AllenCell / AllenCell/benchmarking_representations

Question about size mismatch and alignment of segmentation volumes in NPM1_single_cell_drug_perturbations

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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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