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bdpedigo avatar bdpedigo commented on June 26, 2024

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

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schlegelp avatar schlegelp commented on June 26, 2024

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. b7661e4) 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. This new release now supports (and requires) navis >= 1.0.0 which came with a couple renamed functions
  2. With this release the default max_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.

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bdpedigo avatar bdpedigo commented on June 26, 2024

Awesome, with that release this looks to be working now. Thanks for the help!

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