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| a | b/talk/.ipynb_checkpoints/DiseaseGroup-checkpoint.ipynb | ||
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| 1 | { |
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| 2 | "metadata": { |
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| 3 | "celltoolbar": "Slideshow", |
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| 4 | "name": "", |
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| 5 | "signature": "sha256:5dfa5098b5370799316e25d5c2a66062a5f6b75c6502b8192cbf3896a72c9b71" |
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| 6 | }, |
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| 7 | "nbformat": 3, |
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| 8 | "nbformat_minor": 0, |
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| 9 | "worksheets": [ |
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| 10 | { |
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| 11 | "cells": [ |
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| 12 | { |
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| 13 | "cell_type": "code", |
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| 14 | "collapsed": false, |
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| 15 | "input": [ |
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| 16 | "import numpy as np\n", |
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| 17 | "import pandas as pd\n", |
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| 18 | "import matplotlib.pyplot as plt\n", |
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| 19 | "import seaborn\n", |
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| 20 | "from matplotlib import rcParams\n", |
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| 21 | "rcParams[\"figure.figsize\"] = (14, 8)\n", |
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| 22 | "rcParams[\"xtick.labelsize\"] = 12\n", |
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| 23 | "rcParams[\"ytick.labelsize\"] = 12\n", |
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| 24 | "rcParams[\"font.size\"] = 14\n", |
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| 25 | "rcParams[\"axes.titlesize\"] = 16\n", |
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| 26 | "#rcParams[\"text.usetex\"] = False\n", |
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| 27 | "rcParams[\"font.family\"] = \"Serif\"\n", |
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| 28 | "rcParams[\"figure.dpi\"] = 600\n", |
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| 29 | "\n", |
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| 30 | "\n", |
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| 31 | "a = pd.read_csv(\"../data/villagebay_population.csv\")\n", |
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| 32 | "b = pd.read_csv(\"../data/exposure.csv\")\n", |
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| 33 | "\n", |
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| 34 | "fig, (ax, ax2) = plt.subplots(2, 1, sharex=True)\n", |
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| 35 | "\n", |
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| 36 | "#ax = plt.subplot(211)\n", |
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| 37 | "ax.plot(a.Year, a.VillageBay, c=seaborn.color_palette(\"deep\", 8)[0], lw=3)\n", |
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| 38 | "ax.scatter(a.Year, a.VillageBay, c=seaborn.color_palette(\"deep\", 8)[0], s=50)\n", |
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| 39 | "ax.set_title(\"Village Bay Population\")\n", |
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| 40 | "ax.set_ylim([180, 700])\n", |
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| 41 | "\n", |
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| 42 | "\n", |
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| 43 | "#ax2 = plt.subplot(212, sharex=ax)\n", |
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| 44 | "\n", |
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| 45 | "ax2.plot(b.BirthYear, b.AvgOfLambWS, c=seaborn.color_palette(\"deep\", 8)[2], lw=3)\n", |
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| 46 | "ax2.scatter(b.BirthYear, b.AvgOfLambWS, c=seaborn.color_palette(\"deep\", 8)[2], s=50)\n", |
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| 47 | "ax2.set_title(\"Lamb Winter Survival\")\n", |
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| 48 | "ax2.set_xlim([1984.5, 2013.5])\n", |
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| 49 | "ax2.set_ylim([0, 0.8])\n", |
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| 50 | "\n", |
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| 51 | "plt.savefig(\"figures/population2.jpg\", dpi=300, jpeg_quality=100)\n" |
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| 52 | ], |
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| 53 | "language": "python", |
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| 54 | "metadata": { |
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| 55 | "slideshow": { |
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| 56 | "slide_type": "skip" |
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| 57 | } |
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| 58 | }, |
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| 59 | "outputs": [], |
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| 60 | "prompt_number": 30 |
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| 61 | }, |
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| 62 | { |
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| 63 | "cell_type": "heading", |
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| 64 | "level": 1, |
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| 65 | "metadata": { |
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| 66 | "slideshow": { |
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| 67 | "slide_type": "slide" |
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| 68 | } |
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| 69 | }, |
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| 70 | "source": [ |
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| 71 | "Robust Extraction of Quantitative Information from Histology Images" |
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| 72 | ] |
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| 73 | }, |
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| 74 | { |
