I guess you create the example notebooks somehow automatically with sphinx? Because the descriptive text is written in html which mostly shows up well in the notebook, but the links to other skimage functions do show up weird/broken. I even don't know if it's possible or reasonable to fix that somehow for a locally downloaded notebook, but I just wanted to inform you in case you were not aware.

My example is for http://scikit-image.org/docs/dev/auto_examples/plot_blob.html

The way it's shown in my notebook (ipython 2.3) can be seen here:

https://www.dropbox.com/s/ptzoqfx22yhn5vu/Screenshot%202014-10-08%2017.54.48.pdf?dl=0

If you think it's worth a GH issue, just say the word and I create one.

Regards,

Michael