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| a | b/talk/Untitled0.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:a1c50636bceeed02c8c18724931a58c60be26150f5402e0d284e06e7c7347b67" |
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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": "heading", |
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| 14 | "level": 1, |
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| 15 | "metadata": { |
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| 16 | "slideshow": { |
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| 17 | "slide_type": "slide" |
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| 18 | } |
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| 19 | }, |
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| 20 | "source": [ |
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| 21 | "Robust Extraction of Quantitative Information from Histology Images" |
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| 22 | ] |
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| 23 | }, |
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| 24 | { |
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| 25 | "cell_type": "markdown", |
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| 26 | "metadata": {}, |
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| 27 | "source": [ |
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| 28 | "**Quentin Caudron**" |
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| 29 | ] |
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| 30 | }, |
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| 31 | { |
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| 32 | "cell_type": "markdown", |
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| 33 | "metadata": { |
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| 34 | "slideshow": { |
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| 35 | "slide_type": "slide" |
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| 36 | } |
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| 37 | }, |
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| 38 | "source": [ |
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| 39 | "<img src=\"figures/graphics/soay.jpg\" />" |
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| 40 | ] |
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| 41 | }, |
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| 42 | { |
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| 43 | "cell_type": "markdown", |
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| 44 | "metadata": { |
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| 45 | "slideshow": { |
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| 46 | "slide_type": "subslide" |
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| 47 | } |
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| 48 | }, |
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| 49 | "source": [ |
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| 50 | "<img src=\"figures/population3.png\" width=1200px/>" |
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| 51 | ] |
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| 52 | }, |
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| 53 | { |
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| 54 | "cell_type": "markdown", |
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| 55 | "metadata": { |
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| 56 | "slideshow": { |
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| 57 | "slide_type": "subslide" |
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| 58 | } |
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| 59 | }, |
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| 60 | "source": [ |
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| 61 | "<img src=\"figures/graphics/lit1.jpg\" />" |
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| 62 | ] |
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| 63 | }, |
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| 64 | { |
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| 65 | "cell_type": "markdown", |
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| 66 | "metadata": { |
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| 67 | "slideshow": { |
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| 68 | "slide_type": "fragment" |
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| 69 | } |
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| 70 | }, |
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| 71 | "source": [ |
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| 72 | "<img src=\"figures/graphics/lit2.jpg\" />" |
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| 73 | ] |
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| 74 | }, |
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| 75 | { |
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| 76 | "cell_type": "markdown", |
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| 77 | "metadata": { |
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| 78 | "slideshow": { |
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| 79 | "slide_type": "fragment" |
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| 80 | } |
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| 81 | }, |
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| 82 | "source": [ |
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| 83 | "<img src=\"figures/graphics/lit4.jpg\" />" |
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| 84 | ] |
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| 85 | }, |
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| 86 | { |
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| 87 | "cell_type": "heading", |
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| 88 | "level": 2, |