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| 75 | "cell_type": "heading", |
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| 76 | "level": 4, |
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| 77 | "metadata": {}, |
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| 78 | "source": [ |
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| 79 | "Quentin Caudron" |
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| 80 | ] |
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| 81 | }, |
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| 82 | { |
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| 83 | "cell_type": "heading", |
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| 84 | "level": 2, |
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| 85 | "metadata": { |
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| 86 | "slideshow": { |
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| 87 | "slide_type": "slide" |
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| 88 | } |
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| 89 | }, |
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| 90 | "source": [ |
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| 91 | "The Soay Sheep" |
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| 92 | ] |
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| 93 | }, |
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| 94 | { |
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| 95 | "cell_type": "markdown", |
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| 96 | "metadata": { |
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| 97 | "slideshow": { |
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| 98 | "slide_type": "subslide" |
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| 99 | } |
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| 100 | }, |
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| 101 | "source": [ |
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| 102 | "<img src=\"figures/graphics/soay.jpg\" />" |
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| 103 | ] |
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| 104 | }, |
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| 105 | { |
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| 106 | "cell_type": "markdown", |
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| 107 | "metadata": { |
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| 108 | "slideshow": { |
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| 109 | "slide_type": "subslide" |
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| 110 | } |
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| 111 | }, |
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| 112 | "source": [ |
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| 113 | "<img src=\"figures/graphics/population2.jpg\" />" |
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| 114 | ] |
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| 115 | }, |
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| 116 | { |
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| 117 | "cell_type": "markdown", |
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| 118 | "metadata": { |
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| 119 | "slideshow": { |
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| 120 | "slide_type": "subslide" |
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| 121 | } |
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| 122 | }, |
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| 123 | "source": [ |
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| 124 | "<img src=\"figures/graphics/lit1.jpg\" />" |
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| 125 | ] |
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| 126 | }, |
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| 127 | { |
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| 128 | "cell_type": "markdown", |
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| 129 | "metadata": { |
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| 130 | "slideshow": { |
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| 131 | "slide_type": "fragment" |
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| 132 | } |
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| 133 | }, |
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| 134 | "source": [ |
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| 135 | "<img src=\"figures/graphics/lit2.jpg\" />" |
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| 136 | ] |
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| 137 | }, |
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| 138 | { |
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| 139 | "cell_type": "markdown", |
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| 140 | "metadata": { |
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| 141 | "slideshow": { |
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| 142 | "slide_type": "fragment" |
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| 143 | } |
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| 144 | }, |
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| 145 | "source": [ |
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| 146 | "<img src=\"figures/graphics/lit4.jpg\" />" |
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| 147 | ] |
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| 148 | }, |
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| 149 | { |
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| 150 | "cell_type": "heading", |
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| 151 | "level": 2, |
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| 152 | "metadata": { |
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| 153 | "slideshow": { |
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| 154 | "slide_type": "slide" |
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| 155 | } |
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| 156 | }, |
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| 157 | "source": [ |
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| 158 | "Outline" |
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| 159 | ] |
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| 160 | }, |
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| 161 | { |
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| 162 | "cell_type": "markdown", |
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| 163 | "metadata": {}, |
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| 164 | "source": [ |
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| 165 | "- Methods and data collection\n", |
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| 166 | "- Image processing\n", |
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| 167 | "- Extracted measures\n", |
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| 168 | "- Preliminary analysis\n", |
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| 169 | "- Future directions" |
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| 170 | ] |
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| 171 | }, |
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| 172 | { |
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| 173 | "cell_type": "heading", |
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| 174 | "level": 2, |
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| 175 | "metadata": { |
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| 176 | "slideshow": { |
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| 177 | "slide_type": "slide" |
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| 178 | } |
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| 179 | }, |
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| 180 | "source": [ |
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| 181 | "Data" |
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| 182 | ] |
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| 183 | }, |
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| 184 | { |
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| 185 | "cell_type": "markdown", |
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| 186 | "metadata": {}, |
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| 187 | "source": [ |
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| 188 | "**In the field, winter of 2011 - 2012 :**\n", |
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| 189 | " \n", |
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| 190 | "- Daily study area monitoring for deaths\n", |
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| 191 | "- 143 liver samples collected within a day of death" |
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| 192 | ] |
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| 193 | }, |
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| 194 | { |
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| 195 | "cell_type": "markdown", |
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| 196 | "metadata": { |
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| 197 | "slideshow": { |
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| 198 | "slide_type": "fragment" |
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| 199 | } |
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| 200 | }, |
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| 201 | "source": [ |
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| 202 | "**In the lab :**\n", |
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| 203 | "\n", |
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| 204 | "- Sectioning after paraffin treatment\n", |
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| 205 | "- H&E staining of about 1000 slides" |
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| 206 | ] |
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| 207 | }, |
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| 208 | { |
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| 209 | "cell_type": "markdown", |
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| 210 | "metadata": { |
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| 211 | "slideshow": { |
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| 212 | "slide_type": "fragment" |
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| 213 | } |
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| 214 | }, |
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| 215 | "source": [ |
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| 216 | "**Analysis :**\n", |
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| 217 | "\n", |
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| 218 | "- Pathology standard : semi-quantitative scoring\n", |
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| 219 | "- Image processing" |
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| 220 | ] |
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| 221 | }, |
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| 222 | { |
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| 223 | "cell_type": "heading", |
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| 224 | "level": 3, |
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| 225 | "metadata": { |
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| 226 | "slideshow": { |
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| 227 | "slide_type": "subslide" |
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| 228 | } |
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| 229 | }, |
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| 230 | "source": [ |
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| 231 | "The Field ©" |
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| 232 | ] |
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| 233 | }, |
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| 234 | { |
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| 235 | "cell_type": "markdown", |
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| 236 | "metadata": {}, |
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| 237 | "source": [ |
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| 238 | "Sweat-and-blood-collected in cold, cold Scotland." |
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| 239 | ] |
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| 240 | }, |
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| 241 | { |
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| 242 | "cell_type": "markdown", |
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| 243 | "metadata": { |
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| 244 | "slideshow": { |
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| 245 | "slide_type": "fragment" |
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| 246 | } |
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| 247 | }, |
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| 248 | "source": [ |
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| 249 | "Eight physical measurements :\n", |
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| 250 | "- Age at death\n", |
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| 251 | "- Weight\n", |
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| 252 | "- Sex\n", |
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| 253 | "- Limb length\n", |
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| 254 | "- Environmental \"stress\"" |
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| 255 | ] |
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| 256 | }, |
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| 257 | { |
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| 258 | "cell_type": "heading", |
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| 259 | "level": 3, |
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| 260 | "metadata": { |
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| 261 | "slideshow": { |
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| 262 | "slide_type": "subslide" |
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| 263 | } |
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| 264 | }, |
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| 265 | "source": [ |
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| 266 | "Clinical Pathology" |
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| 267 | ] |
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| 268 | }, |
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| 269 | { |
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| 270 | "cell_type": "markdown", |
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| 271 | "metadata": {}, |
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| 272 | "source": [ |
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| 273 | "Operator-driven visual analysis of 98 slides under microscopy." |
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| 274 | ] |
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| 275 | }, |
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| 276 | { |
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| 277 | "cell_type": "markdown", |
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| 278 | "metadata": { |
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| 279 | "slideshow": { |
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| 280 | "slide_type": "fragment" |
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| 281 | } |
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| 282 | }, |
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| 283 | "source": [ |
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| 284 | "Eleven discrete and continuous measures :\n", |
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| 285 | "\n", |
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| 286 | "- Inflammation\n", |
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| 287 | "- Necrosis\n", |
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| 288 | "- Apoptosis\n", |
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| 289 | "- Hyperplasia\n", |
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| 290 | "- Fibrosis\n", |
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| 291 | "- Hepatitis" |
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| 292 | ] |
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| 293 | }, |
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| 294 | { |
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| 295 | "cell_type": "heading", |
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| 296 | "level": 3, |
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| 297 | "metadata": { |
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| 298 | "slideshow": { |
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| 299 | "slide_type": "subslide" |
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| 300 | } |
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| 301 | }, |
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| 302 | "source": [ |
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| 303 | "Image Processing" |
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| 304 | ] |
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| 305 | }, |
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| 306 | { |
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| 307 | "cell_type": "markdown", |
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| 308 | "metadata": {}, |
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| 309 | "source": [ |
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| 310 | "Automated analysis of 4430 images of slides representing 143 sheep." |
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| 311 | ] |
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| 312 | }, |
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| 313 | { |
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| 314 | "cell_type": "markdown", |
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| 315 | "metadata": { |
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| 316 | "slideshow": { |
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| 317 | "slide_type": "fragment" |
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| 318 | } |
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| 319 | }, |
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| 320 | "source": [ |
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| 321 | "Seven structural and textural measures with varying levels of biological interpretation :\n", |
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| 322 | "\n", |
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| 323 | "- Inflammation\n", |
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| 324 | "- Hyperplasia / tissue density\n", |
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| 325 | "- Best-guess proxies for \"generic degeneration\"" |
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| 326 | ] |
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| 327 | }, |
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| 328 | { |
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| 329 | "cell_type": "heading", |
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| 330 | "level": 2, |
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| 331 | "metadata": { |
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| 332 | "slideshow": { |
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| 333 | "slide_type": "slide" |
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| 334 | } |
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| 335 | }, |
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| 336 | "source": [ |
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| 337 | "Image Processing" |
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| 338 | ] |
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| 339 | }, |
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| 340 | { |
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| 341 | "cell_type": "markdown", |
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| 342 | "metadata": { |
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| 343 | "slideshow": { |
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| 344 | "slide_type": "subslide" |
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| 345 | } |
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| 346 | }, |
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| 347 | "source": [ |
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| 348 | "<img src=\"figures/graphics/sheep.jpg\"></img>" |
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| 349 | ] |
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| 350 | }, |
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| 351 | { |
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| 352 | "cell_type": "markdown", |
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| 353 | "metadata": { |
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| 354 | "slideshow": { |
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| 355 | "slide_type": "subslide" |
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| 356 | } |
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| 357 | }, |
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| 358 | "source": [ |
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| 359 | "<img src=\"figures/graphics/processed.jpg\"></img>" |
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| 360 | ] |
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| 361 | }, |
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| 362 | { |
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| 363 | "cell_type": "heading", |
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| 364 | "level": 3, |
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| 365 | "metadata": { |
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| 366 | "slideshow": { |
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| 367 | "slide_type": "subslide" |
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| 368 | } |
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| 369 | }, |
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| 370 | "source": [ |
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| 371 | "The Challenge" |
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| 372 | ] |
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| 373 | }, |
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| 374 | { |
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| 375 | "cell_type": "markdown", |
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| 376 | "metadata": { |
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| 377 | "slideshow": { |
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| 378 | "slide_type": "-" |
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| 379 | } |
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| 380 | }, |
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| 381 | "source": [ |
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| 382 | "**Information extraction must be**\n", |
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| 383 | "- automagical - no operator input\n", |
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| 384 | "- reasonably quick - restricted computing time\n", |
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| 385 | "- robust - invariant to slicing, staining, field-related variation \n", |
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| 386 | "- unbiased - same algorithms for everyone" |
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| 387 | ] |
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| 388 | }, |
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| 389 | { |
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| 390 | "cell_type": "markdown", |
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| 391 | "metadata": { |
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| 392 | "slideshow": { |
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| 393 | "slide_type": "subslide" |
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| 394 | } |
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| 395 | }, |
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| 396 | "source": [ |
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| 397 | "" |
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| 398 | ] |
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| 399 | }, |
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| 400 | { |
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| 401 | "cell_type": "markdown", |
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| 402 | "metadata": { |
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| 403 | "slideshow": { |
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| 404 | "slide_type": "subslide" |
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| 405 | } |
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| 406 | }, |
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| 407 | "source": [ |
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| 408 | "" |
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| 409 | ] |
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| 410 | }, |
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| 411 | { |
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| 412 | "cell_type": "markdown", |
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| 413 | "metadata": { |
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| 414 | "slideshow": { |
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| 415 | "slide_type": "subslide" |
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| 416 | } |
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| 417 | }, |
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| 418 | "source": [ |
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| 419 | "" |
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| 420 | ] |
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| 421 | }, |
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| 422 | { |
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| 423 | "cell_type": "markdown", |
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| 424 | "metadata": { |
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| 425 | "slideshow": { |
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| 426 | "slide_type": "subslide" |
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| 427 | } |
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| 428 | }, |
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| 429 | "source": [ |
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| 430 | "" |
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| 431 | ] |
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| 432 | }, |
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| 433 | { |
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| 434 | "cell_type": "markdown", |
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| 435 | "metadata": { |
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| 436 | "slideshow": { |
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| 437 | "slide_type": "subslide" |
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| 438 | } |
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| 439 | }, |
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| 440 | "source": [ |
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| 441 | "<img src=\"figures/graphics/gif.gif\"></img>" |
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| 442 | ] |
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| 443 | }, |
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| 444 | { |
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| 445 | "cell_type": "heading", |
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| 446 | "level": 2, |
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| 447 | "metadata": { |
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| 448 | "slideshow": { |
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| 449 | "slide_type": "slide" |
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| 450 | } |
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| 451 | }, |
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| 452 | "source": [ |
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| 453 | "Structural and Textural Measures" |
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| 454 | ] |
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| 455 | }, |
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| 456 | { |
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| 457 | "cell_type": "markdown", |
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| 458 | "metadata": { |
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| 459 | "slideshow": { |
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| 460 | "slide_type": "subslide" |
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| 461 | } |
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| 462 | }, |
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| 463 | "source": [ |
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| 464 | "- characteristic **scale** of sinusoid widths\n", |
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| 465 | "- **directional** amplitude of preferred sinusoid alignment\n", |
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| 466 | "- **tissue to sinusoid** ratio\n", |
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| 467 | "- **count** of inflammatory foci per image\n", |
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| 468 | "- **mean size** of inflammatory foci per image\n", |
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| 469 | "- information **entropy** of sinusoid distribution\n", |
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| 470 | "- **lacunarity** ( clustering ) of sinusoids" |
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| 471 | ] |
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| 472 | }, |
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| 473 | { |
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| 474 | "cell_type": "markdown", |
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| 475 | "metadata": { |
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| 476 | "slideshow": { |
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| 477 | "slide_type": "subslide" |
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| 478 | } |
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| 479 | }, |
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| 480 | "source": [ |
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| 481 | "" |
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| 482 | ] |
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| 483 | }, |
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| 484 | { |
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| 485 | "cell_type": "markdown", |
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| 486 | "metadata": { |
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| 487 | "slideshow": { |
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| 488 | "slide_type": "subslide" |
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| 489 | } |
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| 490 | }, |
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| 491 | "source": [ |
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| 492 | "" |
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| 493 | ] |
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| 494 | }, |
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| 495 | { |
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| 496 | "cell_type": "heading", |
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| 497 | "level": 2, |
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| 498 | "metadata": { |
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| 499 | "slideshow": { |
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| 500 | "slide_type": "slide" |
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| 501 | } |
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| 502 | }, |
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| 503 | "source": [ |
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| 504 | "Exploratory Analysis" |
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| 505 | ] |
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| 506 | }, |
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| 507 | { |
