Tweaks to section titles. Moved info from optional modules over.

docs/installation.rst

@@ -1,8 +1,19 @@
 Installation
-------------
+====
 
-Installation with pip
-^^^^^^^^^^^^^^^^^^^^^
+.. contents:: Table of Contents
+   :depth: 1
+   :backlinks: none
+
+There are currently no required Pythom modules for the core Cell Browser script: ``cbBuild``. 
+Installation instructions for a variety of methods are below, with pip being the 
+recommended method.
+
+Basic installation
+----
+
+With pip (recommended)
+^^^^
 
 To install the Cell Browser using pip, you will need Python2.5+ or Python3+ and pip. With these setup, on a Mac or any Linux system, simply run::
 
@@ -20,45 +31,76 @@ On OSX, if running ``sudo pip`` outputs *command not found*, you will need to se
 
     sudo easy_install pip
 
-Installation with conda
-^^^^^^^^^^^^^^^^^^^^^^^
+With conda
+^^^^
 
 If you would prefer to install the Cell Browser through bioconda, you can run::
 
     conda install -c bioconda ucsc-cell-browser
     
-There should be conda versions for release 0.4.23 onwards. The conda version is managed by
-Pablo Moreno at the EBI and is often a few releases behind. Please indicate in any bug
+There should be conda versions for release 0.4.23 onwards. Please indicate in any bug
 reports if you used conda to install.
 
-Installation with git clone
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
+With git clone
+^^^^
 
 Pip is not required to install the Cell Browser. As an alternative to pip or conda, you can also git clone the repo and
 run the command line scripts under cellbrowser/src::
 
     git clone https://github.com/maximilianh/cellBrowser.git --depth=10
     cd cellBrowser/src
 
-Installation with just wget or curl
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+With wget or curl
+^^^^
 
 You don't use pip, conda or git? You can also download the current master branch::
 
     wget https://github.com/maximilianh/cellBrowser/archive/master.zip
     unzip master.zip
     cellBrowser-master/src/cbBuild
 
-Installation on Windows
-~~~~~~~~~~~~~~~~~~~~~~~
+Notes on Windows Installation
+^^^^
 
 First install the Windows Linux subsystem. 
 Then open the Windows Linux Subsystem bash terminal and run these commands::
 
     sudo apt-get update
     sudo apt-get install python-pip
-    sudo pip install cellbrowser.
+    sudo pip install cellbrowser
+
+Optional modules
+----
+
+To take advantage of some of the advanced features or specialized scripts
+such as ``cbScanpy`` or ``cbSeurat``, you will need to install some extra packages or tools. 
+
+Image sizes
+^^^^^^
+
+To get the image sizes, cbBuild uses either the "file" command or the "identify" command (for JPEGs). 
+You may have to install the ImageMagick package to get the identify command.
+
+Custom Colors
+^^^^
+
+In your cellbrowser.conf you can specify a file with custom colors
+for your metadata values. If this file contains HTML color names instead
+of color codes, you have to install the module webcolors::
+
+    pip install webcolors
+
+Matrices in mtx format
+^^^^^^
+
+To read expression matrices in .mtx format, you have to install scipy::
+
+    pip install scipy
+
+``cbScanpy`` and ``cbSeurat``
+^^^^^^
 
-Email cells@ucsc.edu for more info.
+``cbScanpy`` requires that Scanpy is `installed <https://scanpy.readthedocs.io/en/latest/installation.html>`_. 
 
+``cbSeurat`` requires that both R and `Seurat <https://satijalab.org/seurat/articles/install.html>`_ are installed .