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| 89 | "metadata": { |
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| 90 | "slideshow": { |
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| 91 | "slide_type": "slide" |
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| 92 | } |
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| 93 | }, |
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| 94 | "source": [ |
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| 95 | "Outline" |
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| 96 | ] |
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| 97 | }, |
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| 98 | { |
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| 99 | "cell_type": "markdown", |
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| 100 | "metadata": {}, |
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| 101 | "source": [ |
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| 102 | "- Methods and data collection\n", |
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| 103 | "- Image processing\n", |
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| 104 | "- Extracted measures\n", |
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| 105 | "- Preliminary analysis\n", |
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| 106 | "- Future directions" |
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| 107 | ] |
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| 108 | }, |
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| 109 | { |
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| 110 | "cell_type": "heading", |
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| 111 | "level": 2, |
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| 112 | "metadata": { |
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| 113 | "slideshow": { |
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| 114 | "slide_type": "slide" |
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| 115 | } |
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| 116 | }, |
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| 117 | "source": [ |
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| 118 | "Data" |
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| 119 | ] |
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| 120 | }, |
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| 121 | { |
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| 122 | "cell_type": "markdown", |
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| 123 | "metadata": {}, |
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| 124 | "source": [ |
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| 125 | "**In the field, winter of 2011 - 2012 :**\n", |
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| 126 | " \n", |
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| 127 | "- Daily study area monitoring for deaths\n", |
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| 128 | "- 143 liver samples collected within a day of death" |
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| 129 | ] |
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| 130 | }, |
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| 131 | { |
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| 132 | "cell_type": "markdown", |
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| 133 | "metadata": { |
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| 134 | "slideshow": { |
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| 135 | "slide_type": "fragment" |
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| 136 | } |
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| 137 | }, |
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| 138 | "source": [ |
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| 139 | "<br />**In the lab :**\n", |
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| 140 | "\n", |
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| 141 | "- Sectioning after paraffin treatment\n", |
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| 142 | "- H&E staining of about 1000 slides" |
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| 143 | ] |
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| 144 | }, |
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| 145 | { |
||
| 146 | "cell_type": "markdown", |
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| 147 | "metadata": { |
||
| 148 | "slideshow": { |
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| 149 | "slide_type": "fragment" |
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| 150 | } |
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| 151 | }, |
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| 152 | "source": [ |
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| 153 | "<br />**Analysis :**\n", |
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| 154 | "\n", |
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| 155 | "- Pathology standard : semi-quantitative scoring\n", |
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| 156 | "- Image processing" |
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| 157 | ] |
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| 158 | }, |
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| 159 | { |
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| 160 | "cell_type": "heading", |
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| 161 | "level": 3, |
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| 162 | "metadata": { |
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| 163 | "slideshow": { |
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| 164 | "slide_type": "subslide" |
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| 165 | } |
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| 166 | }, |
