{ "cells": [ { "cell_type": "markdown", "metadata": { "pycharm": { "name": "#%% md\n" } }, "source": [ "# Visualizations" ] }, { "cell_type": "markdown", "metadata": { "pycharm": { "name": "#%% md\n" } }, "source": [ "Polarityjam optionally plots some of the features mentioned above for all cells. All plots are optionally.\n", "If the plots are not needed we recommend to disable plotting in the paramters file to speed up calculation time.\n", "The following visualizations can be generated:\n", "\n", "- cellpose segmentation\n", "- length to width ratio\n", "- elongation\n", "- organelle polarity\n", "- cue intensity ratios\n", "- cue direction asymmetry\n", "- marker expression\n", "- marker polarity\n", "- marker nucleus orientation\n", "- nucleus displacement orientation\n", "- junction features\n", "- junction polarity\n", "- cell corners\n", "- feature of interest\n" ] }, { "cell_type": "markdown", "metadata": { "pycharm": { "name": "#%% md\n" } }, "source": [ "