--- a
+++ b/talk/Untitled0.ipynb
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+  "name": "",
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+ },
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+ "worksheets": [
+  {
+   "cells": [
+    {
+     "cell_type": "heading",
+     "level": 1,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "slide"
+      }
+     },
+     "source": [
+      "Robust Extraction of Quantitative Information from Histology Images"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "**Quentin Caudron**"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "slide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/graphics/soay.jpg\" />"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/population3.png\" width=1200px/>"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/graphics/lit1.jpg\" />"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "fragment"
+      }
+     },
+     "source": [
+      "<img src=\"figures/graphics/lit2.jpg\" />"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "fragment"
+      }
+     },
+     "source": [
+      "<img src=\"figures/graphics/lit4.jpg\" />"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "slide"
+      }
+     },
+     "source": [
+      "Outline"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "- Methods and data collection\n",
+      "- Image processing\n",
+      "- Extracted measures\n",
+      "- Preliminary analysis\n",
+      "- Future directions"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "slide"
+      }
+     },
+     "source": [
+      "Data"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "**In the field, winter of 2011 - 2012 :**\n",
+      "    \n",
+      "- Daily study area monitoring for deaths\n",
+      "- 143 liver samples collected within a day of death"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "fragment"
+      }
+     },
+     "source": [
+      "<br />**In the lab :**\n",
+      "\n",
+      "- Sectioning after paraffin treatment\n",
+      "- H&E staining of about 1000 slides"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "fragment"
+      }
+     },
+     "source": [
+      "<br />**Analysis :**\n",
+      "\n",
+      "- Pathology standard : semi-quantitative scoring\n",
+      "- Image processing"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "The Field"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Sweat-and-blood-collected in cold, cold Scotland."
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "fragment"
+      }
+     },
+     "source": [
+      "Eight physical measurements :\n",
+      "- Age at death\n",
+      "- Weight\n",
+      "- Sex\n",
+      "- Limb length\n",
+      "- Environmental \"stress\""
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "Clinical Pathology"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "-"
+      }
+     },
+     "source": [
+      "Operator-driven visual analysis of 98 slides under microscopy."
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "fragment"
+      }
+     },
+     "source": [
+      "Eleven discrete and continuous measures :\n",
+      "\n",
+      "- Inflammation\n",
+      "- Necrosis\n",
+      "- Apoptosis\n",
+      "- Hyperplasia\n",
+      "- Fibrosis\n",
+      "- Hepatitis"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "Image Processing"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Automated analysis of 4430 images of slides representing 143 sheep."
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "fragment"
+      }
+     },
+     "source": [
+      "Seven structural and textural measures with varying levels of biological interpretation :\n",
+      "\n",
+      "- Inflammation\n",
+      "- Hyperplasia / tissue density\n",
+      "- Best-guess proxies for \"generic degeneration\""
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "slide"
+      }
+     },
+     "source": [
+      "Image Processing"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/graphics/sheep.jpg\"></img>"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/graphics/processed.jpg\"></img>"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "The Challenge"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "-"
+      }
+     },
+     "source": [
+      "**Information extraction must be**\n",
+      "- automagical - no operator input\n",
+      "- reasonably quick - restricted computing time\n",
+      "- robust - invariant to slicing, staining, field-related variation \n",
+      "- unbiased - same algorithms for everyone"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "![image](figures/graphics/robust3.jpg)"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "![image](figures/graphics/robust4.jpg)"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "![image](figures/graphics/robust1.jpg)"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "![image](figures/graphics/robust2.jpg)"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "slide"
+      }
+     },
+     "source": [
+      "Structural and Textural Measures"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "- characteristic **scale** of sinusoid widths\n",
+      "- **directional** amplitude of preferred sinusoid alignment\n",
+      "- **tissue to sinusoid** ratio\n",
+      "- **count** of inflammatory foci per image\n",
+      "- **mean size** of inflammatory foci per image\n",
+      "- information **entropy** of sinusoid distribution\n",
+      "- **lacunarity** ( clustering ) of sinusoids"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/graphics/gif.gif\"></img>"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/graphics/intra3.png\" width=100%/>"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/graphics/inter3.png\"/>"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "slide"
+      }
+     },
+     "source": [
+      "Exploratory Analysis"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "by individual"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/regressions/BDHyperplasia/lm-0.png\" />"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/regressions/PortalInflammation/lm-0.png\" />"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/regressions/PortalInflammation/lm-1.png\" />"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "slide"
+      }
+     },
+     "source": [
+      "Exploratory Analysis"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "controlled for age / cohort"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/regressions/PortalInflammation/mm_0.png\" />"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/regressions/BDHyperplasia/mm_0.png\" />"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/regressions/BDHyperplasia/mm_1.png\" />"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/regressions/TawfikTotal/mm_0.png\" />"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/regressions/Fibrosis/mm_0.png\" />"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/regressions/Hindleg/mm_0.png\" />"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/regressions/Weight/mm_0.png\" />"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "slide"
+      }
+     },
+     "source": [
+      "Further analysis"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Age or cohort effect ?"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/regressions/BDHyperplasia/new/mm_coefs_color_E.png\" width=85%/>"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/regressions/BDHyperplasia/new/mm_coefs_color_CES.png\" width=85%/>"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/regressions/BDHyperplasia/new/mm_coefs_color_RES.png\" width=85%/>"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "slide"
+      }
+     },
+     "source": [
+      "Conclusions"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "- our image measures capture **relevant** and **useful** information\n",
+      "- a number of correlations can be **explained** biologically\n",
+      "- underlying **structure** in the data needs thought\n",
+      "- still no **map** from image or histological measures to condition of individual"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "slide"
+      }
+     },
+     "source": [
+      "Future directions"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "Further exploration of the dataset"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "- 145 sheep ( 89 females )\n",
+      "- 12 age classes\n",
+      "- potential redundancy in various measures"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "- 4460 entries across 31 variables\n",
+      "- 3596 with full image and histological information\n",
+      "- 1196 for which **complete** information is available"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "More data"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "- nutritional information\n",
+      "- immunity data"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "Narrow-field images"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "- 12536 images\n",
+      "- spatial distribution of nuclei"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "![image](figures/graphics/10.jpg)"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "![image](figures/graphics/Processed2.jpg)"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "![image](figures/graphics/Segmented.jpg)"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "<img src=\"figures/graphics/10x.png\" width=100%></src>"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {
+      "slideshow": {
+       "slide_type": "slide"
+      }
+     },
+     "source": [
+      "With thanks to"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Romain Garnier\n",
+      "\n",
+      "Andrea Graham\n",
+      "\n",
+      "Tawfik Aboellail (CSU)\n",
+      "\n",
+      "Bryan Grenfell\n"
+     ]
+    }
+   ],
+   "metadata": {}
+  }
+ ]
+}
\ No newline at end of file