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", ref = "devel")

Load package

library(SpatialExperimentIO)

Xenium ouptut folder structure

A standard Xenium output folder should contain these files for the function readXeniumSXE(). cells.parquet or cells.csv.gz, as well as either cell_feature_matrix.h5 or /cell_feature_matrix are required for just a count matrix at cell-level and its column data. Other transcript, cell/nucleus boundaries, and experiment.xenium .parquet files will have their paths added to metadata(). Genes that are served as control probes can be moved to altExp() by specifying their gene name patterns in the reader readXeniumSXE().

    Xenium_unzipped
        └── outs 
            ├── cells.parquet 
            ├── cell_feature_matrix.h5 
            └── cell_feature_matrix 
                ├── barcodes.tsv 
                ├── features.tsv 
                └── matrix.mtx
            ├── transcripts.parquet 
            ├── cell_boundaries.parquet     
            ├── nucleus_boundaries.parquet  
            └── experiment.xenium

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 for just a count matrix at cell-level and its column data. Additional data fov_positions_file.csv can be merged to colData(). Other transcript and polygon .csv files will be convert and write to .parquet files, and will have their parquet paths added to metadata(). Genes that are served as control probes can be moved to altExp() by specifying their gene name patterns in the reader readCosMxSXE().

    CosMx 
        ├── metadata_file.csv 
        ├── exprMat_file.csv
        ├── fov_positions_file.csv
        ├── tx_file.csv
        └── polygons.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 for just a count matrix at cell-level and its column data. Cell boundaries are multiple .h5 files that are yet to be processed by SpatialExperimentIO. Transcript.csv files are available and is yet to be added as path to parquet in SpatialExperimentIO.

    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 for just a count matrix at cell-level and its column data.

    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 for just a count matrix at cell-level and its column data.

    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):