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| 167 | "source": [ |
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| 168 | "The Field" |
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| 169 | ] |
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| 170 | }, |
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| 171 | { |
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| 172 | "cell_type": "markdown", |
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| 173 | "metadata": {}, |
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| 174 | "source": [ |
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| 175 | "Sweat-and-blood-collected in cold, cold Scotland." |
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| 176 | ] |
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| 177 | }, |
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| 178 | { |
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| 179 | "cell_type": "markdown", |
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| 180 | "metadata": { |
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| 181 | "slideshow": { |
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| 182 | "slide_type": "fragment" |
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| 183 | } |
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| 184 | }, |
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| 185 | "source": [ |
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| 186 | "Eight physical measurements :\n", |
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| 187 | "- Age at death\n", |
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| 188 | "- Weight\n", |
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| 189 | "- Sex\n", |
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| 190 | "- Limb length\n", |
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| 191 | "- Environmental \"stress\"" |
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| 192 | ] |
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| 193 | }, |
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| 194 | { |
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| 195 | "cell_type": "heading", |
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| 196 | "level": 3, |
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| 197 | "metadata": { |
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| 198 | "slideshow": { |
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| 199 | "slide_type": "subslide" |
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| 200 | } |
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| 201 | }, |
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| 202 | "source": [ |
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| 203 | "Clinical Pathology" |
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| 204 | ] |
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| 205 | }, |
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| 206 | { |
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| 207 | "cell_type": "markdown", |
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| 208 | "metadata": { |
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| 209 | "slideshow": { |
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| 210 | "slide_type": "-" |
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| 211 | } |
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| 212 | }, |
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| 213 | "source": [ |
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| 214 | "Operator-driven visual analysis of 98 slides under microscopy." |
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| 215 | ] |
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| 216 | }, |
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| 217 | { |
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| 218 | "cell_type": "markdown", |
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| 219 | "metadata": { |
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| 220 | "slideshow": { |
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| 221 | "slide_type": "fragment" |
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| 222 | } |
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| 223 | }, |
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| 224 | "source": [ |
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| 225 | "Eleven discrete and continuous measures :\n", |
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| 226 | "\n", |
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| 227 | "- Inflammation\n", |
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| 228 | "- Necrosis\n", |
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| 229 | "- Apoptosis\n", |
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| 230 | "- Hyperplasia\n", |
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| 231 | "- Fibrosis\n", |
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| 232 | "- Hepatitis" |
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| 233 | ] |
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| 234 | }, |
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| 235 | { |
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| 236 | "cell_type": "heading", |
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| 237 | "level": 3, |
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| 238 | "metadata": { |
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| 239 | "slideshow": { |
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| 240 | "slide_type": "subslide" |
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| 241 | } |
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| 242 | }, |
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| 243 | "source": [ |
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| 244 | "Image Processing" |
