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SpatialData

for a demo of the class, see the vignette

for visualization capabilites, see SpatialData.plot

for data reading/writing and examples, see SpatialData.data

Introduction

SpatialData provides an interface to Python's SpatialData, and currently includes:

  • reticulate-based use of spatialdata-io for reading of manufacturer data and writing to .zarr
  • on-disk representation of images/labels as ZarrArrays (Rarr) and shapes/points as arrow objects
  • method drafts for visualization and coordinate system handling

In addition, scverse data examples have been made available through Bioconductor's NSF OSN bucket, are accessible from within R, and BiocFileCached; there's also an interface to aligning data into a common (identity) space.

Installation

BiocManager::install("HelenaLC/SpatialData")