{ "cells": [ { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# Create UMAP of single cell features" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "3 png img file paths loaded: \n", "3 tif img file paths loaded: \n" ] } ], "source": [ "from livecellx.sample_data import tutorial_three_image\n", "\n", "dic_dataset, mask_dataset = tutorial_three_image(dic_dataset_path=\"../datasets/test_data_STAV-A549/DIC_data\", mask_dataset_path=\"../datasets/test_data_STAV-A549/mask_data\")" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "100%|██████████| 3/3 [00:07<00:00, 2.43s/it]\n" ] } ], "source": [ "from livecellx.core.io_sc import prep_scs_from_mask_dataset\n", "scs = prep_scs_from_mask_dataset(mask_dataset, dic_dataset)" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "from livecellx.trajectory.feature_extractors import compute_haralick_features, compute_skimage_regionprops\n", "from livecellx.preprocess.utils import normalize_img_to_uint8\n", "for sc in scs:\n", " features = compute_skimage_regionprops(sc, preprocess_img_func=normalize_img_to_uint8, sc_level_normalize=True)" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "skimage_area 22262.000000\n", "skimage_area_bbox 39672.000000\n", "skimage_area_convex 23414.000000\n", "skimage_area_filled 22262.000000\n", "skimage_axis_major_length 263.397536\n", " ... \n", "skimage_orientation -1.053940\n", "skimage_perimeter 660.825469\n", "skimage_perimeter_crofton 629.183347\n", "skimage_solidity 0.950799\n", "t 2.000000\n", "Length: 144, dtype: float64" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "sc.get_feature_pd_series()" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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2 rows × 143 columns
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