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StomataCounter: a neural network for automatic stomata identification and counting

View ORCID ProfileKarl C. Fetter, Sven Eberhardt, Rich S. Barclay, Scott Wing, Stephen R. Keller
doi: https://doi.org/10.1101/327494
Karl C. Fetter
aDepartment of Plant Biology, University of Vermont
bDepartment of Paleobiology, Smithsonian Institution, National Museum of Natural History
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  • ORCID record for Karl C. Fetter
Sven Eberhardt
c
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Rich S. Barclay
bDepartment of Paleobiology, Smithsonian Institution, National Museum of Natural History
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Scott Wing
bDepartment of Paleobiology, Smithsonian Institution, National Museum of Natural History
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Stephen R. Keller
aDepartment of Plant Biology, University of Vermont
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ABSTRACT

  • Stomata regulate important physiological processes in plants and are often phenotyped by researchers in diverse fields of plant biology. Currently, there are no user friendly, fully-automated methods to perform the task of identifying and counting stomata, and stomata density is generally estimated by manually counting stomata.

  • We introduce StomataCounter, an automated stomata counting system using a deep convolutional neural network to identify stomata in a variety of different microscopic images. We use a human-in-the-loop approach to train and refine a neural network on a taxonomically diverse collection of microscopic images.

  • Our network achieves 98.1% identification accuracy on Ginkgo SEM micrographs, and 94.2% transfer accuracy when tested on untrained species.

  • To facilitate adoption of the method, we provide the method in a publicly available website at http://www.stomata.science/.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted March 05, 2019.
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StomataCounter: a neural network for automatic stomata identification and counting
Karl C. Fetter, Sven Eberhardt, Rich S. Barclay, Scott Wing, Stephen R. Keller
bioRxiv 327494; doi: https://doi.org/10.1101/327494
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StomataCounter: a neural network for automatic stomata identification and counting
Karl C. Fetter, Sven Eberhardt, Rich S. Barclay, Scott Wing, Stephen R. Keller
bioRxiv 327494; doi: https://doi.org/10.1101/327494

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