From 0063f8c5510b4f4856d464fb20957b163807ef4e Mon Sep 17 00:00:00 2001 From: Tim Treis Date: Fri, 4 Oct 2024 18:47:41 +0200 Subject: [PATCH] updated to Ilan's PR --- .../10ktp_make_vitessce.py | 8 +++----- .../10ktp_to_lamin.py | 4 +--- 2 files changed, 4 insertions(+), 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 index af15430..7f21b41 100644 --- 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 index eb4a079..ec141ce 100644 --- 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)