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* change notebook names * Update README.md * Text changes for clustering description * testbook fix * Readme adjustements, waiting for Pixie preprint * Add PIxie preprint * added pixie to citation section * added years to citation links * overview fix * bolding fix * Add nuclear filtering functionality to pixel clustering pipeline (#653) * Add nuclear mask filtering to som_utils * Add nuclear filtering method to pixel clustering notebook * Print informative message instead of error if seg_dir is None, and check for valid seg_dir if provided * Remove extra print statement * Update ark/phenotyping/som_utils.py Co-authored-by: Noah F. Greenwald <noahfgreenwald@gmail.com> Co-authored-by: Noah F. Greenwald <noahfgreenwald@gmail.com> * Ensure channel norm and pixel norm files get re-computed if a new set of channels are provided (#654) * Initial commit of normalization updates * Remove capsys call * Provide more robust support by resetting entire pixel_output_dir if new set of channels provided * readme updates * readme updates * improved pairwise spatial enrichment analysis notebook name * fixed mantis-link in readme Co-authored-by: Candace Liu <candace.liu94@gmail.com> Co-authored-by: Sricharan Reddy Varra <srivarra@stanford.edu> Co-authored-by: alex-l-kong <31424707+alex-l-kong@users.noreply.github.com>
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