angelolab / angelolab/ark-analysis

Nuclear signal not being size normalized when generating cell table

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描述

**Describe the bug**

Humza is running a cohort and will be using the nuclear signal for Pixie analysis. The nuclear signal is not normalized in `segmentation_utils.transform_expression_matrix`.

The process for size normalization at https://github.com/angelolab/ark-analysis/blob/main/src/ark/segmentation/segmentation_utils.py#L117-L133 only works for whole cell data, since the `"cell_size"` and `"label"` columns only contain the whole cell channel expression columns in between, not the corresponding nuclear channel expression columns. Additionally, normalization by whole cell size should only happen for whole cell signal; the function does not support nuclear signal normalization by nuclear area.

**Expected behavior**

If nuclear signal is run through Pixie, it should be at least size normalized, if not arcsinh normalized on top of that. `transform_expression_matrix` should account for this so `marker_quantification.create_marker_count_matrices` doesn't append raw nuclear signal as normalized.

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