Characterisation of the three-dimensional structure of earthworm burrow systems using image analysis and mathematical morphology

Capowiez, Yvan; Pierret, Alain; Moran, Chris

doi:10.1007/s00374-003-0647-9

Cited by 52 publications

(27 citation statements)

References 37 publications

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“…From the scarce examples of ecological studies, the most studied animals have been arthropods and annelids, and in a lesser extend other kingdoms such as plants and fungi (Figure 3). It is particularly evident that one of the most popular topics so far is soil ecology (Davey et al., 2011; Harrison, Gardner, Tollner, & Kinard, 1993; Tollner, 1991), and specifically the study of worm burrows (Amossé, Turberg, Kohler‐Milleret, Gobat, & Le Bayon, 2015; Auclerc, Capowiez, Guérold, & Nahmani, 2013; Capowiez, Monestiez, & Belzunces, 2001; Capowiez, Pierret, & Moran, 2003; Francis, Tabley, Butler, & Fraser, 2001; Jégou, Capowiez, & Cluzeau, 2001; Jégou, Cluzeau, Hallaire, Balesdent, & Tréhen, 2000; Jégou, Cluzeau, Wolf, Gandon, & Tréhen, 1998; Jégou, Hallaire, Cluzeau, & Tréhen, 1999; Jégou et al., 2002; Langmaack, Schrader, Rapp‐Bernhardt, & Kotzke, 1999; Pagenkemper et al., 2015; Pelosi, Grandeau, & Capowiez, 2017; Rogasik, Schrader, Onasch, Kiesel, & Gerke, 2014; Schrader, Rogasik, Onasch, & Jegou, 2007), mostly because of the ease of studying this type of sample. Soil can be considered a matrix where the components can be detected through X‐ray CT without any preparation (i.e., staining).…”

Section: Application Of X‐ray Computed Tomography In Ecological Studiesmentioning

confidence: 99%

X‐ray computed tomography and its potential in ecological research: A review of studies and optimization of specimen preparation

Gutiérrez

Ott

Töpperwien

et al. 2018

Ecology and Evolution

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Imaging techniques are a cornerstone of contemporary biology. Over the last decades, advances in microscale imaging techniques have allowed fascinating new insights into cell and tissue morphology and internal anatomy of organisms across kingdoms. However, most studies so far provided snapshots of given reference taxa, describing organs and tissues under “idealized” conditions. Surprisingly, there is an almost complete lack of studies investigating how an organism′s internal morphology changes in response to environmental drivers. Consequently, ecology as a scientific discipline has so far almost neglected the possibilities arising from modern microscale imaging techniques. Here, we provide an overview of recent developments of X‐ray computed tomography as an affordable, simple method of high spatial resolution, allowing insights into three‐dimensional anatomy both in vivo and ex vivo. We review ecological studies using this technique to investigate the three‐dimensional internal structure of organisms. In addition, we provide practical comparisons between different preparation techniques for maximum contrast and tissue differentiation. In particular, we consider the novel modality of phase contrast by self‐interference of the X‐ray wave behind an object (i.e., phase contrast by free space propagation). Using the cricket Acheta domesticus (L.) as model organism, we found that the combination of FAE fixative and iodine staining provided the best results across different tissues. The drying technique also affected contrast and prevented artifacts in specific cases. Overall, we found that for the interests of ecological studies, X‐ray computed tomography is useful when the tissue or structure of interest has sufficient contrast that allows for an automatic or semiautomatic segmentation. In particular, we show that reconstruction schemes which exploit phase contrast can yield enhanced image quality. Combined with suitable specimen preparation and automated analysis, X‐ray CT can therefore become a promising quantitative 3D imaging technique to study organisms′ responses to environmental drivers, in both ecology and evolution.

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Section: Application Of X‐ray Computed Tomography In Ecological Studiesmentioning

confidence: 99%

X‐ray computed tomography and its potential in ecological research: A review of studies and optimization of specimen preparation

Gutiérrez

Ott

Töpperwien

et al. 2018

Ecology and Evolution

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“…A systematic evaluation of the influence of X-ray energy level on the relative attenuation of minerals commonly occurring in soils was presented by Heck and Elliot (2006); the results showed that the X-ray attenuation values of carbonates, gypsum, halite and apatite were more sensitive to changes in excitation voltage (80 to 120 keV) than those of the silicates. As indicated by the variety of X-ray energy Capowiez et al (1998Capowiez et al ( , 2000Capowiez et al ( , 2001Capowiez et al ( , 2003 CT Pace X-ray scanner-General Electric ( (Pierret et al 2002), erosions, dilations (2003) Prospeed SX Advantage, General Electric (2001 140 kV, 160 mA 0.4)0.4)3 resampled into 0.5)0.5 ) 0.5 (2003) Langmaack et al (1999,2002) Siemens Somatom Plus 80 kV, 135 mA 1)1)2 Joschko (1991) AVS Je´gou et al (1998Je´gou et al ( , 1999Je´gou et al ( , 2001Je´gou et al ( , 2002 Siemens Somatom Plus 120 kV, 165 mA Prospeed SX Power system, General Electric 120kV, 160 mA…”

Section: Mineral Constituentsmentioning

confidence: 99%

“…Macropore length, branching intensity, mean vertical deviation and topological parameters such as connectivity were estimated as well. Relatively simple to compute, these operations are implemented in analysis packages such as Khoros, Micromorph and Image-J (Capowiez et al 2003).…”

