Add nuclear filtering functionality to pixel clustering pipeline #653
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ngreenwald
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Aug 16, 2022
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Rather than having this as None, we should tell the user to skip the cell if they don't want to run it
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ngreenwald
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Aug 16, 2022
…eck for valid seg_dir if provided
ngreenwald
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Co-authored-by: Noah F. Greenwald <noahfgreenwald@gmail.com>
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* 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>
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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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What is the purpose of this PR?
Closes #619. Prior to pixel clustering, users may need to filter out non-nuclear marker signal from the nucleus and vice-versa for nuclear marker signal.
How did you implement your changes
Add a function
filter_with_nuclear_masktosom_utilswhich runs this process. The code in #619 provides most of the functionality, however we'll need to make two modifications:seg_dir is not Noneprior to running. Users may run pixel clustering without segmentation labels, however they will not be able to run this function if that's the case because it relies on the_feature_1.tifffiles.channeldefaults toNonein the notebook and function. This is the easiest guard against errors caused by running all the cells at once in the notebook.The cell that calls this function in
example_pixel_clusteringwill be placed after the smoothing process.This PR also solidifies some of the notebook testing, as it was not using the renamed channels after smoothing. This should also apply for the nuclear filtering tests too.