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Question about size mismatch and alignment of segmentation volumes in NPM1_single_cell_drug_perturbations #93

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@wansiyuan12

Hi,

When processing the dataset “NPM1_single_cell_drug_perturbations”, I encountered the following issue:

For each cell,

  • crop_raw and crop_seg_nuc have the same shape (e.g. 22×136×145),
  • while crop_seg (struc_classical) has a larger shape (e.g. 83×145×154).

The struc_classical volume contains empty z-slices at the top and bottom.
In contrast, crop_raw and crop_seg_nuc do not have such empty slices.

Could you please clarify:

  1. Why struc_classical is provided in a different spatial resolution or size compared to crop_raw and crop_seg_nuc?

  2. What is the recommended way for users to align or transform struc_classical to the crop_raw space for downstream analysis?

Thank you for your help.

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