用于全面分析葡萄藤簇结构和浆果特性的分段数据。

IF 7.6 1区 农林科学 Q1 AGRONOMY Plant Phenomics Pub Date : 2024-06-27 eCollection Date: 2024-01-01 DOI:10.34133/plantphenomics.0202
Efrain Torres-Lomas, Jimena Lado-Bega, Guillermo Garcia-Zamora, Luis Diaz-Garcia
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引用次数: 0

摘要

葡萄果穗结构和紧密度是影响疾病易感性、果实质量和产量的复杂性状。这些性状的评估方法包括视觉评分、人工方法和计算机视觉,其中计算机视觉是最具扩展性的方法。现有的大多数计算机视觉处理群集图像的方法通常都依赖于传统的分割或机器学习,这些方法都需要大量的训练,而且通用性有限。Segment Anything Model(SAM)是一种在海量图像数据集上训练的新型基础模型,无需额外训练即可实现自动物体分割。本研究证明,开箱即用的 SAM 在识别二维(2D)群集图像中的单个浆果方面具有很高的准确性。利用该模型,我们成功地分割了约 3,500 幅集群图像,生成了超过 150,000 个浆果掩码,每个掩码都与其集群内的空间坐标相关联。人类识别的浆果与 SAM 预测之间的相关性非常强(Pearson's r2 = 0.96)。虽然由于可见度问题,图像中的可见浆果数量通常会低估实际的群集浆果数量,但我们证明这种差异可以通过线性回归模型进行调整(调整后的 R 2 = 0.87)。我们强调了果穗成像角度的重要性,并指出它对浆果数量和结构有很大影响。我们提出了不同的方法,其中浆果位置信息有助于计算与果丛结构和紧凑程度相关的复杂特征。最后,我们讨论了将 SAM 集成到当前可用的葡萄园图像生成和处理管道中的可能性。
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Segment Anything for Comprehensive Analysis of Grapevine Cluster Architecture and Berry Properties.

Grape cluster architecture and compactness are complex traits influencing disease susceptibility, fruit quality, and yield. Evaluation methods for these traits include visual scoring, manual methodologies, and computer vision, with the latter being the most scalable approach. Most of the existing computer vision approaches for processing cluster images often rely on conventional segmentation or machine learning with extensive training and limited generalization. The Segment Anything Model (SAM), a novel foundation model trained on a massive image dataset, enables automated object segmentation without additional training. This study demonstrates out-of-the-box SAM's high accuracy in identifying individual berries in 2-dimensional (2D) cluster images. Using this model, we managed to segment approximately 3,500 cluster images, generating over 150,000 berry masks, each linked with spatial coordinates within their clusters. The correlation between human-identified berries and SAM predictions was very strong (Pearson's r2 = 0.96). Although the visible berry count in images typically underestimates the actual cluster berry count due to visibility issues, we demonstrated that this discrepancy could be adjusted using a linear regression model (adjusted R 2 = 0.87). We emphasized the critical importance of the angle at which the cluster is imaged, noting its substantial effect on berry counts and architecture. We proposed different approaches in which berry location information facilitated the calculation of complex features related to cluster architecture and compactness. Finally, we discussed SAM's potential integration into currently available pipelines for image generation and processing in vineyard conditions.

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来源期刊
Plant Phenomics
Plant Phenomics Multiple-
CiteScore
8.60
自引率
9.20%
发文量
26
审稿时长
14 weeks
期刊介绍: Plant Phenomics is an Open Access journal published in affiliation with the State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University (NAU) and published by the American Association for the Advancement of Science (AAAS). Like all partners participating in the Science Partner Journal program, Plant Phenomics is editorially independent from the Science family of journals. The mission of Plant Phenomics is to publish novel research that will advance all aspects of plant phenotyping from the cell to the plant population levels using innovative combinations of sensor systems and data analytics. Plant Phenomics aims also to connect phenomics to other science domains, such as genomics, genetics, physiology, molecular biology, bioinformatics, statistics, mathematics, and computer sciences. Plant Phenomics should thus contribute to advance plant sciences and agriculture/forestry/horticulture by addressing key scientific challenges in the area of plant phenomics. The scope of the journal covers the latest technologies in plant phenotyping for data acquisition, data management, data interpretation, modeling, and their practical applications for crop cultivation, plant breeding, forestry, horticulture, ecology, and other plant-related domains.
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