angelolab / ark-analysis / 5273

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Pix preprocessing (#579)

* add channel normalization

* add pixel rowsum normalization

* add new arg to test functions

* Add testing for new pixel matrix preprocessing with channel and pixel normalization

* Add documentation for calculate_pixel_intensity_percentile

* Need to account for all-zero channels in calculate_channel_percentiles

* Missing argument in docstring of calculate_pixel_intensity_percentile

* Accidental uppercase 's' in 'TIFs' for test_calculate_channel_percentages

* First round of comments addressed

* Change addition test in test_create_fov_pixel_data to test row sums to 1

* Add test to check pixel_norm_val filtering works as intended

* add more testing

* switch to dataframe

* standardize with feather files, switch naming

* update tests

* make test less stringent

* change default name in notebook

* remove extra arg

Co-authored-by: alex-l-kong <alkong@ucdavis.edu>
Co-authored-by: alex-l-kong <31424707+alex-l-kong@users.noreply.github.com>

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