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STOmics / Stereopy

A toolkit of spatial transcriptomic analysis.
MIT License
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kernel keep dying while reading stereoseq gef file #122

Closed raman91 closed 1 year ago

raman91 commented 1 year ago

Hi,

I am reading stereoseq gef file using the command :

data = st.io.read_gef(file_path=data_path, bin_type='cell_bins', is_sparse=True). But my jupyter notebook kernel keeps dying.

Do you know how i can solve this issue?

Thank you

junhouhui commented 1 year ago

Hi, could you check if the GEF file is for CellBin or SquareBin, and provide the name of the GEF file if possible? Also, may I ask how much memory is available in the running environment?

raman91 commented 1 year ago

The GEF file is for CellBin

junhouhui commented 1 year ago

Hello, may I ask if it is possible to directly read CellBin GEF files using the Python command line (without using Jupyter notebook) ?To see if there is any error message printed.