Software Image J to study soil pore distribution

Passoni, Sabrina; Borges, Fernando S.; Pires, Luiz F.; Saab, Sérgio da Costa; Cooper, Miguel

doi:10.1590/s1413-70542014000200003

Cited by 26 publications

(16 citation statements)

References 20 publications

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“…Image processing, visualization and quantification were performed with the open‐source software ImageJ (Vs. 1.49s, National Institutes of Health, http://imagej.nih.gov/ij/) and the plugin BoneJ (Martínez, Caniego, & García‐Gutiérrez, ; Passoni, Borges, Pires, Saab, & Cooper, ). Each image data set was cropped to a 1200 μm × 1200 μm × 1600 μm volume for analysis to avoid edge effects.…”

Section: Methodsmentioning

confidence: 99%

Changes in soil macropores: Superposition of the roles of organic nutrient amendments and the greenhouse pattern in vegetable plantations

Wang

Tian

et al. 2019

Soil Use and Management

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Organic farming can potentially mitigate soil compaction, which commonly occurs in vegetable plantations, particularly in greenhouses when compared with open-air systems. Although several studies have addressed the effect of planting patterns on soil pore characteristics, few studies have focused on changes in pore attributes under organic fertilization. We used adjacent fields during green manure planting as a control to compare the differences in soil physicochemical and macropore parameters between 14-year-old greenhouse plots and open-air plots under organic fertilization. Pearson's correlation analysis was performed to analyse the drivers of soil macropore characteristics in vegetable plantations in Jiangsu Province, China. A significant increase in connectivity, fractal dimensions and total macroporosity and a decrease in bulk density after 14 years of organic farming, particularly in the surface layer in the greenhouse, were observed. However, the difference in pores in the plough pan layer was not significant between the treatments. The volume of small pores (50-500 μm) and medium pores (500-1,000 μm) increased significantly (p < 0.05) in both the greenhouse and open-air systems, showing significantly positive relationships with soil organic matter (SOM) and total nitrogen (TN) content. Large pores (>1,000 μm) showed a clear decrease, especially in open-air fields, possibly due to the disappearance of the original straw residues in the surface layer. Small and medium pores in the plough layer increased in greenhouse fields, whereas the opposite occurred in open-air fields. Overall, compared with open-air systems, long-term organic greenhouse patterns had a significantly positive effect on soil pore attributes. K E Y W O R D S different planting patterns, long-term organic fertilization, macropore characteristics, X-ray computed tomography

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Section: Methodsmentioning

confidence: 99%

Changes in soil macropores: Superposition of the roles of organic nutrient amendments and the greenhouse pattern in vegetable plantations

Wang

Tian

et al. 2019

Soil Use and Management

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“…Estimativas do percentual de substrato exposto podem ser obtidas por diferentes ferramentas, como por exemplo, a utilização de softwares especializados para o emprego de análise de imagens, que constituem importantes ferramentas auxiliares (DIAS, 2008). O Image Processing and Analysis In Java (ImageJ®) é um software livre, usado para tratamento e processamento de imagens, constituindo uma ferramenta rápida e eficiente para estimar exposição de substrato e/ou solo, por meio de quantificação de variáveis, aplicação de tratamentos para o processamento e interpretação dos resultados (PASSONI et al, 2014). Pelo ImageJ é possível editar, exibir e analisar em inúmeros formatos (extensões), e o software tem apresentado resultados satisfatórios em diversos tipos de análises do solo e vegetação em ambientes degradados (LAURENCE; CHROMY, 2010).…”

Section: Introductionunclassified

O uso do <em>software</em> Imagej na estimativa de substrato exposto pós controle de gramíneas invasoras

et al. 2018

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Espécies de gramíneas (Poaceae) têm sido recomendadas em processos iniciais de recuperação. Entretanto, necessitam de um controle posterior, para evitar competição com espécies de interesse, especialmente arbóreas. Neste contexto, objetivou-se, por meio do software ImageJ, quantificar o substrato exposto em uma área degradada em Diamantina, MG, sobre a qual foram aplicados distintos métodos de capina para o controle das gramíneas exóticas Urochloa decumbes (Stapf) RD, Wabster e Melinis minutiflora P. Beauv.. Foi realizado o controle das gramíneas por meio da aplicação de diferentes métodos (químico, manual e mecânico), distribuídos em 4 blocos, subdivididos em parcelas e subparcelas. Após 100 dias, por meio de imagens processadas pelo ImajeJ, observou-se que método químico proporcionou a menor exposição do substrato e maior presença de biomassa superficial, diferentemente do método manual, onde houve menor cobertura vegetal. Foi possível quantificar o substrato exposto em ambiente com controle de gramíneas permitindo, de modo eficaz, o planejamento das técnicas de recuperação. O uso do ImageJ se mostrou eficiente, representando uma alternativa para a quantificação de substrato, e diversos estudos inerentes à análise de cobertura vegetal de ambientes degradados.

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“…Analysis in two dimensions (2-D) are frequently employed to investigate soil porosity, due to their low cost and easy access (Pires et al, 2008(Pires et al, , 2009Passoni et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

“…The Noesis Visilog software was used for evaluating the pore system of weathered soils when they are subjected to wetting and drying cycles (Pires et al, 2009). The opensource software ImageJ was successfully used to quantify the total porosity (%), total number of pores and pore size distribution for two Brazilian soils by using soil samples impregnated with resin (Passoni et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Software for micromorphometric characterization of soil pores obtained from 2-D image analysis

Cooper

Boschi

Silva

et al. 2016

Sci. agric. (Piracicaba, Braz.)

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Studies of soil porosity through image analysis are important to an understanding of how the soil functions. However, the lack of a simplified methodology for the quantification of the shape, number, and size of soil pores has limited the use of information extracted from images.The present work proposes a software program for the quantification and characterization of soil porosity from data derived from 2-D images. The user-friendly software was developed in C++ and allows for the classification of pores in terms of size, shape, and combinations of size and shape. Using raw data generated by image analysis systems, the software calculates the following parameters for the characterization of soil porosity: total area of pore (Tap), number of pores, pore shape, pore shape and pore area, and pore shape and equivalent pore diameter (EqDiam). In this paper, the input file with the raw soil porosity data was generated using the Noesis Visilog 5.4 image analysis system; however other image analysis programs can be used, in which case, the input file requires a standard format to permit processing by this software.The software also shows the descriptive statistics (mean, standard deviation, variance, and the coefficient of variation) of the parameters considering the total number of images evaluated. The results show that the software is a complementary tool to any analysis of soil porosity, allowing for a precise and quick analysis.

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Software Image J to study soil pore distribution

Cited by 26 publications

References 20 publications

Changes in soil macropores: Superposition of the roles of organic nutrient amendments and the greenhouse pattern in vegetable plantations

Changes in soil macropores: Superposition of the roles of organic nutrient amendments and the greenhouse pattern in vegetable plantations

O uso do <em>software</em> Imagej na estimativa de substrato exposto pós controle de gramíneas invasoras

Software for micromorphometric characterization of soil pores obtained from 2-D image analysis

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