updated to Ilan's PR

theislab · Oct 4, 2024 · 0063f8c · 0063f8c
1 parent 2e8f230
commit 0063f8c
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Showing 2 changed files with 4 additions and 8 deletions.
diff --git a/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_make_vitessce.py b/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_make_vitessce.py
@@ -41,11 +41,9 @@
 
 wrapper = SpatialDataWrapper(
     spatialdata_url=artifact.path.to_url(),
-    image_path="images/Visium_Adult_Mouse_Brain_hires_image",
-    obs_feature_matrix_path = "tables/table/X",
-    feature_labels_path = "tables/table/var/gene_ids",
-    shapes_path = "shapes/Visium_Adult_Mouse_Brain",
-    coordination_values={"obsType": "spot"}
+    image_elem="images/Visium_Adult_Mouse_Brain_hires_image",
+    shapes_elem = "shapes/Visium_Adult_Mouse_Brain",
+    table_path = "tables/table",
 )
 
 dataset = vc.add_dataset(name='Visium demo').add_object(wrapper)

diff --git a/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_to_lamin.py b/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_to_lamin.py
@@ -11,9 +11,7 @@
 
 ln.settings.transform.stem_uid = "KgGzOw8PUYKO"
 ln.settings.transform.version = "3"
-
-ln.track()
-
+ln.track("KgGzOw8PUYKO7CpM")
 try:
     artifact = ln.Artifact.filter(ulabels__name=uid).one()
     artifact.delete(permanent=True)