Change README to markdown

README.rst → README.md

-===============================
 mito
-===============================
-
-
-.. https://img.shields.io/pypi/v/mito.svg
-        :target: https://pypi.python.org/pypi/mito
-
-.. https://img.shields.io/travis/keithschulze/mito.svg
-        :target: https://travis-ci.org/keithschulze/mito
-
-.. https://readthedocs.org/projects/mito/badge/?version=latest
-        :target: https://mito.readthedocs.io/en/latest/?badge=latest
-        :alt: Documentation Status
-
+====
 
 Tools for analysing mitochondrial distribution in fluoresence microscopy images
 
@@ -28,18 +15,16 @@ is quite nested.
 Installation
 ------------
 
-..code-block:: bash
-
-  pip install -U numpy
-  pip install --process-dependency-links -e https://gitlab.erc.monash.edu.au/skeith/mito.git
-
+```
+pip install -U numpy
+pip install --process-dependency-links -e https://gitlab.erc.monash.edu.au/skeith/mito.git
+```
 
 To use the notebook:
 
-..code-block:: bash
-
-  pip install -U jupyter
-
+```
+pip install -U jupyter
+```
 
 Features
 --------
@@ -57,18 +42,18 @@ Full examples showing how to run the analysis are in the `mito_analysis.ipynb` n
 
 Imports:
 
-..code-block:: python
+```python
 
   # For mito analysis functions and routines
   from mito import mito
 
   # For plotting functions
   from mito import plot
-
+```
 
 Calculate R90%:
 
-..code-block:: python
+```python
 
   import javabridge
   import bioformats
@@ -80,13 +65,13 @@ Calculate R90%:
   output_dir = "/path/to/output_dir"
 
   r90 = process_r90(img_path, treatment="Mock", time="8h", output_dir=output_dir)
-
+```
 
 Credits
 ---------
 
-This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
+This package was created with [Cookiecutter][cc] and the [audreyr/cookiecutter-pypackage][aud] project template.
 
-.. _Cookiecutter: https://github.com/audreyr/cookiecutter
-.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
+[cc]: https://github.com/audreyr/cookiecutter
+[aud]: https://github.com/audreyr/cookiecutter-pypackage