Closed bdpedigo closed 2 years ago
Update - this does work:
neurons = pymaid.find_neurons(
annotations="Paper: Phelps, Hildebrand, Graham et al. 2020"
)
pymaid.adjacency_matrix(neurons)
so maybe specific to the get_connectors
function? Individual connectors aren't that important for me right now so I think this will work, but still curious about how to use that properly
Hi Ben! Your minimal example works for me. Best guess is that this is an issue with missing user data (that data is scrubbed for release on public CATMAID instances). I fixed a few bugs there a while ago (see e.g. b7661e4a1215c9995e3bc9329a9eda8b8872e5be) but haven't pushed a new release since.
With that said: I just released pymaid 2.1.0
which includes this fix. Let me know if that does it for you.
Two side notes:
1.0.0
which came with a couple renamed functionsmax_threads
for CatmaidInstance
went down from 100 to 10 to avoid connection warnings with the sometimes slower public CATMAID servers. If you server/internet connection supports that, you can of course go back up again.Awesome, with that release this looks to be working now. Thanks for the help!
Hi @schlegelp - currently having some trouble with trying to pull some connectivity data from the FANC dataset (which I believe is public and I should not need any credentials for?).
I created a fresh environment and re-installed latest pymaid.
Code I'm trying to run
Output
Any ideas right away as to what could be causing this, or am I using pymaid incorrectly? If nothing jumps out to you I'm happy to look into it further. Looks like something related to pymaid user so I'm guessing I am just not logged in properly or something?