Comments (3)
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
from pymaid.
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:
- This new release now supports (and requires) navis >=
1.0.0
which came with a couple renamed functions - With this release the default
max_threads
forCatmaidInstance
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.
from pymaid.
Awesome, with that release this looks to be working now. Thanks for the help!
from pymaid.
Related Issues (20)
- KeyError: 13 when using 'get_connectors_between' HOT 7
- pymaid.connectivity.cable_overlap raises KeyError exception HOT 2
- get_connectors raises AttributeError when there are no synapses of requested relation_type HOT 1
- navis.cable_overlap on axon/dendrite fragments - non-unique neuron ID problem? HOT 4
- requests.exceptions.ConnectionError: HOT 11
- Unable to fetch data from Platynereis Dataset HOT 5
- Leaked Semaphore Objects when running Navis.cut_skeleton HOT 1
- Using regex for exact matches misbehaves for special characters
- Docs broken
- get_skids_by_name with empty list
- Pymaid seems incompatible with numpy 1.24.0 HOT 3
- Paginate get_entity_graph response as it's very slow HOT 1
- get_volume uses mesh IDs, not volume IDs
- Neuron label logic HOT 2
- Fetching image data from N5 sources HOT 2
- Plotting multi-group neurons with distinct Colors for Axons, Dendrites, and Soma HOT 2
- Exporting skeletons as object files HOT 3
- pymaid.get_annotation_details fails with exception HOT 4
- connection to server reset by peer during get_neuron call HOT 5
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from pymaid.