convert/from_cells2stats_to_h5mu

Description

Convert spatial data resulting from Aviti Teton sequencers that have been processed by the Element Biosciences cells2stats workflow to H5MU format.

This component processes cells2stats count matrices to create a standardized H5MU file for downstream analysis.

The component reads:

Parquet file containing the count matrix and metadata
Panel.json with target and batch information

And outputs an H5MU file with:

Count data as the main .X matrix
Spatial coordinates in obsm
Cell Paint intensities in obsm (optional)
Nuclear count data as a layer (optional)
CellProfiler morphology metrics in obsm (optional)
Unassigned targets in obsm (optional)

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.h5mu"  
modality: [ "rna" ]  
obsm_coordinates: [ "spatial" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \  
  -revision v0.1.0 \  
  -main-script target/nextflow/convert/from_cells2stats_to_h5mu/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	Path to the cells2stats output bundle. Expected folder structure (showing required files only): ├── Cytoprofiling/ │ └── Instrument/ │ └── RawCellStats.parquet └── Panel.json

Name

Type & Properties

--input

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output H5MU file path.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--output

file

required

output

--output_compression

string

Options

Name	Type & Properties	Description
--modality	string	The modality to which the processed data will be written to in the H5MU file.
--obsm_coordinates	string	Key name to store the spatial coordinates (in pixels) in obsm. If present, spatial coordinates in micrometers will be stored under {obsm_coordinates}_um. The column names will be stored in uns.
--layer_nuclear_counts	string	Name for nuclear counts layer. If specified, nuclear count data will be stored as a separate layer in the AnnData object.
--obsm_cell_paint	string	Key name for storing Cell Paint target intensities in obsm. If provided, Cell Paint target intensity data will be stored as a separate matrix in the obsm field. The column names will be stored in uns.
--obsm_cell_paint_nuclear	string	Key name for storing Nuclear Cell Paint target intensities in obsm. If provided, Nuclear Cell Paint target intensity data will be stored as a separate matrix in the obsm field. The column names will be stored in uns.
--obsm_cell_profiler	string	Key name for storing CellProfiler morphology metrics in obsm. If provided, CellProfiler morphology metrics will be stored as a separate matrix in the obsm field. The column names will be stored in uns.
--obsm_unassigned_targets	string	Key name for storing any unassigned target data in obsm. If provided, unassigned target data will be stored as a separate matrix in the obsm field. The column names will be stored in uns.

Name

Type & Properties

--modality

string

--obsm_coordinates

string

--layer_nuclear_counts

string

--obsm_cell_paint

string

--obsm_cell_paint_nuclear

string

--obsm_cell_profiler

string

--obsm_unassigned_targets

string