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ValueError in stlearn.Read10X step #313

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TLC199676 opened this issue Oct 8, 2024 · 0 comments
Open

ValueError in stlearn.Read10X step #313

TLC199676 opened this issue Oct 8, 2024 · 0 comments

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@TLC199676
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Dear developers,

I encountered the problems when I tried to load the SpaceRanger resutls in python. My data was obtained from FFPE samples processed by SpaceRanger 3.1.0.
I ran the code as below and got the error:
import stlearn as st import scanpy as sc sample_233_st = st.Read10X(path="H:/spatial/spaceranger/B115-18-233/outs", count_file="filtered_feature_bc_matrix.h5", library_id="233", load_images=True, quality="hires", image_path="H:/spatial/spaceranger/B115-18-233/outs/spatial/tissue_hires_image.png")
1728307109634

Besides, I also used scanpy.read_visium to successfully load it
sample_233 = sc.read_visium(path=data_dir, count_file="filtered_feature_bc_matrix.h5", library_id="sample_233",load_images=True,source_image_path=data_dir+"/spatial")
Then I tried to lauch the interactive interface by stlearn.pl.gene_plot_interactive
st.pl.gene_plot_interactive(sample_233)
It also reported an error:
1728375618190

I am so appreciate for any advice
Thanks a lot
Tan Licheng

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