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| 508 | "cell_type": "heading", |
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| 509 | "level": 3, |
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| 510 | "metadata": {}, |
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| 511 | "source": [ |
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| 512 | "by individual" |
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| 513 | ] |
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| 514 | }, |
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| 515 | { |
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| 516 | "cell_type": "markdown", |
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| 517 | "metadata": { |
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| 518 | "slideshow": { |
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| 519 | "slide_type": "subslide" |
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| 520 | } |
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| 521 | }, |
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| 522 | "source": [ |
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| 523 | "<img src=\"figures/regressions/BDHyperplasia/lm-0.png\" />" |
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| 524 | ] |
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| 525 | }, |
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| 526 | { |
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| 527 | "cell_type": "markdown", |
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| 528 | "metadata": { |
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| 529 | "slideshow": { |
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| 530 | "slide_type": "subslide" |
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| 531 | } |
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| 532 | }, |
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| 533 | "source": [ |
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| 534 | "<img src=\"figures/regressions/PortalInflammation/lm-0.png\" />" |
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| 535 | ] |
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| 536 | }, |
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| 537 | { |
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| 538 | "cell_type": "markdown", |
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| 539 | "metadata": { |
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| 540 | "slideshow": { |
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| 541 | "slide_type": "subslide" |
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| 542 | } |
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| 543 | }, |
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| 544 | "source": [ |
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| 545 | "<img src=\"figures/regressions/PortalInflammation/lm-1.png\" />" |
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| 546 | ] |
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| 547 | }, |
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| 548 | { |
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| 549 | "cell_type": "heading", |
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| 550 | "level": 2, |
||
| 551 | "metadata": { |
||
| 552 | "slideshow": { |
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| 553 | "slide_type": "slide" |
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| 554 | } |
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| 555 | }, |
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| 556 | "source": [ |
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| 557 | "Exploratory Analysis" |
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| 558 | ] |
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| 559 | }, |
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| 560 | { |
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| 561 | "cell_type": "heading", |
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| 562 | "level": 3, |
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| 563 | "metadata": {}, |
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| 564 | "source": [ |
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| 565 | "controlled for age / cohort" |
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| 566 | ] |
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| 567 | }, |
||
| 568 | { |
||
| 569 | "cell_type": "markdown", |
||
| 570 | "metadata": { |
||
| 571 | "slideshow": { |
||
| 572 | "slide_type": "subslide" |
||
| 573 | } |
||
| 574 | }, |
||
| 575 | "source": [ |
||
| 576 | "<img src=\"figures/regressions/PortalInflammation/mm_0.png\" />" |
||
| 577 | ] |
||
| 578 | }, |
||
| 579 | { |
||
| 580 | "cell_type": "markdown", |
||
| 581 | "metadata": { |
||
| 582 | "slideshow": { |
||
| 583 | "slide_type": "subslide" |
||
| 584 | } |
||
| 585 | }, |
||
| 586 | "source": [ |
||
| 587 | "<img src=\"figures/regressions/BDHyperplasia/mm_0.png\" />" |
||
| 588 | ] |
||
| 589 | }, |
||
| 590 | { |
||
| 591 | "cell_type": "markdown", |
||
| 592 | "metadata": { |
||
| 593 | "slideshow": { |
||
| 594 | "slide_type": "subslide" |
||
| 595 | } |
||
| 596 | }, |
||
| 597 | "source": [ |
||
| 598 | "<img src=\"figures/regressions/BDHyperplasia/mm_1.png\" />" |
||
| 599 | ] |
||
| 600 | }, |
||
| 601 | { |
||
| 602 | "cell_type": "markdown", |
||
| 603 | "metadata": { |
||
| 604 | "slideshow": { |
||
| 605 | "slide_type": "subslide" |
||
| 606 | } |
||
| 607 | }, |
||
| 608 | "source": [ |
||
| 609 | "<img src=\"figures/regressions/TawfikTotal/mm_0.png\" />" |
||
| 610 | ] |
||
| 611 | }, |
||
| 612 | { |
||
| 613 | "cell_type": "markdown", |
||
| 614 | "metadata": { |
||
| 615 | "slideshow": { |
||
| 616 | "slide_type": "subslide" |
||
| 617 | } |
||
| 618 | }, |
||
| 619 | "source": [ |
||
| 620 | "<img src=\"figures/regressions/Fibrosis/mm_0.png\" />" |
||
| 621 | ] |
||
| 622 | }, |
||
| 623 | { |
||
| 624 | "cell_type": "markdown", |
||
| 625 | "metadata": { |
||
| 626 | "slideshow": { |
||
| 627 | "slide_type": "subslide" |
||
| 628 | } |
||
| 629 | }, |
||
| 630 | "source": [ |
||
| 631 | "<img src=\"figures/regressions/PortalInflammation/mm_0.png\" />" |
||
| 632 | ] |
||
| 633 | }, |
||
| 634 | { |
||
| 635 | "cell_type": "markdown", |
||
| 636 | "metadata": { |
||
| 637 | "slideshow": { |
||
| 638 | "slide_type": "subslide" |
||
| 639 | } |
||
| 640 | }, |
||
| 641 | "source": [ |
||
| 642 | "<img src=\"figures/regressions/Hindleg/mm_0.png\" />" |
||
| 643 | ] |
||
| 644 | }, |
