convert/from_xenium_to_spatialdata

Description

Converts the output from 10X Genomics Xenium dataset into a SpatialData objcet.
By default, the following files will be converted:

experiment.xenium: File containing specifications.
nucleus_boundaries.parquet: Polygons of nucleus boundaries.
cell_boundaries.parquet: Polygons of cell boundaries.
transcripts.parquet: File containing transcripts.
cell_feature_matrix.h5: File containing cell feature matrix.
cells.parquet: File containing cell metadata.
morphology_mip.ome.tif: File containing morphology mip.
morphology_focus.ome.tif: File containing morphology focus.

Type

python_script

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.zarr"  
cells_boundaries: [ true ]  
nucleus_boundaries: [ true ]  
cells_labels: [ true ]  
transcripts: [ true ]  
nucleus_labels: [ true ]  
morphology_mip: [ true ]  
morphology_focus: [ true ]  
aligned_images: [ true ]  
cells_table: [ true ]  
n_jobs: [ 1 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/convert/from_xenium_to_spatialdata/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input folder. Must contain the output from a xenium run.
--output -o	file output	Zarr directory where the SpatialData object will be stored
--cells_boundaries	boolean	Whether to read cell boundaries (polygons).
--nucleus_boundaries	boolean	Whether to read nucleus boundaries (polygons).
--cells_as_circles	boolean_true	Whether to read cells also as circles (the center and the radius of each circle is computed from the corresponding labels cell).
--cells_labels	boolean	Whether to read cell labels (raster). The polygonal version of the cell labels are simplified for visualization purposes, and using the raster version is recommended for analysis.
--transcripts	boolean	Whether to read transcripts.
--nucleus_labels	boolean	Whether to read nucleus labels (raster). The polygonal version of the nucleus labels are simplified for visualization purposes, and using the raster version is recommended for analysis.
--morphology_mip	boolean	Whether to read the morphology mip image (available in versions < 2.0.0).
--morphology_focus	boolean	Whether to read the morphology focus image.
--aligned_images	boolean	Whether to also parse, when available, additional H&E or IF aligned images. For more control over the aligned images being read, in particular, to specify the axes of the aligned images, please set this parameter to False and use the xenium_aligned_image function directly.
--cells_table	boolean	Whether to read the cell annotations in the AnnData table.
--n_jobs	integer

Name

Type & Properties

--input

-i

file

required

--output

-o

file

output

--cells_boundaries

boolean

--nucleus_boundaries

boolean

--cells_as_circles

boolean_true

--cells_labels

boolean

--transcripts

boolean

--nucleus_labels

boolean

--morphology_mip

boolean

--morphology_focus

boolean

--aligned_images

boolean

--cells_table

boolean

--n_jobs

integer