
task. For a single experiment, this manual annotation task takes several hours. |
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