Package: sosta 1.5.1

Samuel Gunz

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

sosta (Spatial Omics STructure Analysis) is a package for analyzing spatial omics data to explore tissue organization at the anatomical structure level. It reconstructs anatomically relevant structures based on molecular features or cell types. It further calculates a range of metrics at the structure level to quantitatively describe tissue architecture. The package is designed to integrate with other packages for the analysis of spatial omics data.

Authors:Samuel Gunz [aut, cre], Mark D. Robinson [aut, fnd]

sosta_1.5.1.tar.gz
sosta_1.5.1.zip(r-4.7)sosta_1.5.1.zip(r-4.6)sosta_1.5.1.zip(r-4.5)
sosta_1.5.1.tgz(r-4.6-any)sosta_1.5.1.tgz(r-4.5-any)
sosta_1.5.1.tar.gz(r-4.7-any)sosta_1.5.1.tar.gz(r-4.6-any)
sosta_1.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
sosta/json (API)

# Install 'sosta' in R:

install.packages('sosta', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sgunz/sosta/issues

Pkgdown/docs site:https://sgunz.github.io

Datasets:

sostaSPE - Example SpatialExperiment Object with Simulated Tissue Images and Point Patterns

On BioConductor:sosta-1.5.1(bioc 3.24)sosta-1.4.0(bioc 3.23)

software spatial transcriptomics visualization

6.53 score 7 stars 20 scripts 28 exports 118 dependencies

Last updated from:0c7092a6af. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	527
linux-devel-x86_64	OK	494
source / vignettes	OK	770
linux-release-x86_64	OK	516
macos-release-arm64	OK	442
macos-oldrel-arm64	OK	311
windows-devel	OK	363
windows-release	OK	368
windows-oldrel	OK	375
wasm-release	OK	202

Exports:.df2ppp .intensityImage .intensityThreshold .SPE2df assingCellsToStructures binaryImageToSF cellTypeProportions createPointPatternTissue estimateReconstructionParametersSPE findIntensityThreshold getDimXY meanShapeMetrics minBoundaryDistances minCellTypeStructDist normalizeCoordinates reconstructShapeDensity reconstructShapeDensityImage reconstructShapeDensitySPE shapeIntensityImage shapeMetrics simulateTissueBlobs spatialCoords2SF SPE2ppp stCalculateCurvature stCalculateShapeCurl stFeatureAxes totalShapeMetrics xyCoordinates

Dependencies:abind askpass base64enc Biobase BiocFileCache BiocGenerics bit bit64 bitops blob bslib cachem class classInt cli cpp11 curl DBI dbplyr DelayedArray deldir digest dplyr e1071 EBImage evaluate farver fastmap fftwtools filelock fontawesome fs generics GenomicRanges ggplot2 glue goftest gtable highr htmltools htmlwidgets httr2 IRanges isoband jpeg jquerylib jsonlite KernSmooth knitr labeling lattice lifecycle locfit magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nlme openssl patchwork pillar pkgconfig png polyclip proxy purrr R6 rappdirs RColorBrewer Rcpp RCurl rjson rlang rmarkdown RSQLite s2 S4Arrays S4Vectors S7 sass scales Seqinfo sf SingleCellExperiment smoothr SparseArray SpatialExperiment spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment sys tensor terra tibble tidyr tidyselect tiff tinytex units utf8 vctrs viridisLite withr wk xfun XVector yaml

01 -- Overview of sosta

Rendered fromStructureReconstructionVignette.Rmdusingknitr::rmarkdown

Last update: 2026-03-23
Started: 2025-03-21

02 -- Reconstruction and analysis of pancreatic islets from IMC data

Rendered fromImcDiabetesIsletsVignette.Rmdusingknitr::rmarkdown

Last update: 2025-04-14
Started: 2025-03-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Function to convert 'data.frame' to 'ppp' object	.df2ppp
Function to estimate the intensity image of a point pattern	.intensityImage
Function to estimate the intensity threshold for the reconstruction of spatial structures	.intensityThreshold
Function to convert 'SpatialExperiment' object to a data frame	.SPE2df
Function to assign points / coordinates to structures	assingCellsToStructures
Converts a binary matrix to an sf polygon	binaryImageToSF
Calculate the proportion of each cell type within spatial structures	cellTypeProportions
Create a Point Pattern on a Simulated Tissue Image	createPointPatternTissue
Estimate reconstruction parameters from a set of images	estimateReconstructionParametersSPE
Estimate the intensity threshold for the reconstruction of spatial structures	findIntensityThreshold
Function to get the dimension based on dim of y axis	getDimXY
Calculate mean shape metrics of a set of polygons	meanShapeMetrics
Compute minimum boundary distances for each cell within its corresponding image structures	minBoundaryDistances
Compute minimum distances from each cell types to structure boundaries per structure	minCellTypeStructDist
Function to normalize coordinates between zero and one while keep scaling	normalizeCoordinates
Reconstruct polygon from point pattern density	reconstructShapeDensity
Reconstruct structure from spe object with given image id	reconstructShapeDensityImage
Reconstruct structure from spatial experiment object per image id	reconstructShapeDensitySPE
Intensity plot	shapeIntensityImage
Calculate a set of shape metrics of a single polygon	shapeMetrics
Simulate Tissue Blobs	simulateTissueBlobs
Example SpatialExperiment Object with Simulated Tissue Images and Point Patterns	sostaSPE
Function to convert spatialCoords to an sf object	spatialCoords2SF
Function to convert spatial coordinates of a 'SpatialExperiment' object to a 'ppp' object	SPE2ppp
Calculate curvature of sf object	stCalculateCurvature
Calculate curl of a polygon	stCalculateShapeCurl
Calculate the length of feature axes of a single sf polygon	stFeatureAxes
Calculate a set of shape metrics of a set of polygons	totalShapeMetrics
Function to extract x y coordinates from binary image	xyCoordinates