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AFM  

Atomic Force Microscope Image Analysis
View on CRAN: Click here


Download and install AFM package within the R console
Install from CRAN:
install.packages("AFM")

Install from Github:
library("remotes")
install_github("cran/AFM")

Install by package version:
library("remotes")
install_version("AFM", "2.0")



Attach the package and use:
library("AFM")
Maintained by
Mathieu Beauvais
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-10-29
Latest Update: 2020-10-07
Description:
Provides Atomic Force Microscope images analysis such as Gaussian mixes identification, Power Spectral Density, roughness against lengthscale, experimental variogram and variogram models, fractal dimension and scale, 2D network analysis. The AFM images can be exported to STL format for 3D printing.
How to cite:
Mathieu Beauvais (2015). AFM: Atomic Force Microscope Image Analysis. R package version 2.0, https://cran.r-project.org/web/packages/AFM. Accessed 21 Nov. 2024.
Previous versions and publish date:
1.0.0 (2015-10-29 15:36), 1.1.0 (2015-12-01 16:17), 1.2.0 (2016-02-26 23:23), 1.2.1 (2016-04-12 00:57), 1.2.2 (2016-09-01 01:33), 1.2.4 (2018-04-28 08:21), 1.2.6 (2019-06-08 09:40)
Other packages that cited AFM R package
View AFM citation profile
Other R packages that AFM depends, imports, suggests or enhances
Complete documentation for AFM
Functions, R codes and Examples using the AFM R package
Some associated functions: AFM . AFMFractalDimensionAnalyser-getFractalDimensions . AFMImage-class . AFMImage-extractAFMImage . AFMImage-filterAFMImage . AFMImage-getHolesStatistics . AFMImage-importFromNanoscope . AFMImage-invertBinaryAFMImage . AFMImage-isBinary . AFMImage-makeBinaryAFMImage . AFMImage-multiplyHeightsAFMImage . AFMImage-sampleAFMImage . AFMImage-saveOnDisk . AFMImage-simplifyAFMImage . AFMImage3DModelAnalysis-class . AFMImageAnalyser-class-initialize . AFMImageAnalyser-class . AFMImageCollagenNetwork . AFMImageFractalDimensionMethod-class . AFMImageFractalDimensionsAnalysis-class . AFMImageGaussianMixAnalysis-class . AFMImageNetworksAnalysis-class . AFMImageOfAluminiumInterface . AFMImageOfNormallyDistributedHeights . AFMImageOfOnePeak . AFMImageOfRegularPeaks . AFMImagePSDAnalysis-class . AFMImagePSDSlopesAnalysis-class . AFMImageVariogramAnalyser-calculateDirectionalVariograms . AFMImageVariogramAnalyser-calculateOmnidirectionalVariogram . AFMImageVariogramAnalyser-getAutomaticWidthForVariogramCalculation . AFMImageVariogramAnalysis-class . AFMImageVariogramAnalysis-evaluateVariogramModels-method . AFMImageVariogramAnalysis-getDTModelEvaluation-method . AFMImageVariogramAnalysis-getDTModelSillRange-method . AFMImageVariogramAnalysis-updateProgress-method . AFMImageVariogramModel-class . AFMVariogramAnalyser-getSpplotFromAFMImage . AFMVariogramAnalyser-saveSpplotFromAFMImage . AreNodesConnected . PSD1DAgainstFrequency-methods . PSD2DAgainstFrequency-methods . RoughnessByLengthScale-methods . addNode . analyse . calculate3DModel-methods . calculateGaussianMixture . calculateHolesCharacteristics . calculateIgraph . calculateNetworkParameters . calculateNetworkSkeleton . calculateNetworks-methods . calculatePhysicalDistanceFromPath . calculateShortestPaths . canBeRemoved . checkIsotropy . checkNormality . createGraph . displayColoredNetworkWithVerticesSize . displayHolesIn3D . displayIn3D . displaygridIgraphPlot . displaygridIgraphPlotFromEdges . dnormalmix . existsEdge . existsSegment . exportToSTL . fusionCloseNodes . generateAFMImageReport . generateCheckReport . generatePolygonEnvelope . generateReport . generateReportFromNanoscopeImageDirectory . get3DImageFullfilename . getAllPointsToRemove . getAngle . getAutoIntersectionForOmnidirectionalVariogram . getAutoIntersectionForRoughnessAgainstLengthscale . getBresenham2DSegment . getCircleSpatialPoints . getCoordinatesFromVertexId . getIntersectionForRoughnessAgainstLengthscale . getIntersectionPointWithBorder . getListOfDiameters . getLogLogOmnidirectionalSlopeGraph . getMaxCircleMatrix . getNetworkGridLayout . getNetworkParameters-methods . getNyquistSpatialFrequency-methods . getPaddedAFMImage . getRoughnessParameters-methods . getSurroundingVertexesList . getTopologyAFMImage . getTriangle . getVertexId . gridIgraphPlot . identifyEdgesFromCircles . identifyIsolatedNodes . identifyMaxCircleRadius . identifyNodesAndEdges . identifyNodesWithCircles . isAdjacentToBetterVertex . isAngleBetweenEdgesAlwaysSuperiorToMinAngle . loglike.normalmix . omniVariogramSlopeAnalysis-class . performAllPSDCalculation . performGaussianMixCalculation . pnormmix . printVariogramModelEvaluations . putAnalysisOnDisk-methods . putImagesFromAnalysisOnDisk . removeLonguestEdge . removeNode . runAFMApp . saveOnDiskIntersectionForRoughnessAgainstLengthscale . shiftFFT2D . shiftedPSDuv . simplifyNetwork . thinImage . totalRMSRoughness . transformAFMImageForNetworkAnalysis-methods . 
Some associated R codes: AFM3DPrinter.R . AFMFractalDimensionAnalyser.R . AFMGaussianMixAnalyser.R . AFMImage.R . AFMImageAnalyser.R . AFMNetworksAnalyser.R . AFMPSDAnalyser.R . AFMReportMaker.R . AFMVariogramAnalyser.R . pkgname.R . runAFMApp.R .  Full AFM package functions and examples
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