Hello teams,

Thank you for developing and maintaining this tool. I am working on the single-cell level xenium data and followed the tutorial 2 to extract transcripts for individual cells. However, I encountered a few issues when I tried to match the cell_id from transcripts and cellvit results.

• In some samples (e.g. NCBI783), the format of cell_id in transcripts is like b'aagigajm-1', while in the cellvit results, they are in [1,2,3....]. So it is impossible to match the cell type information from cellvit with transcripts.
• In other samples, although their cell_id are in the same format, but they do not seem to match. e.g. Assuming that I am working on a cell with cell_id=100, when I examined he_x,he_y from cell_id==100 transcripts that are overlaid with nucleus, I found they are actually from cell_id=9563 in the cellvit results.

In summary, are cell_ids in the transcripts and cellvit results representing the same cell?

Look forward to hearing from you.

Best,
Yumin