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Microscope image based fully automated stomata detection and pore measurement method for grapevines

Overview of attention for article published in Plant Methods, November 2017
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (72nd percentile)
  • Good Attention Score compared to outputs of the same age and source (73rd percentile)

Mentioned by

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9 tweeters

Citations

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32 Dimensions

Readers on

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73 Mendeley
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Title
Microscope image based fully automated stomata detection and pore measurement method for grapevines
Published in
Plant Methods, November 2017
DOI 10.1186/s13007-017-0244-9
Pubmed ID
Authors

Hiranya Jayakody, Scarlett Liu, Mark Whitty, Paul Petrie

Abstract

Stomatal behavior in grapevines has been identified as a good indicator of the water stress level and overall health of the plant. Microscope images are often used to analyze stomatal behavior in plants. However, most of the current approaches involve manual measurement of stomatal features. The main aim of this research is to develop a fully automated stomata detection and pore measurement method for grapevines, taking microscope images as the input. The proposed approach, which employs machine learning and image processing techniques, can outperform available manual and semi-automatic methods used to identify and estimate stomatal morphological features. First, a cascade object detection learning algorithm is developed to correctly identify multiple stomata in a large microscopic image. Once the regions of interest which contain stomata are identified and extracted, a combination of image processing techniques are applied to estimate the pore dimensions of the stomata. The stomata detection approach was compared with an existing fully automated template matching technique and a semi-automatic maximum stable extremal regions approach, with the proposed method clearly surpassing the performance of the existing techniques with a precision of 91.68% and an F1-score of 0.85. Next, the morphological features of the detected stomata were measured. Contrary to existing approaches, the proposed image segmentation and skeletonization method allows us to estimate the pore dimensions even in cases where the stomatal pore boundary is only partially visible in the microscope image. A test conducted using 1267 images of stomata showed that the segmentation and skeletonization approach was able to correctly identify the stoma opening 86.27% of the time. Further comparisons made with manually traced stoma openings indicated that the proposed method is able to estimate stomata morphological features with accuracies of 89.03% for area, 94.06% for major axis length, 93.31% for minor axis length and 99.43% for eccentricity. The proposed fully automated solution for stomata detection and measurement is able to produce results far superior to existing automatic and semi-automatic methods. This method not only produces a low number of false positives in the stomata detection stage, it can also accurately estimate the pore dimensions of partially incomplete stomata images. In addition, it can process thousands of stomata in minutes, eliminating the need for researchers to manually measure stomata, thereby accelerating the process of analysing plant health.

Twitter Demographics

The data shown below were collected from the profiles of 9 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 73 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 73 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 19 26%
Student > Ph. D. Student 13 18%
Student > Bachelor 6 8%
Student > Master 4 5%
Student > Postgraduate 3 4%
Other 7 10%
Unknown 21 29%
Readers by discipline Count As %
Agricultural and Biological Sciences 25 34%
Engineering 6 8%
Biochemistry, Genetics and Molecular Biology 6 8%
Computer Science 5 7%
Physics and Astronomy 3 4%
Other 6 8%
Unknown 22 30%

Attention Score in Context

This research output has an Altmetric Attention Score of 6. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 11 May 2018.
All research outputs
#3,892,159
of 16,236,576 outputs
Outputs from Plant Methods
#204
of 797 outputs
Outputs of similar age
#87,425
of 321,875 outputs
Outputs of similar age from Plant Methods
#25
of 93 outputs
Altmetric has tracked 16,236,576 research outputs across all sources so far. Compared to these this one has done well and is in the 75th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 797 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.0. This one has gotten more attention than average, scoring higher than 74% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 321,875 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 72% of its contemporaries.
We're also able to compare this research output to 93 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 73% of its contemporaries.