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| 245 | ] |
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| 246 | }, |
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| 247 | { |
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| 248 | "cell_type": "markdown", |
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| 249 | "metadata": {}, |
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| 250 | "source": [ |
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| 251 | "Automated analysis of 4430 images of slides representing 143 sheep." |
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| 252 | ] |
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| 253 | }, |
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| 254 | { |
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| 255 | "cell_type": "markdown", |
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| 256 | "metadata": { |
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| 257 | "slideshow": { |
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| 258 | "slide_type": "fragment" |
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| 259 | } |
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| 260 | }, |
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| 261 | "source": [ |
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| 262 | "Seven structural and textural measures with varying levels of biological interpretation :\n", |
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| 263 | "\n", |
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| 264 | "- Inflammation\n", |
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| 265 | "- Hyperplasia / tissue density\n", |
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| 266 | "- Best-guess proxies for \"generic degeneration\"" |
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| 267 | ] |
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| 268 | }, |
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| 269 | { |
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| 270 | "cell_type": "heading", |
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| 271 | "level": 2, |
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| 272 | "metadata": { |
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| 273 | "slideshow": { |
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| 274 | "slide_type": "slide" |
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| 275 | } |
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| 276 | }, |
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| 277 | "source": [ |
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| 278 | "Image Processing" |
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| 279 | ] |
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| 280 | }, |
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| 281 | { |
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| 282 | "cell_type": "markdown", |
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| 283 | "metadata": { |
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| 284 | "slideshow": { |
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| 285 | "slide_type": "subslide" |
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| 286 | } |
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| 287 | }, |
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| 288 | "source": [ |
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| 289 | "<img src=\"figures/graphics/sheep.jpg\"></img>" |
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| 290 | ] |
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| 291 | }, |
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| 292 | { |
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| 293 | "cell_type": "markdown", |
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| 294 | "metadata": { |
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| 295 | "slideshow": { |
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| 296 | "slide_type": "subslide" |
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| 297 | } |
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| 298 | }, |
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| 299 | "source": [ |
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| 300 | "<img src=\"figures/graphics/processed.jpg\"></img>" |
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| 301 | ] |
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| 302 | }, |
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| 303 | { |
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| 304 | "cell_type": "heading", |
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| 305 | "level": 3, |
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| 306 | "metadata": { |
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| 307 | "slideshow": { |
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| 308 | "slide_type": "subslide" |
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| 309 | } |
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| 310 | }, |
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| 311 | "source": [ |
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| 312 | "The Challenge" |
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| 313 | ] |
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| 314 | }, |
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| 315 | { |
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| 316 | "cell_type": "markdown", |
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| 317 | "metadata": { |
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| 318 | "slideshow": { |
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| 319 | "slide_type": "-" |
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| 320 | } |
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| 321 | }, |
