Refactor format module #27
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gwaybio
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Mar 2, 2023
roshankern
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Mar 9, 2023
* refactor locate data module (#25) * Idr stream module refactor (#26) * Co-authored-by: Jenna Tomkinson <jenna.tomkinson@ucdenver.edu> * add files for CP run * remove run cellpose plugin * refactor idrstreams * create python merge files * remove unecessary create folder line * docs * change conda environments with bash file * black formatting * Refactor format module (#27) * rerun module * rerun script * rerun notebook * greg suggestion * Refactor normalize module (#29) * rerun format module * refactor raw data umaps * update utils * run umaps notebook * reconvert jupyter notebook * normalize training data * rerun pipeline * jenna suggestions * Refactor umaps module (#30) * rerun notebook * docs, convert notebook * Update 4.analyze_data/README.md Co-authored-by: Erik Serrano <31600622+axiomcura@users.noreply.github.com> * documentation --------- Co-authored-by: Erik Serrano <31600622+axiomcura@users.noreply.github.com> * remove unecessary line from gitignore * fix typo * move constants outside of for loop --------- Co-authored-by: Erik Serrano <31600622+axiomcura@users.noreply.github.com>
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This PR is ready for review!
In this small PR, the format module is rerun, with the path to the training features changed and the accessor for the outlines changed (a
DPprefix is added to theObject_Outlinescolumn as this data came from the DP IDR_stream).