Section: Characterization Of Soil Physical Propertiesmentioning

confidence: 99%

“…Despite its non-destructive and non-invasive nature, X-ray CT has been used only in relatively few studies of the root system and soil interactions (Hainsworth and Aylmore 1983;Tollner et al 1987Tollner et al , 1994Grose et al 1996;Zwiggelaar et al 1997). More numerous are the investigations on the influence of earthworms on soil structure (Joschko et al 1991(Joschko et al , 1993Daniel et al 1997;Capowiez et al 1998Capowiez et al , 2000Capowiez et al , 2001Capowiez et al , 2003Je´gou et al 1998Je´gou et al , 1999Je´gou et al , 2000Je´gou et al , 2001Langmaack et al 1999Langmaack et al , 2002Francis et al 2001;Pierret et al 2002;Bastardie et al 2003).…”

Section: Characterization Of Soil Biotamentioning

confidence: 99%

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Application of X-ray computed tomography to soil science: A literature review

Taina¹,

Heck²,

Elliot³

2008

Can. J. Soil. Sci.

265

128

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T. R. 2008. Application of X-ray computed tomography to soil science: A literature review. Can. J. Soil Sci. 88: 1Á20. The study of the spatial configuration of soil, in its complexity, requires an understanding of the interrelations and interactions between the diverse soil constituents, at various levels of organization. Investigations of the spatial arrangement of the mineral and organic components of soil have benefited from the development of techniques for structural analysis. X-ray computed tomography (CT) is a non-destructive and non-invasive technique that has been successfully used for three-dimensional (3D) examination of soil. Valuable information has been obtained by the application of CT for the description and quantitative measurements of soil structure elements, especially of soil pores and pore network features. In many studies, X-ray CT has been used to investigate the hydro-physical characteristics of the soil, in a functional and temporal manner. A dynamic approach has also been utilized in the evaluation of the biotic factor influence on soil. The analysis of soil solid phases, by X-ray CT, has been challenging due to the similar X-ray attenuation of different solid constituents. However, the use of multiple X-ray energy levels has facilitated the discrimination of minerals in soil. The aim of this review and synthesis is to offer a perspective on the major issues related to application of the technique, general attempted solutions and possible directions in the utilization of X-ray CT in soil research. Relevant scanning parameters, procedures for CT image reconstruction, algorithms for the quantification of soil characteristics and results are presented for each type of application.Key words: X-ray computed tomography, energy level, spatial resolution, segmentation, soil mineral and organic constituents, soil physical and hydro-physical properties, soil biota Taina, I. A., Heck, R. J. et Elliot, T. R. 2008. Application de la tomographie aux rayons X a`la science du sol : survol de la litte´rature. Can. J. Soil Sci. 88: 1Á20. Pour e´tudier la configuration spatiale du sol dans toute sa complexite´, il faut comprendre les relations et les interactions des fractions du sol a`diffe´rents niveaux d'organisation. Les recherches sur l'organisation spatiale des couches mine´rales et organiques du sol ont profite´du de´veloppement de techniques d'analyse structurale. La tomographie aux rayons X assiste´e par ordinateur (TXAO) est une technique non destructive et non invasive qu'on a applique´e avec succe`s a`l'analyse tridimensionnelle du sol. L'usage de la TXAO pour de´crire et quantifier les e´le´ments structuraux du sol, surtout les pores et les particularite´s de leurs re´seaux, a permis de glaner quelques pre´cieuses informations. Maintes e´tudes rapportent qu'on s'est servi de la TXAO pour pre´ciser les proprie´te´s hydrophysiques du sol sur le plan fonctionnel ou temporel. On a aussi recouru a`une approche dynamique pour e´valuer l'influence des facteurs biotiques sur le sol. L'analyse des p...

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“…for earthworm burrow systems Capowiez et al, 2003Capowiez et al, , 2011. All effects connected to friction in the macropore (which includes the inclination 20 of the macropore gallery and pore roughness) are implicitly summed up in equation 8.…”

mentioning

confidence: 99%

Ecohydrological particle model based on representative domains

Jackisch¹,

Zehe²

2017

Preprint

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Abstract. Non-uniform infiltration and subsurface flow in structured soils is observed in most natural settings. It arises from imperfect lateral mixing of fast advective flow in structures and diffusive flow in the soil matrix and remains one of the most challenging topics with respect to match observation and modelling of water and solutes at the plot scale.This study extends the fundamental introduction of a space-domain random walk of water particles as alternative approach to the Richards equation for diffusive flow (Zehe and Jackisch, 2016) to a stochastic-physical model framework simulating 5 soil water flow in a representative, structured soil domain. The central objective of the proposed model is the simulation of non-uniform flow fingerprints in different ecohydrological settings and antecedent states by making maximum use of field observables for parameterisation. Avoiding non-observable parameters for macropore-matrix exchange, an energy-balance approach to govern film flow in representative flow paths is employed. We present the echoRD model (ecohydrological particle model based on representative domains) and a series of application test cases. 10The model proves as a powerful alternative to existing dual-domain models, driven on experimental data and with selfcontrolled, dynamic macropore-matrix exchange from the topologically semi-explicitly defined structures.

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Characterisation of the three-dimensional structure of earthworm burrow systems using image analysis and mathematical morphology

Cited by 52 publications

References 37 publications

X‐ray computed tomography and its potential in ecological research: A review of studies and optimization of specimen preparation

X‐ray computed tomography and its potential in ecological research: A review of studies and optimization of specimen preparation

Application of X-ray computed tomography to soil science: A literature review

Ecohydrological particle model based on representative domains

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