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| 322 | "source": [ |
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| 323 | "**Information extraction must be**\n", |
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| 324 | "- automagical - no operator input\n", |
||
| 325 | "- reasonably quick - restricted computing time\n", |
||
| 326 | "- robust - invariant to slicing, staining, field-related variation \n", |
||
| 327 | "- unbiased - same algorithms for everyone" |
||
| 328 | ] |
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| 329 | }, |
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| 330 | { |
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| 331 | "cell_type": "markdown", |
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| 332 | "metadata": { |
||
| 333 | "slideshow": { |
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| 334 | "slide_type": "subslide" |
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| 335 | } |
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| 336 | }, |
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| 337 | "source": [ |
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| 338 | "" |
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| 339 | ] |
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| 340 | }, |
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| 341 | { |
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| 342 | "cell_type": "markdown", |
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| 343 | "metadata": { |
||
| 344 | "slideshow": { |
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| 345 | "slide_type": "subslide" |
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| 346 | } |
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| 347 | }, |
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| 348 | "source": [ |
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| 349 | "" |
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| 350 | ] |
||
| 351 | }, |
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| 352 | { |
||
| 353 | "cell_type": "markdown", |
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| 354 | "metadata": { |
||
| 355 | "slideshow": { |
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| 356 | "slide_type": "subslide" |
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| 357 | } |
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| 358 | }, |
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| 359 | "source": [ |
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| 360 | "" |
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| 361 | ] |
||
| 362 | }, |
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| 363 | { |
||
| 364 | "cell_type": "markdown", |
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| 365 | "metadata": { |
||
| 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 | "" |
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| 372 | ] |
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| 373 | }, |
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| 374 | { |
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| 375 | "cell_type": "heading", |
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| 376 | "level": 2, |
||
| 377 | "metadata": { |
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| 378 | "slideshow": { |
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| 379 | "slide_type": "slide" |
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| 380 | } |
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| 381 | }, |
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| 382 | "source": [ |
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| 383 | "Structural and Textural Measures" |
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| 384 | ] |
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| 385 | }, |
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| 386 | { |
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| 387 | "cell_type": "markdown", |
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| 388 | "metadata": { |
||
| 389 | "slideshow": { |
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| 390 | "slide_type": "subslide" |
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| 391 | } |
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| 392 | }, |
||
| 393 | "source": [ |
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| 394 | "- characteristic **scale** of sinusoid widths\n", |
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| 395 | "- **directional** amplitude of preferred sinusoid alignment\n", |
||
| 396 | "- **tissue to sinusoid** ratio\n", |
||
| 397 | "- **count** of inflammatory foci per image\n", |
||
| 398 | "- **mean size** of inflammatory foci per image\n", |
||
| 399 | "- information **entropy** of sinusoid distribution\n", |
||
| 400 | "- **lacunarity** ( clustering ) of sinusoids" |
||
| 401 | ] |
||
| 402 | }, |
||
| 403 | { |
||
| 404 | "cell_type": "markdown", |
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| 405 | "metadata": { |
||
| 406 | "slideshow": { |
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| 407 | "slide_type": "subslide" |
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| 408 | } |
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| 409 | }, |
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| 410 | "source": [ |
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| 411 | "<img src=\"figures/graphics/gif.gif\"></img>" |
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| 412 | ] |
||
| 413 | }, |
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| 414 | { |
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| 415 | "cell_type": "markdown", |
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| 416 | "metadata": { |
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| 417 | "slideshow": { |
