convert/from_spaceranger_hd_to_spatialdata

spaceranger

visium_hd

segmentation

spatialdata

Description

Converts the output from 10X Genomics Space Ranger for Visium HD into a
SpatialData object.

By default it reads the segmented cells (per-cell count matrix and cell
boundary polygons) that Space Ranger 4.x writes to segmented_outputs/. Set
--mode bins to instead read a binned output (binned_outputs/square_<N>um/)
at the bin size given by --bin_size. In both cases the loaded table is
renamed to "table" so that downstream components stay technology-agnostic.

Type

python_script

Keywords

spaceranger

visium_hd

segmentation

spatialdata

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.zarr"  
mode: [ "segmented_cells" ]  
bin_size: [ 8 ]  
output_type: [ "filtered" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \  
  -revision v0.6.0 \  
  -main-script target/nextflow/convert/from_spaceranger_hd_to_spatialdata/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input folder containing the output from a Space Ranger run for Visium HD and a `*_feature_slice.h5` file. Must contain a `segmented_outputs/` directory for `--mode segmented_cells`, or `binned_outputs/` for `--mode bins`.
--output -o	file required output	Zarr directory where the SpatialData object will be stored.
--mode	string	Which output to load into the table: `segmented_cells` (per-cell counts and cell boundary polygons from `segmented_outputs/`) or `bins` (binned counts from `binned_outputs/square_<bin_size>um/`).
--bin_size	integer	Bin size in microns to load when `--mode bins`. Visium HD captures data at 2 µm and aggregates it into 8 µm and 16 µm square bins.
--output_type	string	Which count matrix to load: `filtered` (barcodes under tissue only) or `raw` (all barcodes). Applies to both the segmented-cell and binned matrices.
--output_layer	string	If provided, the count matrix is also stored as a named layer (`table.layers[output_layer]`) in addition to `.X`.
--dataset_id	string	Identifier used to name the spatial elements (shapes and images) in the SpatialData object. If not provided, it is inferred from the `*_feature_slice.h5` file name in the input directory.

Name

Type & Properties

--input

-i

file

required

--output

-o

file

required

output

--mode

string

--bin_size

integer

--output_type

string

--output_layer

string

--dataset_id

string