You’ve encountered a problem? See if you can find it in below table. If not, please get in touch via issues on Github.




Fetching data

Fetching any data throws an exception <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate very failed>.

Have a look at this blog post.


3D plots with VisPy as backend use only one quarter of the canvas.

Try installing the developer version from GitHub ( As one-liner:

git clone && cd vispy && python install --user

3D plots using Plotly are too small and all I can see is a chunk of legend.

Sometimes plotly does not scale the plot correctly. The solution is to play around with the width parameter:

fig = navis.plot3d(neurons, backend='plotly', width=1200)

Opening a vispy 3D viewer, throws a long list of errors ending with something like this:

RuntimeError: Error while fetching file
Dataset fetching aborted (<urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:847)>)

For reasons beyond me, vispy does not include the font to render text so it has to download it on first use. If this fails with an SSL error, do the following once:

import navis
import ssl
ssl._create_default_https_context = ssl._create_unverified_context
v = navis.Viewer()

This temporarily disables SSL verification to allow download of the font. I recommend restarting the Python session afterwards!


Instead of a progress bar, I get some odd message (e.g. Hbox(children=...) when using pymaid in a Jupyter notebook.

You probably have ipywidgets not installed or not configured properly. One work-around is to force pymaid to use standard progress bars using pymaid.set_pbars():