<commit_before>{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<h1 align=\"center\">Focused Ion Beam Scanning Electron Microscopy Image Segmentation</h1>\n",
    "\n",
    "\n",
    "**Summary:**\n",
    "1. SimpleITK supports a large number of filters that facilitate classical segmentation algorithms (variety of thresholding algorithms, watersheds...).\n",
    "2. Once your data is segmented SimpleITK enables you to efficiently post process the segmentation (e.g. label distinct objects, analyze object shapes).\n",
    "\n",
    "This notebook will illustrate the use of SimpleITK for segmentation of bacteria from a 3D Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) image. The specific bacterium is <a href=\"https://en.wikipedia.org/wiki/Bacillus_subtilis\">bacillus subtilis</a>, a rod shaped organism naturally found in soil and plants. The bacteria have been subjected to stress to initiate the process of forming an endospore. These endospores can be seen as a generally dark ellipsoid inside the individual bacterium. \n",
    "\n",
    "Data provided courtesy of the [Laboratory of Cell Biology](https://electron.nci.nih.gov/), Center for Cancer Research, National Cancer Institute, National Institutes of Health."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import SimpleITK as sitk\n",
    "import pandas as pd\n",
    "\n",
    "%matplotlib notebook\n",
    "\n",
    "import matplotlib.pyplot as plt\n",
    "import gui\n",
    "from math import ceil\n",
    "\n",
    "%run update_path_to_download_script\n",<commit_msg>Removed lab link which no longer exists.<commit_after>{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<h1 align=\"center\">Focused Ion Beam Scanning Electron Microscopy Image Segmentation</h1>\n",
    "\n",
    "\n",
    "**Summary:**\n",
    "1. SimpleITK supports a large number of filters that facilitate classical segmentation algorithms (variety of thresholding algorithms, watersheds...).\n",
    "2. Once your data is segmented SimpleITK enables you to efficiently post process the segmentation (e.g. label distinct objects, analyze object shapes).\n",
    "\n",
    "This notebook will illustrate the use of SimpleITK for segmentation of bacteria from a 3D Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) image. The specific bacterium is <a href=\"https://en.wikipedia.org/wiki/Bacillus_subtilis\">bacillus subtilis</a>, a rod shaped organism naturally found in soil and plants. The bacteria have been subjected to stress to initiate the process of forming an endospore. These endospores can be seen as a generally dark ellipsoid inside the individual bacterium. \n",
    "\n",
    "Data provided courtesy of the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import SimpleITK as sitk\n",
    "import pandas as pd\n",
    "\n",
    "%matplotlib notebook\n",
    "\n",
    "import matplotlib.pyplot as plt\n",
    "import gui\n",
    "from math import ceil\n",
    "\n",
    "%run update_path_to_download_script\n",
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