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When tissue_positions.csv rather than tissue_positions_list.csv is in the spatial directory for a Visium dataset, the resulting AnnData object has:
tissue_positions.csv
tissue_positions_list.csv
It looks like this the issue could be that it should be header=0 rather than header=1 in this line:
header=0
header=1
squidpy/src/squidpy/read/_read.py
Line 87 in 945e127
squidpy 1.2.3 and later
The text was updated successfully, but these errors were encountered:
michalk8
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Description
When
tissue_positions.csv
rather thantissue_positions_list.csv
is in the spatial directory for a Visium dataset, the resulting AnnData object has:Minimal reproducible example
Traceback
It looks like this the issue could be that it should be
header=0
rather thanheader=1
in this line:squidpy/src/squidpy/read/_read.py
Line 87 in 945e127
Version
squidpy 1.2.3 and later
The text was updated successfully, but these errors were encountered: