--- a
+++ b/talk/DiseaseGroup.py
@@ -0,0 +1,388 @@
+# -*- coding: utf-8 -*-
+# <nbformat>3.0</nbformat>
+
+# <codecell>
+
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+import seaborn
+from matplotlib import rcParams
+rcParams["figure.figsize"] = (14, 8)
+rcParams["xtick.labelsize"] = 12
+rcParams["ytick.labelsize"] = 12
+rcParams["font.size"] = 14
+rcParams["axes.titlesize"] = 16
+#rcParams["text.usetex"] = False
+rcParams["font.family"] = "Serif"
+rcParams["figure.dpi"] = 600
+
+
+a = pd.read_csv("../data/villagebay_population.csv")
+b = pd.read_csv("../data/exposure.csv")
+
+fig, (ax, ax2) = plt.subplots(2, 1, sharex=True)
+
+#ax = plt.subplot(211)
+ax.plot(a.Year, a.VillageBay, c=seaborn.color_palette("deep", 8)[0], lw=3)
+ax.scatter(a.Year, a.VillageBay, c=seaborn.color_palette("deep", 8)[0], s=50)
+ax.set_title("Village Bay Population")
+ax.set_ylim([180, 700])
+
+
+#ax2 = plt.subplot(212, sharex=ax)
+
+ax2.plot(b.BirthYear, b.AvgOfLambWS, c=seaborn.color_palette("deep", 8)[2], lw=3)
+ax2.scatter(b.BirthYear, b.AvgOfLambWS, c=seaborn.color_palette("deep", 8)[2], s=50)
+ax2.set_title("Lamb Winter Survival")
+ax2.set_xlim([1984.5, 2013.5])
+ax2.set_ylim([0, 0.8])
+
+plt.savefig("figures/population2.jpg", dpi=300, jpeg_quality=100)
+
+# <headingcell level=1>
+
+# Robust Extraction of Quantitative Information from Histology Images
+
+# <headingcell level=4>
+
+# Quentin Caudron
+
+# <headingcell level=2>
+
+# The Soay Sheep
+
+# <markdowncell>
+
+# <img src="figures/graphics/soay.jpg" />
+
+# <markdowncell>
+
+# <img src="figures/graphics/population2.jpg" />
+
+# <markdowncell>
+
+# <img src="figures/graphics/lit1.jpg" />
+
+# <markdowncell>
+
+# <img src="figures/graphics/lit2.jpg" />
+
+# <markdowncell>
+
+# <img src="figures/graphics/lit4.jpg" />
+
+# <headingcell level=2>
+
+# Outline
+
+# <markdowncell>
+
+# - Methods and data collection
+# - Image processing
+# - Extracted measures
+# - Preliminary analysis
+# - Future directions
+
+# <headingcell level=2>
+
+# Data
+
+# <markdowncell>
+
+# **In the field, winter of 2011 - 2012 :**
+#     
+# - Daily study area monitoring for deaths
+# - 143 liver samples collected within a day of death
+
+# <markdowncell>
+
+# **In the lab :**
+# 
+# - Sectioning after paraffin treatment
+# - H&E staining of about 1000 slides
+
+# <markdowncell>
+
+# **Analysis :**
+# 
+# - Pathology standard : semi-quantitative scoring
+# - Image processing
+
+# <headingcell level=3>
+
+# The Field &copy;
+
+# <markdowncell>
+
+# Sweat-and-blood-collected in cold, cold Scotland.
+
+# <markdowncell>
+
+# Eight physical measurements :
+# - Age at death
+# - Weight
+# - Sex
+# - Limb length
+# - Environmental "stress"
+
+# <headingcell level=3>
+
+# Clinical Pathology
+
+# <markdowncell>
+
+# Operator-driven visual analysis of 98 slides under microscopy.
+
+# <markdowncell>
+
+# Eleven discrete and continuous measures :
+# 
+# - Inflammation
+# - Necrosis
+# - Apoptosis
+# - Hyperplasia
+# - Fibrosis
+# - Hepatitis
+
+# <headingcell level=3>
+
+# Image Processing
+
+# <markdowncell>
+
+# Automated analysis of 4430 images of slides representing 143 sheep.
+
+# <markdowncell>
+
+# Seven structural and textural measures with varying levels of biological interpretation :
+# 
+# - Inflammation
+# - Hyperplasia / tissue density
+# - Best-guess proxies for "generic degeneration"
+
+# <headingcell level=2>
+
+# Image Processing
+
+# <markdowncell>
+
+# <img src="figures/graphics/sheep.jpg"></img>
+
+# <markdowncell>
+
+# <img src="figures/graphics/processed.jpg"></img>
+
+# <headingcell level=3>
+
+# The Challenge
+
+# <markdowncell>
+
+# **Information extraction must be**
+# - automagical - no operator input
+# - reasonably quick - restricted computing time
+# - robust - invariant to slicing, staining, field-related variation 
+# - unbiased - same algorithms for everyone
+
+# <markdowncell>
+
+# ![image](figures/graphics/robust3.jpg)
+
+# <markdowncell>
+
+# ![image](figures/graphics/robust4.jpg)
+
+# <markdowncell>
+
+# ![image](figures/graphics/robust1.jpg)
+
+# <markdowncell>
+
+# ![image](figures/graphics/robust2.jpg)
+
+# <markdowncell>
+
+# <img src="figures/graphics/gif.gif"></img>
+
+# <headingcell level=2>
+
+# Structural and Textural Measures
+
+# <markdowncell>
+
+# - characteristic **scale** of sinusoid widths
+# - **directional** amplitude of preferred sinusoid alignment
+# - **tissue to sinusoid** ratio
+# - **count** of inflammatory foci per image
+# - **mean size** of inflammatory foci per image
+# - information **entropy** of sinusoid distribution
+# - **lacunarity** ( clustering ) of sinusoids
+
+# <markdowncell>
+
+# ![image](figures/graphics/intra.png)
+
+# <markdowncell>
+
+# ![image](figures/graphics/inter2.png)
+
+# <headingcell level=2>
+
+# Exploratory Analysis
+
+# <headingcell level=3>
+
+# by individual
+
+# <markdowncell>
+
+# <img src="figures/regressions/BDHyperplasia/lm-0.png" />
+
+# <markdowncell>
+
+# <img src="figures/regressions/PortalInflammation/lm-0.png" />
+
+# <markdowncell>
+
+# <img src="figures/regressions/PortalInflammation/lm-1.png" />
+
+# <headingcell level=2>
+
+# Exploratory Analysis
+
+# <headingcell level=3>
+
+# controlled for age / cohort
+
+# <markdowncell>
+
+# <img src="figures/regressions/PortalInflammation/mm_0.png" />
+
+# <markdowncell>
+
+# <img src="figures/regressions/BDHyperplasia/mm_0.png" />
+
+# <markdowncell>
+
+# <img src="figures/regressions/BDHyperplasia/mm_1.png" />
+
+# <markdowncell>
+
+# <img src="figures/regressions/TawfikTotal/mm_0.png" />
+
+# <markdowncell>
+
+# <img src="figures/regressions/Fibrosis/mm_0.png" />
+
+# <markdowncell>
+
+# <img src="figures/regressions/PortalInflammation/mm_0.png" />
+
+# <markdowncell>
+
+# <img src="figures/regressions/Hindleg/mm_0.png" />
+
+# <markdowncell>
+
+# <img src="figures/regressions/Weight/mm_0.png" />
+
+# <headingcell level=2>
+
+# Further analysis
+
+# <headingcell level=3>
+
+# Age or cohort effect ?
+
+# <markdowncell>
+
+# <img src="figures/regressions/BDHyperplasia/mm_coefs_color_E.png" />
+
+# <markdowncell>
+
+# <img src="figures/regressions/BDHyperplasia/mm_coefs_color_CES.png" />
+
+# <markdowncell>
+
+# <img src="figures/regressions/BDHyperplasia/mm_coefs_color_RES.png" />
+
+# <headingcell level=2>
+
+# Conclusions
+
+# <markdowncell>
+
+# - our image measures capture **relevant** and **useful** information
+# - a number of correlations can be **explained** biologically
+# - underlying **structure** in the data needs thought
+# - still no **map** from image or histological measures to condition of individual
+
+# <headingcell level=2>
+
+# Future directions
+
+# <headingcell level=3>
+
+# Further exploration of the dataset
+
+# <markdowncell>
+
+# - 145 sheep ( 89 females )
+# - 12 age classes
+# - potential redundancy in various measures
+
+# <markdowncell>
+
+# - 4460 entries across 27 variables
+# - 3330 with full image and histological information
+# - 1196 for which **complete** information is available
+
+# <headingcell level=3>
+
+# More data
+
+# <markdowncell>
+
+# - nutritional information
+# - immunity data
+
+# <headingcell level=3>
+
+# Narrow-field images
+
+# <markdowncell>
+
+# - 12536 images
+# - spatial distribution of nuclei
+
+# <markdowncell>
+
+# ![image](figures/graphics/10.jpg)
+
+# <markdowncell>
+
+# ![image](figures/graphics/Processed2.jpg)
+
+# <markdowncell>
+
+# ![image](figures/graphics/Segmented.jpg)
+
+# <markdowncell>
+
+# <img src="figures/graphics/10x.png" width=100%></src>
+
+# <headingcell level=2>
+
+# With thanks to
+
+# <markdowncell>
+
+# Romain Garnier
+# 
+# Andrea Graham
+# 
+# Tawfik Aboellail (CSU)
+# 
+# Bryan Grenfell
+