Space Ranger1.0, printed on 03/24/2023
Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image. Space Ranger includes two pipelines relevant to spatial gene expression experiments:
spaceranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Visium-prepared sequencing runs and to convert barcode and read data to FASTQ files.
spaceranger count takes a bright
field slide image and FASTQ files from
spaceranger mkfastq and performs alignment, tissue detection, fiducial
detection, and barcode/UMI counting. The pipeline uses the
Visium spatial barcodes to generate feature-spot
matrices, determine clusters, and perform gene expression analysis.
These pipelines combine Visium-specific algorithms with the widely used RNA-seq aligner STAR. Output is delivered in standard BAM, MEX, CSV, HDF5, TIFF, PNG, JPEG and HTML formats that are augmented with spatial information.
Space Ranger combines algorithms for processing Visium slide images with the robust gene expression analysis used in Cell Ranger.
spaceranger count pipline performs the following
automated image processing tasks:
These image processing tasks are described further in the Image Processing section.
The automated alignment and tissue identification processes require
images taken with proper tissue placement and image exposure. Samples
where these conditions cannot be met can still be processed by
using Loupe Browser to manually align the spot pattern and
identify tissue in the slide image. When this "manual workflow" is
spaceranger count pipeline
will still take the full resolution image as input in order to
prepare data for visualzation within Loupe Browser. Note that both
Loupe and Space Ranger must be given the same image for a given