scikit-image: Image processing in Python

Walt, Stéfan van der; Schönberger, Johannes L.; Nunez-Iglesias, Juan; Boulogne, François; Warner, Joshua D.; Yager, Neil; Gouillart, Emmanuelle; Yu, Tony

doi:10.7287/peerj.preprints.336

Cited by 92 publications

(97 citation statements)

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“…Drainage area is calculated from the model topography (Figure a) using the Landlab FlowDirectorD8 and FlowAccumulator components (Hobley et al, ), and channels are identified with a threshold drainage area. The selected channels are analyzed with a connected components algorithm (Van der Walt et al, ) to map connected channel systems across the fault (Figure b). Thalweg locations are automatically identified where channels intersect profiles on both sides of the fault.…”

Section: Methodsmentioning

confidence: 99%

Offset Channels May Not Accurately Record Strike‐Slip Fault Displacement: Evidence From Landscape Evolution Models

et al. 2019

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Slip distribution, slip rate, and slip per event for strike‐slip faults are commonly determined by correlating offset stream channels—under the assumption that they record seismic slip—but offset channels are formed by the interplay of tectonic and geomorphic processes. To constrain offset channel development under known tectonic and geomorphic conditions, we use numerical landscape evolution simulations along a theoretical strike‐slip fault with uniform and steady uplift, erosion, and diffusion. We investigate the influence of four tectonic parameters (fault zone width, earthquake recurrence interval, variance of the recurrence interval, and total slip relative to channel spacing) on offset channel development through multiple earthquake cycles. Analysis of >3,000 automatically measured offsets from >135 simulations suggests ~30% variability in individual measurements, but modeled displacement is recovered by averaging multiple measurements. However, the average of multiple offset measurements systematically underestimates modeled slip except when the fault zone is less than ~5 m wide, total slip is less than channel spacing, and offsets are measured shortly after an earthquake. In these simulations, postearthquake landscape evolution widens the geomorphic expression of the fault zone and modifies apparent channel offsets. We distinguish this “geomorphic fault zone” from the tectonic fault zone (zone of coseismic distributed deformation). This study highlights the capability of landscape evolution models to explore a range of conditions not easily defined in natural examples and the importance of averaging multiple measurements. Our results verify that paleoseismic studies must consider how geomorphic change has modified offset markers and use caution interpreting slip histories with multiple earthquakes.

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Section: Methodsmentioning

confidence: 99%

Offset Channels May Not Accurately Record Strike‐Slip Fault Displacement: Evidence From Landscape Evolution Models

et al. 2019

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“…Paper sheets with leaves were digitized using either a flatbed scanner or a digital photo camera. The obtained images were further processed using the Python module scikit‐image (Van der Walt et al., ). Individual leaves were segmented using an intensity thresholding approach.…”

Section: Methodsmentioning

confidence: 99%

Compensatory mechanisms to climate change in the widely distributed species Silene vulgaris

2019

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The adaptation of plants to future climatic conditions is crucial for their survival. Not surprisingly, phenotypic responses to climate change have already been observed in many plant populations. These responses may be due to evolutionary adaptive changes or phenotypic plasticity. Especially plant species with a wide geographic range are either expected to show genetic differentiation in response to differing climate conditions or to have a high phenotypic plasticity. We investigated phenotypic responses and plasticity as an estimate of the adaptive potential in the widespread species Silene vulgaris. In a greenhouse experiment, 25 European populations covering a geographic range from the Canary Islands to Sweden were exposed to three experimental precipitation and two temperature regimes mimicking a possible climate‐change scenario for central Europe. We hypothesized that southern populations have a better performance under high temperature and drought conditions, as they are already adapted to a comparable environment. We found that our treatments significantly influenced the plants, but did not reveal a latitudinal difference in response to climate treatments for most plant traits. Only flower number showed a stronger plasticity in northern European populations (e.g. Swedish populations) where numbers decreased more drastically with increased temperature and decreased precipitation treatment. Synthesis. The significant treatment response in Silene vulgaris, independent of population origin – except for the number of flowers produced – suggests a high degree of universal phenotypic plasticity in this widely distributed species. This reflects the likely adaptation strategy of the species and forms the basis for a successful survival strategy during upcoming climatic changes. However, as flower number, a strongly fitness‐related trait, decreased more strongly in northern populations under a climate‐change scenario, there might be limits to adaptation even in this widespread, plastic species.

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“…In addition to end-user software, open-source libraries for scripting languages such as MATLAB or Python (Coelho, 2013; van der Walt et al, 2014) offer access to skeletonization methods. In particular, Python and its scientific libraries have become widely used in interdisciplinary research and education (Deutsch, 2014).…”

Section: Discussionmentioning

confidence: 99%

A practical introduction to skeletons for the plant sciences

Bucksch

2014

Appl Plant Sci

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Before the availability of digital photography resulting from the invention of charged couple devices in 1969, the measurement of plant architecture was a manual process either on the plant itself or on traditional photographs. The introduction of cheap digital imaging devices for the consumer market enabled the wide use of digital images to capture the shape of plant networks such as roots, tree crowns, or leaf venation. Plant networks contain geometric traits that can establish links to genetic or physiological characteristics, support plant breeding efforts, drive evolutionary studies, or serve as input to plant growth simulations. Typically, traits are encoded in shape descriptors that are computed from imaging data. Skeletons are one class of shape descriptors that are used to describe the hierarchies and extent of branching and looping plant networks. While the mathematical understanding of skeletons is well developed, their application within the plant sciences remains challenging because the quality of the measurement depends partly on the interpretation of the skeleton. This article is meant to bridge the skeletonization literature in the plant sciences and related technical fields by discussing best practices for deriving diameters and approximating branching hierarchies in a plant network.

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scikit-image: Image processing in Python

Cited by 92 publications

References 0 publications

Offset Channels May Not Accurately Record Strike‐Slip Fault Displacement: Evidence From Landscape Evolution Models

Offset Channels May Not Accurately Record Strike‐Slip Fault Displacement: Evidence From Landscape Evolution Models

Compensatory mechanisms to climate change in the widely distributed species Silene vulgaris

A practical introduction to skeletons for the plant sciences

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