Merge pull request #518 from juanchopanza/notebook-tutorial-summit16

Update jupyter tutorial notebook.

Author: juanchopanza

ipynb/tutorial.ipynb

@@ -15,25 +15,30 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "source": [
     "<h2>1. Installation</h2>\n",
-    "NeuroM is supported for Linux and OS X. Windows users are advised to use [VirtualBox](https://www.virtualbox.org/)\n",
+    "[NeuroM](http://neurom.readthedocs.io/en/latest/index.html) is supported for Linux and OS X. Windows users are advised to use [VirtualBox](https://www.virtualbox.org/)\n",
     "\n",
     "It is assumed that the following packages are installed on your system:\n",
     "\n",
-    "* Python 2.7\n",
-    "* numpy >= 1.8.0\n",
-    "* scipy >= 0.13.3\n",
-    "* h5py >= 2.2.1 (optional)\n",
-    "* matplotlib >= 1.3.1\n",
+    "* Python >= 2.7\n",
+    "* pip >= 8.1.0\n",
     "* ipython\n",
-    "* pip\n",
     "* virtualenv\n",
-    "* git\n",
     "\n",
     "These are available as packages in most Linux distributions. For OS X, please refer to [MacPorts](http://www.macports.org/) if you don’t already use a different package manager.\n",
     "\n",
+    "The following packages will be installed automatically with NeuroM if not pre-installed in your system.\n",
+    "* numpy >= 1.8.0\n",
+    "* scipy >= 0.17.0\n",
+    "* h5py >= 2.2.1 (optional)\n",
+    "* matplotlib >= 1.3.1\n",
+    "* pyyaml >= 3.10\n",
+    "\n",
+    "\n",
     "<h3> 1.1 Virtualenv set-up </h3>\n",
     "\n",
     "<code>\n",
@@ -63,25 +68,27 @@
     "\n",
     "<h3>2.1 Check the validity of a morphology file </h3>\n",
     "\n",
-    "The application \"morph_check\" allows you to apply semantic checks to a morphology file before loading it into NeuroM.\n",
+    "The application [morph_check](http://neurom.readthedocs.io/en/latest/morph_check.html) allows you to apply semantic checks to a morphology file before loading it into NeuroM.\n",
     "\n",
     "<code>\n",
-    "(nrm)$ morph_check -h                       # shows help for the script to check a morphology\n",
+    "(nrm)$ morph_check -h  # shows help for morphology checking script\n",
     "</code>\n",
     "\n",
     "Try it yourself! You can go to [NeuroMorpho](http://neuromorpho.org) to download a neuronal morphology and perform the semantic checks.\n",
     "\n",
     "<code>\n",
-    "(nrm)$ morph_check  path/to/file/filename\n",
+    "(nrm)$ morph_check  path/to/files/filename\n",
     "<code>\n",
     "\n",
     "<h3>2.2 Extract basic morphometrics of a sample morphology </h3>\n",
     "\n",
-    "Let's start by running an example of basic measurement extraction:\n",
+    "The application [morph_stats](http://neurom.readthedocs.io/en/latest/morph_stats.html) extracts various morphometrics for one or many morphologies.\n",
+    "Its contents can be easily configured via a configuration file, as shown in the [online documentation](http://neurom.readthedocs.io/en/latest/morph_stats.html)\n",
     "\n",
     "<code>\n",
-    "(nrm)$ cd NeuroM\n",
-    "(nrm)$ ./examples/get_features.py\n",
+    "(nrm)$ morph_stats -h  # shows help for the morphometrics extraction script\n",
+    "(nrm)$ morph_stats path/to/files/filename # analyze single morphology file\n",
+    "(nrm)$ morph_stats path/to/files          # analyze many morphology files\n",
     "</code>\n",
     "\n",
     "<h3>2.3 Basic morphometrics with the neurom and neurom.viewer modules</h3>\n",