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)

Converts the output from NanoString experiment into a MuData objcet.

• <dataset_id>_exprMat_file.csv: File containing the counts.

• <dataset_id>_metadata_file: File containing the spatial coordinates and additional cell-level metadata.

• <dataset_id>_fov_file.csv: File containing the coordinates of all the fields of view.
  In addition to reading the regular Nanostring output, it loads CellComposite and CellLabels directories, if present,
  containing the images.

Creates a SpatialExperiment object from the downloaded unzipped CosMx directory for Nanostring
CosMx spatial gene expression data, and saves it as a SpatialExperiment object.
The constructor assumes the downloaded unzipped CosMx Folder has the following structure:

Mandatory files
· | — *_exprMat_file.csv
· | — *_metadata_file.csv
Optional files, by default added to the metadata() as a list of paths (will be converted to parquet):
· | —*_fov_positions_file.csv
· | — *_tx_file.csv
· | — *_polygons.csv

Converts a single modality of an h5mu file into a Seurat object with a Field of View (FOV)
built from centroid coordinates of spatially-resolved single cells.

Reads in an H5MU file and saves it as a SpatialData Zarr store.

Converts an h5mu file into a SpatialExperiment object.

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/.

Converts the output bundle from spaceranger into an h5mu file.

Reads in the Tables field stored in a SpatialData object and converts it to an h5mu file.

Converts the output from Xenium to a single .h5mu file, where the count matrix is written to the rna modality.
The following files are expected to be present in the Xenium output bundle:
├── cell_feature_matrix.h5
├── cells.parquet
├── experiment.xenium
└── metrics_summary.csv