||
| 645 | { |
||
| 646 | "cell_type": "markdown", |
||
| 647 | "metadata": { |
||
| 648 | "slideshow": { |
||
| 649 | "slide_type": "subslide" |
||
| 650 | } |
||
| 651 | }, |
||
| 652 | "source": [ |
||
| 653 | "<img src=\"figures/regressions/Weight/mm_0.png\" />" |
||
| 654 | ] |
||
| 655 | }, |
||
| 656 | { |
||
| 657 | "cell_type": "heading", |
||
| 658 | "level": 2, |
||
| 659 | "metadata": { |
||
| 660 | "slideshow": { |
||
| 661 | "slide_type": "slide" |
||
| 662 | } |
||
| 663 | }, |
||
| 664 | "source": [ |
||
| 665 | "Further analysis" |
||
| 666 | ] |
||
| 667 | }, |
||
| 668 | { |
||
| 669 | "cell_type": "heading", |
||
| 670 | "level": 3, |
||
| 671 | "metadata": {}, |
||
| 672 | "source": [ |
||
| 673 | "Age or cohort effect ?" |
||
| 674 | ] |
||
| 675 | }, |
||
| 676 | { |
||
| 677 | "cell_type": "markdown", |
||
| 678 | "metadata": { |
||
| 679 | "slideshow": { |
||
| 680 | "slide_type": "subslide" |
||
| 681 | } |
||
| 682 | }, |
||
| 683 | "source": [ |
||
| 684 | "<img src=\"figures/regressions/BDHyperplasia/mm_coefs_color_E.png\" />" |
||
| 685 | ] |
||
| 686 | }, |
||
| 687 | { |
||
| 688 | "cell_type": "markdown", |
||
| 689 | "metadata": { |
||
| 690 | "slideshow": { |
||
| 691 | "slide_type": "subslide" |
||
| 692 | } |
||
| 693 | }, |
||
| 694 | "source": [ |
||
| 695 | "<img src=\"figures/regressions/BDHyperplasia/mm_coefs_color_CES.png\" />" |
||
| 696 | ] |
||
| 697 | }, |
||
| 698 | { |
||
| 699 | "cell_type": "markdown", |
||
| 700 | "metadata": { |
||
| 701 | "slideshow": { |
||
| 702 | "slide_type": "subslide" |
||
| 703 | } |
||
| 704 | }, |
||
| 705 | "source": [ |
||
| 706 | "<img src=\"figures/regressions/BDHyperplasia/mm_coefs_color_RES.png\" />" |
||
| 707 | ] |
||
| 708 | }, |
||
| 709 | { |
||
| 710 | "cell_type": "heading", |
||
| 711 | "level": 2, |
||
| 712 | "metadata": { |
||
| 713 | "slideshow": { |
||
| 714 | "slide_type": "slide" |
||
| 715 | } |
||
| 716 | }, |
||
| 717 | "source": [ |
||
| 718 | "Conclusions" |
||
| 719 | ] |
||
| 720 | }, |
||
| 721 | { |
||
| 722 | "cell_type": "markdown", |
||
| 723 | "metadata": {}, |
||
| 724 | "source": [ |
||
| 725 | "- our image measures capture **relevant** and **useful** information\n", |
||
| 726 | "- a number of correlations can be **explained** biologically\n", |
||
| 727 | "- underlying **structure** in the data needs thought\n", |
||
| 728 | "- still no **map** from image or histological measures to condition of individual" |
||
| 729 | ] |
||
| 730 | }, |
||
| 731 | { |
||
| 732 | "cell_type": "heading", |
||
| 733 | "level": 2, |
||
| 734 | "metadata": { |
||
| 735 | "slideshow": { |
||
| 736 | "slide_type": "slide" |
||
| 737 | } |
||
| 738 | }, |
||
| 739 | "source": [ |
||
| 740 | "Future directions" |
||
| 741 | ] |
||
| 742 | }, |
||
| 743 | { |
||
| 744 | "cell_type": "heading", |
||
| 745 | "level": 3, |
||
| 746 | "metadata": { |
||
| 747 | "slideshow": { |
||
| 748 | "slide_type": "subslide" |
||
| 749 | } |
||
| 750 | }, |
||
| 751 | "source": [ |
||
| 752 | "Further exploration of the dataset" |
||
| 753 | ] |
||
| 754 | }, |
||
| 755 | { |
||
| 756 | "cell_type": "markdown", |
||
| 757 | "metadata": { |
||
| 758 | "slideshow": { |
||
| 759 | "slide_type": "-" |
||
| 760 | } |
||
| 761 | }, |
||
| 762 | "source": [ |
||
| 763 | "- 145 sheep ( 89 females )\n", |
||
| 764 | "- 12 age classes\n", |
||
| 765 | "- potential redundancy in various measures" |
||
| 766 | ] |
||
| 767 | }, |
||
| 768 | { |
||
| 769 | "cell_type": "markdown", |
||
| 770 | "metadata": { |
||
| 771 | "slideshow": { |
||
| 772 | "slide_type": "fragment" |
||
| 773 | } |
||
| 774 | }, |
||
| 775 | "source": [ |
||
| 776 | "- 4460 entries across 27 variables\n", |
||
| 777 | "- 3330 with full image and histological information\n", |
||
| 778 | "- 1196 for which **complete** information is available" |
||
| 779 | ] |
||
| 780 | }, |
||
| 781 | { |
||
| 782 | "cell_type": "heading", |
||
| 783 | "level": 3, |
||
| 784 | "metadata": { |
||
| 785 | "slideshow": { |
||
| 786 | "slide_type": "subslide" |
||
| 787 | } |
||
| 788 | }, |
||
| 789 | "source": [ |
||
| 790 | "More data" |
||
| 791 | ] |
||
| 792 | }, |
||
| 793 | { |
||
| 794 | "cell_type": "markdown", |
||
| 795 | "metadata": {}, |
||
| 796 | "source": [ |
||
| 797 | "- nutritional information\n", |
||
| 798 | "- immunity data" |
||
| 799 | ] |
||
| 800 | }, |
||
| 801 | { |
||
| 802 | "cell_type": "heading", |
||
| 803 | "level": 3, |
||
| 804 | "metadata": { |
||
| 805 | "slideshow": { |
||
| 806 | "slide_type": "subslide" |
||
| 807 | } |
||
| 808 | }, |
||
| 809 | "source": [ |
||
| 810 | "Narrow-field images" |
||
| 811 | ] |
||
| 812 | }, |
||
| 813 | { |
||
| 814 | "cell_type": "markdown", |
||
| 815 | "metadata": {}, |
||
| 816 | "source": [ |
||
| 817 | "- 12536 images\n", |
||
| 818 | "- spatial distribution of nuclei" |
||
| 819 | ] |
||
| 820 | }, |
||
| 821 | { |
||
| 822 | "cell_type": "markdown", |
||
| 823 | "metadata": { |
||
| 824 | "slideshow": { |
||
| 825 | "slide_type": "subslide" |
||
| 826 | } |
||
| 827 | }, |
||
| 828 | "source": [ |
||
| 829 | "" |
||
| 830 | ] |
||
| 831 | }, |
||
| 832 | { |
||
| 833 | "cell_type": "markdown", |
||
| 834 | "metadata": { |
||
| 835 | "slideshow": { |
||
| 836 | "slide_type": "subslide" |
||
| 837 | } |
||
| 838 | }, |
||
| 839 | "source": [ |
||
| 840 | "" |
||
| 841 | ] |
||
| 842 | }, |
||
| 843 | { |
||
| 844 | "cell_type": "markdown", |
||
| 845 | "metadata": { |
||
| 846 | "slideshow": { |
||
| 847 | "slide_type": "subslide" |
||
| 848 | } |
||
| 849 | }, |
||
| 850 | "source": [ |
||
| 851 | "" |
||
| 852 | ] |
||
| 853 | }, |
||
| 854 | { |
||
| 855 | "cell_type": "markdown", |
||
| 856 | "metadata": { |
||
| 857 | "slideshow": { |
||
| 858 | "slide_type": "subslide" |
||
| 859 | } |
||
| 860 | }, |
||
| 861 | "source": [ |
||
| 862 | "<img src=\"figures/graphics/10x.png\" width=100%></src>" |
||
| 863 | ] |
||
| 864 | }, |
||
| 865 | { |
||
| 866 | "cell_type": "heading", |
||
| 867 | "level": 2, |
||
| 868 | "metadata": { |
||
| 869 | "slideshow": { |
||
| 870 | "slide_type": "slide" |
||
| 871 | } |
||
| 872 | }, |
||
| 873 | "source": [ |
||
| 874 | "With thanks to" |
||
| 875 | ] |
||
| 876 | }, |
||
| 877 | { |
||
| 878 | "cell_type": "markdown", |
||
| 879 | "metadata": {}, |
||
| 880 | "source": [ |
||
| 881 | "Romain Garnier\n", |
||
| 882 | "\n", |
||
| 883 | "Andrea Graham\n", |
||
| 884 | "\n", |
||
| 885 | "Tawfik Aboellail (CSU)\n", |
||
| 886 | "\n", |
||
| 887 | "Bryan Grenfell\n" |
||
| 888 | ] |
||
| 889 | } |
||
| 890 | ], |
||
| 891 | "metadata": {} |
||
| 892 | } |
||
| 893 | ] |
||
| 894 | } |