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| 418 | "slide_type": "subslide" |
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| 419 | } |
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| 420 | }, |
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| 421 | "source": [ |
||
| 422 | "<img src=\"figures/graphics/intra3.png\" width=100%/>" |
||
| 423 | ] |
||
| 424 | }, |
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| 425 | { |
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| 426 | "cell_type": "markdown", |
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| 427 | "metadata": { |
||
| 428 | "slideshow": { |
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| 429 | "slide_type": "subslide" |
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| 430 | } |
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| 431 | }, |
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| 432 | "source": [ |
||
| 433 | "<img src=\"figures/graphics/inter3.png\"/>" |
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| 434 | ] |
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| 435 | }, |
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| 436 | { |
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| 437 | "cell_type": "heading", |
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| 438 | "level": 2, |
||
| 439 | "metadata": { |
||
| 440 | "slideshow": { |
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| 441 | "slide_type": "slide" |
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| 442 | } |
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| 443 | }, |
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| 444 | "source": [ |
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| 445 | "Exploratory Analysis" |
||
| 446 | ] |
||
| 447 | }, |
||
| 448 | { |
||
| 449 | "cell_type": "markdown", |
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| 450 | "metadata": {}, |
||
| 451 | "source": [ |
||
| 452 | "by individual" |
||
| 453 | ] |
||
| 454 | }, |
||
| 455 | { |
||
| 456 | "cell_type": "markdown", |
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| 457 | "metadata": { |
||
| 458 | "slideshow": { |
||
| 459 | "slide_type": "subslide" |
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| 460 | } |
||
| 461 | }, |
||
| 462 | "source": [ |
||
| 463 | "<img src=\"figures/regressions/BDHyperplasia/lm-0.png\" />" |
||
| 464 | ] |
||
| 465 | }, |
||
| 466 | { |
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| 467 | "cell_type": "markdown", |
||
| 468 | "metadata": { |
||
| 469 | "slideshow": { |
||
| 470 | "slide_type": "subslide" |
||
| 471 | } |
||
| 472 | }, |
||
| 473 | "source": [ |
||
| 474 | "<img src=\"figures/regressions/PortalInflammation/lm-0.png\" />" |
||
| 475 | ] |
||
| 476 | }, |
||
| 477 | { |
||
| 478 | "cell_type": "markdown", |
||
| 479 | "metadata": { |
||
| 480 | "slideshow": { |
||
| 481 | "slide_type": "subslide" |
||
| 482 | } |
||
| 483 | }, |
||
| 484 | "source": [ |
||
| 485 | "<img src=\"figures/regressions/PortalInflammation/lm-1.png\" />" |
||
| 486 | ] |
||
| 487 | }, |
||
| 488 | { |
||
| 489 | "cell_type": "heading", |
||
| 490 | "level": 2, |
||
| 491 | "metadata": { |
||
| 492 | "slideshow": { |
||
| 493 | "slide_type": "slide" |
||
| 494 | } |
||
| 495 | }, |
||
| 496 | "source": [ |
||
| 497 | "Exploratory Analysis" |
||
| 498 | ] |
||
| 499 | }, |
||
| 500 | { |
||
| 501 | "cell_type": "markdown", |
||
| 502 | "metadata": {}, |
||
| 503 | "source": [ |
||
| 504 | "controlled for age / cohort" |
||
| 505 | ] |
||
| 506 | }, |
||
| 507 | { |
||
| 508 | "cell_type": "markdown", |
||
| 509 | "metadata": { |
||
| 510 | "slideshow": { |
||
| 511 | "slide_type": "subslide" |
||
| 512 | } |
||
| 513 | }, |
||
| 514 | "source": [ |
||
| 515 | "<img src=\"figures/regressions/PortalInflammation/mm_0.png\" />" |
||
| 516 | ] |
||
| 517 | }, |
||
| 518 | { |
||
| 519 | "cell_type": "markdown", |
||
| 520 | "metadata": { |
||
| 521 | "slideshow": { |
||
| 522 | "slide_type": "subslide" |
||
| 523 | } |
||
| 524 | }, |
||
| 525 | "source": [ |
||
| 526 | "<img src=\"figures/regressions/BDHyperplasia/mm_0.png\" />" |
||
| 527 | ] |
||
| 528 | }, |
||
| 529 | { |
||
| 530 | "cell_type": "markdown", |
||
| 531 | "metadata": { |
||
| 532 | "slideshow": { |
||
| 533 | "slide_type": "subslide" |
||
| 534 | } |
||
| 535 | }, |
||
| 536 | "source": [ |
||
| 537 | "<img src=\"figures/regressions/BDHyperplasia/mm_1.png\" />" |
||
| 538 | ] |
||
| 539 | }, |
||
| 540 | { |
||
| 541 | "cell_type": "markdown", |
||
| 542 | "metadata": { |
||
| 543 | "slideshow": { |
||
| 544 | "slide_type": "subslide" |
||
| 545 | } |
||
| 546 | }, |
||
| 547 | "source": [ |
||
| 548 | "<img src=\"figures/regressions/TawfikTotal/mm_0.png\" />" |
||
| 549 | ] |
||
| 550 | }, |
||
| 551 | { |
||
| 552 | "cell_type": "markdown", |
||
| 553 | "metadata": { |
||
| 554 | "slideshow": { |
||
| 555 | "slide_type": "subslide" |
||
| 556 | } |
||
| 557 | }, |
||
| 558 | "source": [ |
||
| 559 | "<img src=\"figures/regressions/Fibrosis/mm_0.png\" />" |
||
| 560 | ] |
||
| 561 | }, |
||
| 562 | { |
||
| 563 | "cell_type": "markdown", |
||
| 564 | "metadata": { |
||
| 565 | "slideshow": { |
||
| 566 | "slide_type": "subslide" |
||
| 567 | } |
||
| 568 | }, |
||
| 569 | "source": [ |
||
| 570 | "<img src=\"figures/regressions/Hindleg/mm_0.png\" />" |
||
| 571 | ] |
||
| 572 | }, |
||
| 573 | { |
||
| 574 | "cell_type": "markdown", |
||
| 575 | "metadata": { |
||
| 576 | "slideshow": { |
||
| 577 | "slide_type": "subslide" |
||
| 578 | } |
||
| 579 | }, |
||
| 580 | "source": [ |
||
| 581 | "<img src=\"figures/regressions/Weight/mm_0.png\" />" |
||
| 582 | ] |
||
| 583 | }, |
||
| 584 | { |
||
| 585 | "cell_type": "heading", |
||
| 586 | "level": 2, |
||
| 587 | "metadata": { |
||
| 588 | "slideshow": { |
||
| 589 | "slide_type": "slide" |
||
| 590 | } |
||
| 591 | }, |
||
| 592 | "source": [ |
