Convert example documentation to markdown

[martinitus]

Currently the readme files in the example directory are written in rich text format. Maybe it would be better to have that in markdown. then they can easily be read online via github.

[stephenlenzi]

okay - I will upload these later today

[martinitus]

I updated the rtf files in pr #19. However, at the moment files that are referenced in the documentation are missing in the repo:

• the ilastik project
• the tif images for cell population
• the tif images for subcellular example

We need to upload these files somewhere and provide a link to them in the documentation. Optimal would be to update the notebooks to automatically download the files if they are not available in the notebook directory.

@fjohenning Does the schmitz lab have an official website where we could host this data for the public? The just create a tar.bz2 archive from the three files and upload it there! An alternative solution would be a Dropbox link, but thats not really guaranteed to remain valid :-/

[martinitus]

@stephenlenzi @fjohenning please review the changes in the doc/example/notebooks directory!
Dont forget to change the branch on github website (top left: master -> markdown-documentation)

[martinitus]

todo: integrate notebook documentation on samuroi.readthedocs.org using sphinx notebook tool

[stephenlenzi]

the changes look good to me.
a few things I should probably do:

todo: ensure all paths are relative
todo: remove %matplotlib inline as the manual corrections require a pop-out/interactive matplotlib widget
todo: all comments as text cells