Workflow cheat sheet

Workflow cheat sheet#

I want to…	Use	Result
Open a slide	`zs.open_wsi(...)`	`WSIData`
Use sample data	`zs.datasets.sample(...)`	`WSIData`
Find tissue with image processing	`zs.pp.find_tissues(...)`	tissue shapes
Find tissue with a model	`zs.seg.tissue(...)`	tissue shapes
Create tiles	`zs.pp.tile_tissues(...)`	tile shapes and specification
Compute tissue properties	`zs.tl.tissue_props(...)`	columns on tissue shapes
Build tile neighbors	`zs.pp.tile_graph(...)`	spatial graph metadata
Segment cells	`zs.seg.cells(...)`	cell shapes, optionally features
Run semantic segmentation	`zs.seg.semantic(...)`	class shapes
Extract tile embeddings	`zs.tl.feature_extraction(...)`	feature table
Predict from tile images	`zs.tl.tile_prediction(...)`	columns on tile shapes
Predict from embeddings	`zs.tl.feature_prediction(...)`	prediction table
Aggregate features	`zs.tl.feature_aggregation(...)`	data inside feature table
Identify spatial domains	`zs.tl.spatial_domain(...)`	columns on tile shapes
Visualize tissue	`zs.pl.tissue(...)`	plot
Visualize tile values	`zs.pl.tiles(...)`	plot
Visualize spatial shapes	`zs.pl.annotations(...)`	plot
Import annotations	`zs.io.load_annotations(...)`	annotation shapes
Export annotations	`zs.io.export_annotations(...)`	GeoDataFrame or GeoJSON
Score segmentation	`zs.metrics.segmentation`	metric values

Use the API reference for complete signatures and the How-To guides for decisions and failure modes.