{ "cells": [ { "cell_type": "code", "execution_count": 1, "id": "02288901", "metadata": { "lines_to_next_cell": 2 }, "outputs": [], "source": [ "from skimage.io import imread\n", "import pyclesperanto_prototype as cle # version 0.22.0" ] }, { "cell_type": "markdown", "id": "948f789a", "metadata": {}, "source": [ "## Loading 'blobs'" ] }, { "cell_type": "code", "execution_count": 2, "id": "d88bf584", "metadata": { "lines_to_next_cell": 2 }, "outputs": [ { "data": { "text/plain": [ "array([[ 40, 32, 24, ..., 216, 200, 200],\n", " [ 56, 40, 24, ..., 232, 216, 216],\n", " [ 64, 48, 24, ..., 240, 232, 232],\n", " ...,\n", " [ 72, 80, 80, ..., 48, 48, 48],\n", " [ 80, 80, 80, ..., 48, 48, 48],\n", " [ 96, 88, 80, ..., 48, 48, 48]], dtype=uint8)" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "image0_b = imread(\"/projects/p_scads_trainings/BIAS/blobs.tif\")\n", "image0_b" ] }, { "cell_type": "markdown", "id": "853ced0a", "metadata": {}, "source": [ "## gaussian blur" ] }, { "cell_type": "code", "execution_count": 3, "id": "ce6be712", "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "
\n", "\n", "\n", "cle._ image
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shape(254, 256)
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" ], "text/plain": [ "cl.OCLArray([[ 41.428753, 34.696438, 27.733936, ..., 220.92714 , 211.21164 ,\n", " 206.71573 ],\n", " [ 47.421425, 38.878723, 30.323011, ..., 228.32323 , 220.60194 ,\n", " 216.83534 ],\n", " [ 48.121437, 40.610855, 33.357384, ..., 235.32935 , 229.7049 ,\n", " 226.88821 ],\n", " ...,\n", " [ 74.4386 , 76.32904 , 77.03725 , ..., 48.000324, 48.00075 ,\n", " 48.001007],\n", " [ 81.793655, 81.17787 , 79.80763 , ..., 48. , 48. ,\n", " 48. ],\n", " [ 88.816925, 85.382095, 81.478806, ..., 48. , 48. ,\n", " 48. ]], dtype=float32)" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "image1_gb = cle.gaussian_blur(image0_b, None, 1.0, 1.0, 0.0)\n", "image1_gb" ] }, { "cell_type": "markdown", "id": "7b675a36", "metadata": {}, "source": [ "## threshold otsu" ] }, { "cell_type": "code", "execution_count": 4, "id": "8f4bc144", "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "
\n", "\n", "\n", "cle._ image
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shape(254, 256)
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" ], "text/plain": [ "cl.OCLArray([[0, 0, 0, ..., 1, 1, 1],\n", " [0, 0, 0, ..., 1, 1, 1],\n", " [0, 0, 0, ..., 1, 1, 1],\n", " ...,\n", " [0, 0, 0, ..., 0, 0, 0],\n", " [0, 0, 0, ..., 0, 0, 0],\n", " [0, 0, 0, ..., 0, 0, 0]], dtype=uint8)" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "image2_to = cle.threshold_otsu(image1_gb)\n", "image2_to" ] }, { "cell_type": "markdown", "id": "f5f69e98", "metadata": {}, "source": [ "## connected components labeling box" ] }, { "cell_type": "code", "execution_count": 5, "id": "6af0436b", "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "
\n", "\n", "\n", "cle._ image
\n", "\n", "\n", "\n", "\n", "\n", "
shape(254, 256)
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" ], "text/plain": [ "cl.OCLArray([[ 0, 0, 0, ..., 59, 59, 59],\n", " [ 0, 0, 0, ..., 59, 59, 59],\n", " [ 0, 0, 0, ..., 59, 59, 59],\n", " ...,\n", " [ 0, 0, 0, ..., 0, 0, 0],\n", " [ 0, 0, 0, ..., 0, 0, 0],\n", " [ 0, 0, 0, ..., 0, 0, 0]], dtype=uint32)" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "image3_cclb = cle.connected_components_labeling_box(image2_to)\n", "image3_cclb" ] } ], "metadata": { "jupytext": { "cell_metadata_filter": "-all", "main_language": "python", "notebook_metadata_filter": "-all" }, "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.17" } }, "nbformat": 4, "nbformat_minor": 5 }