Introduction

The SpatialExperimentIO package provides a set of functions to import Xenium (10x Genomics), CosMx (Nanostring), MERSCOPE (Vizgen), STARmapPLUS (Wang et al., 2023, Broad Institute), and seqFISH (Spatial Genomics) data into a SpatialExperiment or SingleCellExperimentclass object.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SpatialExperimentIO")

Development version

You can also install the development version of SpatialExperimentIO from GitHub with:

# install.packages("devtools")
devtools::install_github("estellad/SpatialExperimentIO")

Load package

library(SpatialExperimentIO)

Xenium ouptut folder structure

A standard Xenium output folder should contain these files for the function readXeniumSXE(). cells.csv.gz and either cell_feature_matrix.h5 or /cell_feature_matrix are required.

    Xenium_unzipped
        └── outs 
            ├── cells.csv.gz 
            ├── cell_feature_matrix.h5 
            └── cell_feature_matrix 
                ├── barcodes.tsv 
                ├── features.tsv 
                └── matrix.mtx
    

CosMx output folder structure

A standard CosMx output folder should contain these files for the function readCosMxSXE(). Both metadata_file.csv and exprMat_file.csv are required.

    CosMx 
        ├── metadata_file.csv 
        └── exprMat_file.csv

MERSCOPE output folder structure

A standard MERSCOPE output folder should contain these files for the function readMerscopeSXE(). Both cell_metadata.csv and cell_by_gene.csv are required.

    MERSCOPE 
        ├── cell_metadata.csv 
        └── cell_by_gene.csv

STARmap PLUS output folder structure

A standard STARmap PLUS output folder should contain these files for the function readStarmapplusSXE(). Both spatial.csv and raw_expression_pd.csv are required.

    STARmap_PLUS 
        ├── spatial.csv 
        └── raw_expression_pd.csv

seqFISH output folder structure

A standard seqFISH output folder should contain these files for the function readSeqfishSXE(). Both CellCoordinates.csv and CellxGene.csv are required.

    seqFISH 
        ├── CellCoordinates.csv 
        └── CellxGene.csv

Usage

Taking Xenium as an example, providing a path to the folder that stores all the required files (i.e. /outs ) would return a SpatialExperiment object.

spe <- readXeniumSXE(dir)
spe
# class: SpatialExperiment 
# dim: 4 6 
# metadata(0):
# assays(1): counts
# rownames(4): AATK ABL1 ACKR3 ACKR4
# rowData names(3): ID Symbol Type
# colnames(6): 1 2 ... 5 6
# colData names(9): X cell_id ... nucleus_area sample_id
# reducedDimNames(0):
# mainExpName: NULL
# altExpNames(0):
# spatialCoords names(2) : x_centroid y_centroid
# imgData names(0):