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Towards Automated Analysis of Grain Spikes in Greenhouse Images Using Neural Network Approaches: A Comparative Investigation of Six Methods

Automated analysis of small and optically variable plant organs, such as grain spikes, is highly demanded in quantitative plant science and breeding. Previous works primarily focused on the detection of prominently visible spikes emerging on the top of the grain plants growing in field conditions. H...

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Autores principales: Ullah, Sajid, Henke, Michael, Narisetti, Narendra, Panzarová, Klára, Trtílek, Martin, Hejatko, Jan, Gladilin, Evgeny
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8621358/
https://www.ncbi.nlm.nih.gov/pubmed/34833515
http://dx.doi.org/10.3390/s21227441
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author Ullah, Sajid
Henke, Michael
Narisetti, Narendra
Panzarová, Klára
Trtílek, Martin
Hejatko, Jan
Gladilin, Evgeny
author_facet Ullah, Sajid
Henke, Michael
Narisetti, Narendra
Panzarová, Klára
Trtílek, Martin
Hejatko, Jan
Gladilin, Evgeny
author_sort Ullah, Sajid
collection PubMed
description Automated analysis of small and optically variable plant organs, such as grain spikes, is highly demanded in quantitative plant science and breeding. Previous works primarily focused on the detection of prominently visible spikes emerging on the top of the grain plants growing in field conditions. However, accurate and automated analysis of all fully and partially visible spikes in greenhouse images renders a more challenging task, which was rarely addressed in the past. A particular difficulty for image analysis is represented by leaf-covered, occluded but also matured spikes of bushy crop cultivars that can hardly be differentiated from the remaining plant biomass. To address the challenge of automated analysis of arbitrary spike phenotypes in different grain crops and optical setups, here, we performed a comparative investigation of six neural network methods for pattern detection and segmentation in RGB images, including five deep and one shallow neural network. Our experimental results demonstrate that advanced deep learning methods show superior performance, achieving over 90% accuracy by detection and segmentation of spikes in wheat, barley and rye images. However, spike detection in new crop phenotypes can be performed more accurately than segmentation. Furthermore, the detection and segmentation of matured, partially visible and occluded spikes, for which phenotypes substantially deviate from the training set of regular spikes, still represent a challenge to neural network models trained on a limited set of a few hundreds of manually labeled ground truth images. Limitations and further potential improvements of the presented algorithmic frameworks for spike image analysis are discussed. Besides theoretical and experimental investigations, we provide a GUI-based tool (SpikeApp), which shows the application of pre-trained neural networks to fully automate spike detection, segmentation and phenotyping in images of greenhouse-grown plants.
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spelling pubmed-86213582021-11-27 Towards Automated Analysis of Grain Spikes in Greenhouse Images Using Neural Network Approaches: A Comparative Investigation of Six Methods Ullah, Sajid Henke, Michael Narisetti, Narendra Panzarová, Klára Trtílek, Martin Hejatko, Jan Gladilin, Evgeny Sensors (Basel) Article Automated analysis of small and optically variable plant organs, such as grain spikes, is highly demanded in quantitative plant science and breeding. Previous works primarily focused on the detection of prominently visible spikes emerging on the top of the grain plants growing in field conditions. However, accurate and automated analysis of all fully and partially visible spikes in greenhouse images renders a more challenging task, which was rarely addressed in the past. A particular difficulty for image analysis is represented by leaf-covered, occluded but also matured spikes of bushy crop cultivars that can hardly be differentiated from the remaining plant biomass. To address the challenge of automated analysis of arbitrary spike phenotypes in different grain crops and optical setups, here, we performed a comparative investigation of six neural network methods for pattern detection and segmentation in RGB images, including five deep and one shallow neural network. Our experimental results demonstrate that advanced deep learning methods show superior performance, achieving over 90% accuracy by detection and segmentation of spikes in wheat, barley and rye images. However, spike detection in new crop phenotypes can be performed more accurately than segmentation. Furthermore, the detection and segmentation of matured, partially visible and occluded spikes, for which phenotypes substantially deviate from the training set of regular spikes, still represent a challenge to neural network models trained on a limited set of a few hundreds of manually labeled ground truth images. Limitations and further potential improvements of the presented algorithmic frameworks for spike image analysis are discussed. Besides theoretical and experimental investigations, we provide a GUI-based tool (SpikeApp), which shows the application of pre-trained neural networks to fully automate spike detection, segmentation and phenotyping in images of greenhouse-grown plants. MDPI 2021-11-09 /pmc/articles/PMC8621358/ /pubmed/34833515 http://dx.doi.org/10.3390/s21227441 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ullah, Sajid
Henke, Michael
Narisetti, Narendra
Panzarová, Klára
Trtílek, Martin
Hejatko, Jan
Gladilin, Evgeny
Towards Automated Analysis of Grain Spikes in Greenhouse Images Using Neural Network Approaches: A Comparative Investigation of Six Methods
title Towards Automated Analysis of Grain Spikes in Greenhouse Images Using Neural Network Approaches: A Comparative Investigation of Six Methods
title_full Towards Automated Analysis of Grain Spikes in Greenhouse Images Using Neural Network Approaches: A Comparative Investigation of Six Methods
title_fullStr Towards Automated Analysis of Grain Spikes in Greenhouse Images Using Neural Network Approaches: A Comparative Investigation of Six Methods
title_full_unstemmed Towards Automated Analysis of Grain Spikes in Greenhouse Images Using Neural Network Approaches: A Comparative Investigation of Six Methods
title_short Towards Automated Analysis of Grain Spikes in Greenhouse Images Using Neural Network Approaches: A Comparative Investigation of Six Methods
title_sort towards automated analysis of grain spikes in greenhouse images using neural network approaches: a comparative investigation of six methods
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8621358/
https://www.ncbi.nlm.nih.gov/pubmed/34833515
http://dx.doi.org/10.3390/s21227441
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