splitting.yaml Reference

This configuration file corresponds to spatialsnake useful_tool --option=splitting and is used to split objects by sample, label, or spatial range.

Parameter	Default	Description
`output_zarr_path`	`results`	Root directory for exported `zarr` objects
`split_by`	`sample`	Splitting mode, such as `sample`, `group`, `clusters`, `celltype`, `ROI`, or `image`
`output_dir`	`results/useful_results`	Output directory
`shape_elements`	`None`	Shape element used when splitting by image
`max_x` / `min_x` / `max_y` / `min_y`	`0`	Coordinate boundaries used for image-based splitting
`barcodes`	`None`	Labels to retain, separated by commas
`roi_csv`	`""`	Path to an ROI table or ROI directory

Tuning suggestions

For label-based splitting, start with split_by together with barcodes.
For local tissue cropping, use split_by=image and define the coordinate boundaries at the same time.
If you perform multiple rounds of splitting, keep output_dir fixed to simplify output management.