SpatialData.data package provides utilities for accessing example SpatialData datasets. Data from a variety of spatial omics technologies (Visium, Visium HD, Xenium, MERFISH etc.) has been made available as SpatialData (zipped) .zarr stores.

These scverse SpatialData examples are available through the following S3 buckets:

sandbox: (Default) scverse’s spatialdata-sandbox (https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html)
biocOSN: Bioc’s NSF OSN bucket,

Installation

if(!requireNamespace("BiocManager"))
  install.packages("BiocManager")
BiocManager::install("spatialdataR")
BiocManager::install("SpatialData.data")

library(spatialdataR)
#> Warning: package 'spatialdataR' was built under R version 4.6.1
#> 
#> Attaching package: 'spatialdataR'
#> The following object is masked from 'package:stats':
#> 
#>     filter
library(SpatialData.data)

To interrogate either of two S3 buckets you will need paws.storage installed.

if(!requireNamespace("paws.storage"))
  install.packages("paws.storage")
library(paws.storage)
Sys.setenv(AWS_REGION = "us-east-1")

Load SpatialData (.zarr) from Archives

Any spatialdata dataset can be retrieved (once) into some location, and read into R.

(x <- SD.data_load("ColorectalCarcinomaMIBITOF"))
#> checking Bioconductor OSN bucket...
#> class: SpatialData
#> - images(3):
#>   - point16_image (3,1024,1024)
#>   - point23_image (3,1024,1024)
#>   - point8_image (3,1024,1024)
#> - labels(3):
#>   - point16_labels (1024,1024)
#>   - point23_labels (1024,1024)
#>   - point8_labels (1024,1024)
#> - points(0):
#> - shapes(0):
#> - tables(1):
#>   - table (36,3309) [point8_labels,point16_labels,point23_labels]
#> coordinate systems(3):
#> - point16(2): point16_image point16_labels
#> - point23(2): point23_image point23_labels
#> - point8(2): point8_image point8_labels

You can view a list of available datasets using:

SD.data_list()
#>  [1] "MouseIntestineVisHD"        "MouseBrainVisHD"           
#>  [3] "MouseBrainVis"              "LungAdenocarcinomaMCMICRO" 
#>  [5] "MouseBrainMERFISH"          "MouseLiverMERFISH"         
#>  [7] "ColorectalCarcinomaMIBITOF" "MulticancerSteinbock"      
#>  [9] "JanesickBreastVisiumEnh"    "JanesickBreastXeniumRep1"  
#> [11] "JanesickBreastXeniumRep2"   "HumanLungMulti_10x"        
#> [13] "SpaceMHelaniH3T3"

Introduction

Installation

Load SpatialData (.zarr) from Archives