Open lg907 opened 4 days ago
Hi, to fix please replace .pp.get_elements()
with .subset()
, and please ensure you pass a list to subset()
.
So your code becomes:
(
visium_sdata.subset(["ST8059050"])
.pl.render_images(elements="ST8059050_hires_image")
.pl.render_shapes(elements="ST8059050", color="mt-Co3")
.pl.show()
)
.pp.get_elements()
and automatically calls .subset()
, saying that the .pp.get_elements()
is now deprecated and will be removed in one next release? Thanks.
Hello, I am attempting to follow the 10x Visium example notebook (https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/technology_visium.html#technology-focus-10x-genomics-visium) and are encountering issues when attempting to colour the visium spots by gene expression.
Running:
Gives the following output:
All previous code worked and gave outputs consistent with the example notebook.
I am using spatialdata 0.2.3 with python 3.11.10 on MacOS.