Outputs and key naming

Outputs and key naming#

Most LazySlide operations add results to wsi. Defaults can be changed with key_added.

Operation	Default result	Location
`pp.find_tissues`	`tissues`	`wsi.shapes`
`pp.tile_tissues`	`tiles`	`wsi.shapes`
`seg.tissue`	`tissues`	`wsi.shapes`
`seg.cells`	`cells`	`wsi.shapes`
`seg.cells(..., extract_features=True)`	`cells_features`	`wsi.tables`
`seg.semantic`	`anatomical_structures`	`wsi.shapes`
`io.load_annotations`	`annotations`	`wsi.shapes`
`tl.feature_extraction`	`{model}_{tile_key}`	`wsi.tables`
`tl.feature_aggregation`	`agg_slide` or `agg_{by}`	inside feature `AnnData`

print(list(wsi.shapes))
print(list(wsi.tables))
print(list(wsi.images))
print(list(wsi.attrs))

Many APIs accept a short feature key and add the tile suffix automatically:

zs.tl.feature_extraction(wsi, "uni")
zs.pl.tiles(wsi, feature_key="uni", color="0")

The stored table is normally uni_tiles. With a custom tile set, it becomes uni_{tile_key}.

Encode the meaningful variant, not every parameter:

tissue_key = "tissues_entropy"
tile_key = "tiles_20x"
feature_name = "uni_experiment_a"

Keep the complete parameter set in a machine-readable run configuration. Keys should remain short enough to pass between functions without mistakes.