spatial-experiment
data type. Expand to view the properties of spatial-experiment
datasets:
Properties
image
, darkimage
, colorizedimage
, or cytaimage
.Used as an input to Spaceranger Count as --<image_type> <image>
.See the Spaceranger Count documentation for more information.slide
input to Spaceranger Count. See the Spaceranger Count documentation for more information.loupe-alignment
input to Spaceranger Count. See the Spaceranger Count documentation for more information.area
input to Spaceranger Count. See the Spaceranger Count documentation for more information.Sudmeier, et al. (2022) “Distinct phenotypic states and spatial distribution of CD8+ T cell clonotypes in human brain metastases.” Cell Reports Medicine, 3(5), 100620
GRCH38-2020-A
) and mouse (mm10-2020-A
) genomes. We packaged them into the spatial-reference
datasets.
Depending on your experimental workflow, you may also need a spatial probe file for data processing. 10x also has probesets available for human and mouse, which we have packaged into the spatial-probes
datasets.
spaceranger-count
pipeline takes as input a dataset of the spatial-experiment
type and a dataset of the spatial-reference
type. The spatial-experiment
dataset contains most of the Spaceranger Count required inputs as properties. The reference transcriptome is stored in the spatial-reference
dataset. When you run this pipeline on Mantle, all the hardware provisioning is taken care of for you.
spaceranger-count
pipeline outputs all the files generated by Spaceranger Count, and a spaceranger-outputs
dataset. The spaceranger-outputs
data type has
path_to_output_dir
as a property, which contains the path to the directory containing the Spaceranger Count outputs.
The output dataset is used as an input to a downstream analysis notebook, and serves to link the Spaceranger Count outputs to the input datasets.
pt15_spatial_gene_expression
notebook, which ran in the spatial-transcriptomics-analysis
analysis environment.