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)
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 |
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. |
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. |
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 v0.6.0 \
-main-script target/nextflow/convert/from_cells2stats_to_h5mu/main.nf \
-params-file params.yaml Relationships
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Uses
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