A package for the analysis of anatomical tissue structures in spatial omics data

Documentation for package ‘sosta’ version 0.99.4

.intensityImage	Function to estimate the intensity image of a point pattern
.intensityThreshold	Function to estimate the intensity threshold for the reconstruction of spatial structures
binaryImageToSF	Converts a binary matrix to an sf polygon
estimateReconstructionParametersSPE	Estimate reconstruction parameters from a set of images
findIntensityThreshold	Estimate the intensity threshold for the reconstruction of spatial structures
getDimXY	Function to get the dimension based on dim of y axis
meanShapeMetrics	Calculate mean shape metrics of a set of polygons
normalizeCoordinates	Function to normalize coordinates between zero and one while keep scaling
reconstructShapeDensity	Reconstruct polygon from point pattern density
reconstructShapeDensityImage	Reconstruct structure from spe object with given image id
reconstructShapeDensitySPE	Reconstruct structure from spatial experiment object per image id
shapeIntensityImage	Intensity plot
shapeMetrics	Calculate a set of shape metrics of a polygon
SPE2ppp	Function to convert spatial coordinates of a 'SpatialExperiment' object to a 'ppp' object
st_calculateCurvature	Title
st_calculateShapeCurl	Calculate curl of a polygon
st_feature_axes	Calculate the length of feature axes of an sf polygon
totalShapeMetrics	Calculate a set of shape metrics of a set of polygons
xyCoordinates	Function to extract x y coordinates from binary image