Errors in final cells of Xenium H&E Alignment tutorial: NameError for `tpointsI` and AttributeError for `.to_csv()

[albert239825]

Title: Errors in final cells: NameError for tpointsI and AttributeError for .to_csv()

Description
In the last two cells of the tutorial, there are two errors:

1. NameError: name 'tpointsI' is not defined
   • The code uses tpointsI.numpy() in np.hstack((df, tpointsI.numpy())), but tpointsI is never defined. It looks like the intended variable might be tpointsJ instead, or another point transformation variable.
2. AttributeError: 'numpy.ndarray' object has no attribute 'to_csv'
   • After using np.hstack, the result is a NumPy array, which doesn’t have a .to_csv() method. Converting to a pandas DataFrame before calling .to_csv() would fix this.

These issues occur in docs/notebooks/xenium-heimage-alignment.ipynb.

Proposed Fixes

1. Replace tpointsI with the correct variable (likely tpointsJ).
2. Instead of using np.hstack, add the aligned coordinates directly to the original DataFrame and then export it. For example:

   # Create a copy of the original DataFrame
   df_results = df.copy()
   
   # Add aligned coordinates to the DataFrame
   df_results['aligned_y'] = tpointsJ[:, 0].detach().numpy()
   df_results['aligned_x'] = tpointsJ[:, 1].detach().numpy()
   
   # Save the new DataFrame as a compressed CSV
   df_results.to_csv(
       '../xenium_data/Xenium_Breast_Cancer_Rep1_STalign_to_HE.csv.gz',
       compression='gzip',
       index=False
   )