Colab demo notebook - Githubissues

lhilbert commented 4 years ago

Hi, very naively trying to get the demos to run in a Colab notebook...my first notebook :-/

This is as far as I got...it seems the demo files are run, but it doesn't manage to import all that's needed.

https://gist.github.com/lhilbert/2de0ee7b8ef3885a19c8c4f0265397da

VolkerH commented 4 years ago

you also need to install the ssi package itself. I did that with python setup.py install from the cloned folder into my conda environment, not quite sure how it works in colab.

VolkerH commented 4 years ago

Just gave this a try .. there are a few things you need to do:

from your ssi-code folder run !python setup.py install
if that is successful you can run the demos from that folder (if you cd into the demo folder your paths won't be correct), i.e. !python ssi/demo/demo2D.py.
Note that this will run the network, but crash on the displaying the results as you cannot run napari from colab. You will have to change the lines that visualize the results to use matplotlib (or similar) or write the results to your gdrive (see for example my modified version here (not tested on colab)

Note that I just happen to be playing with this code at the same time as you and am not connected to the project.

royerlab / ssi-code

Colab demo notebook #20