Public-domain software for root image analysis

Costa, Mírian Cristina Gomes; Cunha, Isabela Maria de Lima; Jorge, Lúcio André de Castro; Araújo, Isabel Cristina da Silva

doi:10.1590/s0100-06832014000500001

Cited by 24 publications

(15 citation statements)

References 28 publications

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“…The coefficients of determination values were quite different from those obtained from Safira. However, the determination of coefficient R² = 0.733 is better than the low values of determination coefficient (R² = 0.514 and 0.453), in root length measures of banana (Costa et al, 2014). This indicates that our method explains root length better than Safira.…”

Section: Test With Soybean Rootsmentioning

confidence: 69%

“…In 0-20 cm soil layers, where these values are strong, we can concluded that reference method shows an increase in root length compared to the tested software (Our Method and Safira). Overall, the software developed to facilitate root studies using image processing are positively correlated with the conventional method (Costa et al, 2014). In studies using image processing, which compared WinRHIZO™ with the Tennant method, the morphological root parameters of winter wheat generated by these two methods were positively correlated, but significantly different (Wang and Zhang, 2009).…”

Section: Test With Soybean Rootsmentioning

confidence: 99%

“…2b. The threshold value for estimated root length can vary widely and, because of this, most image analysis software uses manual threshold (Kaspar and Ewing, 1997;Kimura et al, 1999;Kano et al, 2011;Costa et al, 2014). However, it was difficult to determine the proper threshold value manually, because of the continuous change in estimates of root length with changing threshold values (Tajima and Kato, 2011).…”

Section: Application Of Software In Image Samplesmentioning

confidence: 99%

“…In Brazil, Embrapa (Brazilian Enterprise for Agricultural Research) also developed computational systems to assist in the evaluation of root systems: SIARCS® (Jorge and Crestana, 1996) and Safira (Safira, 2018), developed in the Java language. Costa et al (2014) used samples of roots of banana to compare the root lengths achieved by ImageJ, Safira and the reference method (Tennant). The determination coefficient between the reference method and each software was calculated resulting in R² = 0.514 and 0.453, using ImageJ and Safira, respectively.…”

Section: Introductionmentioning

confidence: 99%

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A computational method to assist evaluation of root length of soybean based on digital image processing

et al. 2019

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The evaluation of the root system is important for better understanding the effects of nutrient management on soil and plant nutri-tion. However, root system studies and culture are slow and show low accuracy. In this context, digital image processing may be an alternative. The objective of this research was to develop a computational method to assist evaluation of the soybean root growth. Initially, the free and open access software, available at: http://rm.deinfo.uepg.br/, was developed in Java platform with the OpenCV library supply through the plug-in JavaCV. To evaluate the software, copper wires with 10 mm, 20 mm, and 50 mm of length manually measured using callipers. They were scanned with a resolution of 300 dpi and then images were loaded in the software. Variation coefficients between 0.01 and 2.99 % were obtained. Subsequently, the samples of soybean roots were scanned and the results of developed software and Safira software were correlated with those from the line-intersect method. The determination coefficients (R² = 0.999) of the developed software, on average, were better than those obtained with Safira software (R² = 0.733), when compar-ing with the line-intersect method. Therefore, the proposed method was accurate for length measurements of soybean roots.

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Section: Test With Soybean Rootsmentioning

confidence: 69%

Section: Test With Soybean Rootsmentioning

confidence: 99%

Section: Application Of Software In Image Samplesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

A computational method to assist evaluation of root length of soybean based on digital image processing

et al. 2019

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“…The challenge for root studies is to improve techniques and methods for root sampling and root system architecture quantification7. A rich number of sampling and phenotyping methods for crop roots in the field have been proposed, including soil profiles8, monoliths9, nail plates, probes10, rhizotron8, trenching11, shovelomics12 and digitalization and visualization of roots in field1314. These methods supply a number of parameters, e.g.…”

mentioning

confidence: 99%

Phenotyping for the dynamics of field wheat root system architecture

Chen

Ding

Błaszkiewicz

et al. 2017

Sci Rep

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We investigated a method to quantify field-state wheat RSA in a phenotyping way, depicting the 3D topology of wheat RSA in 14d periods. The phenotyping procedure, proposed for understanding the spatio-temporal variations of root-soil interaction and the RSA dynamics in the field, is realized with a set of indices of mm scale precision, illustrating the gradients of both wheat root angle and elongation rate along soil depth, as well as the foraging potential along the side directions. The 70d was identified as the shifting point distinguishing the linear root length elongation from power-law development. Root vertical angle in the 40 mm surface soil layer was the largest, but steadily decreased along the soil depth. After 98d, larger root vertical angle appeared in the deep soil layers. PAC revealed a stable root foraging potential in the 0–70d period, which increased rapidly afterwards (70–112d). Root foraging potential, explained by MaxW/MaxD ratio, revealed an enhanced gravitropism in 14d period. No-till post-paddy wheat RLD decreased exponentially in both depth and circular directions, with 90% roots concentrated within the top 20 cm soil layer. RER along soil depth was either positive or negative, depending on specific soil layers and the sampling time.

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Quantitative proteomic analysis reveals altered enzyme expression profile in Zea mays roots during the early stages of colonization by Herbaspirillum seropedicae

et al. 2021

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The use of plant growth-promoting bacteria as agricultural inoculants of plants should be encouraged because of their prominent role in biological nitrogen fixation, the increase of nutrient uptake by roots, abiotic stress mitigation, and disease control. The complex mechanisms underlying the association between plant and beneficial bacteria have been increasingly studied, and proteomic tools can expand our perception regarding the fundamental molecular processes modulated by the interaction. In this study, we investigated the changes in protein expression in maize roots in response to treatment with the endophytic diazotrophic Herbaspirillum seropedicae and the activities of enzymes related to nitrogen metabolism. To identify maize proteins whose expression levels were altered in the presence of bacteria, a label-free quantitative proteomic approach was employed. Using this approach, we identified 123 differentially expressed proteins, of which 34 were upregulated enzymes, in maize roots cultivated with H. seropedicae. The maize root colonization of H. seropedicae modulated the differential expression of enzymes involved in the stress response, such as peroxidases, phenylalanine ammonia-lyase, and glutathione transferase. The differential protein profile obtained in the inoculated roots reflects the effect of colonization on plant growth and development compared with control plants. K E Y W O R D S biostimulation, endophytes, label-free proteomics, N 2 -fixation 1 INTRODUCTION The enhanced use of fertilizers for supporting agriculture has led to deterioration of the environment [1]. Nitrogen fertilization of nonleguminous crops is one of the most expensive inputs to increase agri-cultural yields [2]. The use of plant growth-promoting bacteria (PGPB)as agricultural plant inoculants should be encouraged because of their prominent role in biological nitrogen fixation (BNF) and the increased root nutrient absorption, which mitigate abiotic stress and help in disease control. Herbaspirillum seropedicae has been studied because of its

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Public-domain software for root image analysis

Cited by 24 publications

References 28 publications

A computational method to assist evaluation of root length of soybean based on digital image processing

A computational method to assist evaluation of root length of soybean based on digital image processing

Phenotyping for the dynamics of field wheat root system architecture

Quantitative proteomic analysis reveals altered enzyme expression profile in Zea mays roots during the early stages of colonization by Herbaspirillum seropedicae

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