||
| 593 | "Further analysis" |
||
| 594 | ] |
||
| 595 | }, |
||
| 596 | { |
||
| 597 | "cell_type": "markdown", |
||
| 598 | "metadata": {}, |
||
| 599 | "source": [ |
||
| 600 | "Age or cohort effect ?" |
||
| 601 | ] |
||
| 602 | }, |
||
| 603 | { |
||
| 604 | "cell_type": "markdown", |
||
| 605 | "metadata": { |
||
| 606 | "slideshow": { |
||
| 607 | "slide_type": "subslide" |
||
| 608 | } |
||
| 609 | }, |
||
| 610 | "source": [ |
||
| 611 | "<img src=\"figures/regressions/BDHyperplasia/new/mm_coefs_color_E.png\" width=85%/>" |
||
| 612 | ] |
||
| 613 | }, |
||
| 614 | { |
||
| 615 | "cell_type": "markdown", |
||
| 616 | "metadata": { |
||
| 617 | "slideshow": { |
||
| 618 | "slide_type": "subslide" |
||
| 619 | } |
||
| 620 | }, |
||
| 621 | "source": [ |
||
| 622 | "<img src=\"figures/regressions/BDHyperplasia/new/mm_coefs_color_CES.png\" width=85%/>" |
||
| 623 | ] |
||
| 624 | }, |
||
| 625 | { |
||
| 626 | "cell_type": "markdown", |
||
| 627 | "metadata": { |
||
| 628 | "slideshow": { |
||
| 629 | "slide_type": "subslide" |
||
| 630 | } |
||
| 631 | }, |
||
| 632 | "source": [ |
||
| 633 | "<img src=\"figures/regressions/BDHyperplasia/new/mm_coefs_color_RES.png\" width=85%/>" |
||
| 634 | ] |
||
| 635 | }, |
||
| 636 | { |
||
| 637 | "cell_type": "heading", |
||
| 638 | "level": 2, |
||
| 639 | "metadata": { |
||
| 640 | "slideshow": { |
||
| 641 | "slide_type": "slide" |
||
| 642 | } |
||
| 643 | }, |
||
| 644 | "source": [ |
||
| 645 | "Conclusions" |
||
| 646 | ] |
||
| 647 | }, |
||
| 648 | { |
||
| 649 | "cell_type": "markdown", |
||
| 650 | "metadata": {}, |
||
| 651 | "source": [ |
||
| 652 | "- our image measures capture **relevant** and **useful** information\n", |
||
| 653 | "- a number of correlations can be **explained** biologically\n", |
||
| 654 | "- underlying **structure** in the data needs thought\n", |
||
| 655 | "- still no **map** from image or histological measures to condition of individual" |
||
| 656 | ] |
||
| 657 | }, |
||
| 658 | { |
||
| 659 | "cell_type": "heading", |
||
| 660 | "level": 2, |
||
| 661 | "metadata": { |
||
| 662 | "slideshow": { |
||
| 663 | "slide_type": "slide" |
||
| 664 | } |
||
| 665 | }, |
||
| 666 | "source": [ |
||
| 667 | "Future directions" |
||
| 668 | ] |
||
| 669 | }, |
||
| 670 | { |
||
| 671 | "cell_type": "heading", |
||
| 672 | "level": 3, |
||
| 673 | "metadata": { |
||
| 674 | "slideshow": { |
||
| 675 | "slide_type": "subslide" |
||
| 676 | } |
||
| 677 | }, |
||
| 678 | "source": [ |
||
| 679 | "Further exploration of the dataset" |
||
| 680 | ] |
||
| 681 | }, |
||
| 682 | { |
||
| 683 | "cell_type": "markdown", |
||
| 684 | "metadata": {}, |
||
| 685 | "source": [ |
||
| 686 | "- 145 sheep ( 89 females )\n", |
||
| 687 | "- 12 age classes\n", |
||
| 688 | "- potential redundancy in various measures" |
||
| 689 | ] |
||
| 690 | }, |
||
| 691 | { |
||
| 692 | "cell_type": "markdown", |
||
| 693 | "metadata": {}, |
||
| 694 | "source": [ |
||
| 695 | "- 4460 entries across 31 variables\n", |
||
| 696 | "- 3596 with full image and histological information\n", |
||
| 697 | "- 1196 for which **complete** information is available" |
||
| 698 | ] |
||
| 699 | }, |
||
| 700 | { |
||
| 701 | "cell_type": "heading", |
||
| 702 | "level": 3, |
||
| 703 | "metadata": { |
||
| 704 | "slideshow": { |
||
| 705 | "slide_type": "subslide" |
||
| 706 | } |
||
| 707 | }, |
||
| 708 | "source": [ |
||
| 709 | "More data" |
||
| 710 | ] |
||
| 711 | }, |
||
| 712 | { |
||
| 713 | "cell_type": "markdown", |
||
| 714 | "metadata": {}, |
||
| 715 | "source": [ |
||
| 716 | "- nutritional information\n", |
||
| 717 | "- immunity data" |
||
| 718 | ] |
||
| 719 | }, |
||
| 720 | { |
||
| 721 | "cell_type": "heading", |
||
| 722 | "level": 3, |
||
| 723 | "metadata": { |
||
| 724 | "slideshow": { |
||
| 725 | "slide_type": "subslide" |
||
| 726 | } |
||
| 727 | }, |
||
| 728 | "source": [ |
||
| 729 | "Narrow-field images" |
||
| 730 | ] |
||
| 731 | }, |
||
| 732 | { |
||
| 733 | "cell_type": "markdown", |
||
| 734 | "metadata": {}, |
||
| 735 | "source": [ |
||
| 736 | "- 12536 images\n", |
||
| 737 | "- spatial distribution of nuclei" |
||
| 738 | ] |
||
| 739 | }, |
||
| 740 | { |
||
| 741 | "cell_type": "markdown", |
||
| 742 | "metadata": { |
||
| 743 | "slideshow": { |
||
| 744 | "slide_type": "subslide" |
||
| 745 | } |
||
| 746 | }, |
||
| 747 | "source": [ |
||
| 748 | "" |
||
| 749 | ] |
||
| 750 | }, |
||
| 751 | { |
||
| 752 | "cell_type": "markdown", |
||
| 753 | "metadata": { |
||
| 754 | "slideshow": { |
||
| 755 | "slide_type": "subslide" |
||
| 756 | } |
||
| 757 | }, |
||
| 758 | "source": [ |
||
| 759 | "" |
||
| 760 | ] |
||
| 761 | }, |
||
| 762 | { |
||
| 763 | "cell_type": "markdown", |
||
| 764 | "metadata": { |
||
| 765 | "slideshow": { |
||
| 766 | "slide_type": "subslide" |
||
| 767 | } |
||
| 768 | }, |
||
| 769 | "source": [ |
||
| 770 | "" |
||
| 771 | ] |
||
| 772 | }, |
||
| 773 | { |
||
| 774 | "cell_type": "markdown", |
||
| 775 | "metadata": { |
||
| 776 | "slideshow": { |
||
| 777 | "slide_type": "subslide" |
||
| 778 | } |
||
| 779 | }, |
||
| 780 | "source": [ |
||
| 781 | "<img src=\"figures/graphics/10x.png\" width=100%></src>" |
||
| 782 | ] |
||
| 783 | }, |
||
| 784 | { |
||
| 785 | "cell_type": "heading", |
||
| 786 | "level": 2, |
||
| 787 | "metadata": { |
||
| 788 | "slideshow": { |
||
| 789 | "slide_type": "slide" |
||
| 790 | } |
||
| 791 | }, |
||
| 792 | "source": [ |
||
| 793 | "With thanks to" |
||
| 794 | ] |
||
| 795 | }, |
||
| 796 | { |
||
| 797 | "cell_type": "markdown", |
||
| 798 | "metadata": {}, |
||
| 799 | "source": [ |
||
| 800 | "Romain Garnier\n", |
||
| 801 | "\n", |
||
| 802 | "Andrea Graham\n", |
||
| 803 | "\n", |
||
| 804 | "Tawfik Aboellail (CSU)\n", |
||
| 805 | "\n", |
||
| 806 | "Bryan Grenfell\n" |
||
| 807 | ] |
||
| 808 | } |
||
| 809 | ], |
||
| 810 | "metadata": {} |
||
| 811 | } |
||
| 812 | ] |
||
| 813 | } |