DeepPod: a convolutional neural network based quantification of fruit number in Arabidopsis.

GigaScience
Azam HamidinekooChuan Lu

Abstract

High-throughput phenotyping based on non-destructive imaging has great potential in plant biology and breeding programs. However, efficient feature extraction and quantification from image data remains a bottleneck that needs to be addressed. Advances in sensor technology have led to the increasing use of imaging to monitor and measure a range of plants including the model Arabidopsis thaliana. These extensive datasets contain diverse trait information, but feature extraction is often still implemented using approaches requiring substantial manual input. The computational detection and segmentation of individual fruits from images is a challenging task, for which we have developed DeepPod, a patch-based 2-phase deep learning framework. The associated manual annotation task is simple and cost-effective without the need for detailed segmentation or bounding boxes. Convolutional neural networks (CNNs) are used for classifying different parts of the plant inflorescence, including the tip, base, and body of the siliques and the stem inflorescence. In a post-processing step, different parts of the same silique are joined together for silique detection and localization, whilst taking into account possible overlapping among the silique...Continue Reading

References

Apr 23, 2010·The Plant Journal : for Cell and Molecular Biology·Maarten Koornneef, David Meinke
Nov 15, 2011·Trends in Plant Science·Robert T Furbank, Mark Tester
Jan 29, 2014·Proceedings of the National Academy of Sciences of the United States of America·Tao ZhengJohn H Doonan
Mar 21, 2015·Plant Methods·Frank LiebischAndreas Hund
Apr 30, 2015·Journal of Experimental Botany·Johanna A Bac-MolenaarJoost J B Keurentjes
May 29, 2015·Nature·Yann LeCunGeoffrey Hinton
Jul 4, 2015·Plant, Cell & Environment·Johanna A Bac-MolenaarDick Vreugdenhil
Oct 24, 2015·The Plant Journal : for Cell and Molecular Biology·Maxwell S BushJohn H Doonan
Dec 15, 2015·Trends in Plant Science·Arti SinghSoumik Sarkar
Oct 8, 2016·Frontiers in Plant Science·Sharada P MohantyMarcel Salathé
Nov 9, 2016·Frontiers in Plant Science·Anyela V CamargoAlison R Bentley
Apr 14, 2017·Plant Methods·Hsiang Sing NaikBaskar Ganapathysubramanian
Jul 25, 2017·Frontiers in Plant Science·Jordan R Ubbens, Ian Stavness
Jul 25, 2017·Current Opinion in Plant Biology·Nadia ShakoorTodd C Mockler
Aug 2, 2017·Computational Intelligence and Neuroscience·Guan WangJianxin Wang
Nov 23, 2017·Frontiers in Plant Science·Amanda RamcharanDavid P Hughes
Apr 22, 2018·Medical Image Analysis·Azam HamidinekooReyer Zwiggelaar
Aug 9, 2018·Plant Methods·Sarah Taghavi NaminJustin O Borevitz

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Citations

Apr 13, 2021·Frontiers in Plant Science·Morteza GhahremaniJohn H Doonan

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Methods Mentioned

BETA
feature extraction
rosette

Key Resources (RRID) Mentioned

SCR_017413

Software Mentioned

SciCrunch
YOLO
Basic
CuDNN
AlexNet
ImageJ
DenseNet
CUDA
DIGITS
MATLAB

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