transform.yaml Reference

This configuration file corresponds to spatialsnake useful_tool --option=transform and is used for conversion among zarr, h5ad, and Seurat-compatible formats.

Parameter	Default	Description
`output_dir`	`results/useful_results`	Output directory for converted files
`save_image`	`True`	Whether to export image data when converting from `zarr` to `h5ad`
`transform_from`	`h5ad`	Input format
`transform_to`	`h5ad`	Output format, such as `h5ad`, `zarr`, or `seurat`

Tuning suggestions

For cross-ecosystem interoperability, keeping save_image=True is usually helpful for reproducible spatial visualization.
Reserve sufficient disk space before converting large objects.
For data sharing, exporting h5ad or seurat is often the most convenient choice for downstream collaborators.