Merge pull request #332 from quentinblampey/merscope_use_z

LucaMarconato · web-flow · commit c6d659e4e0a8 · 2025-10-22T15:48:34.000+02:00
Use `global_z` in the merscope coordinates
diff --git a/src/spatialdata_io/readers/merscope.py b/src/spatialdata_io/readers/merscope.py
@@ -302,7 +302,7 @@ def _get_points(transcript_path: Path, transformations: dict[str, BaseTransforma
     transcript_df = dd.read_csv(transcript_path)
     transcripts = PointsModel.parse(
         transcript_df,
-        coordinates={"x": MerscopeKeys.GLOBAL_X, "y": MerscopeKeys.GLOBAL_Y},
+        coordinates={"x": MerscopeKeys.GLOBAL_X, "y": MerscopeKeys.GLOBAL_Y, "z": MerscopeKeys.GLOBAL_Z},
         transformations=transformations,
         feature_key=MerscopeKeys.GENE_KEY,
     )

Original file line number	Diff line number	Diff line change
`@@ -302,7 +302,7 @@ def _get_points(transcript_path: Path, transformations: dict[str, BaseTransforma`
`302`	`302`	`transcript_df = dd.read_csv(transcript_path)`
`303`	`303`	`transcripts = PointsModel.parse(`
`304`	`304`	`transcript_df,`
`305`		`- coordinates={"x": MerscopeKeys.GLOBAL_X, "y": MerscopeKeys.GLOBAL_Y},`
	`305`	`+ coordinates={"x": MerscopeKeys.GLOBAL_X, "y": MerscopeKeys.GLOBAL_Y, "z": MerscopeKeys.GLOBAL_Z},`
`306`	`306`	`transformations=transformations,`
`307`	`307`	`feature_key=MerscopeKeys.GENE_KEY,`
`308`	`308`	`)`