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navis-org / navis

Python library for analysis of neuroanatomical data.
https://navis-org.github.io/navis/
GNU General Public License v3.0
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split_axon_dendrite fails for big neurons #123

Open katie-marquand opened 1 year ago

katie-marquand commented 1 year ago

If the neuron has too many synapses the geodesic distance matrix can't be initialised because it takes too much memory.

schlegelp commented 12 months ago

Sorry for taking so long. I'm afraid I don't have an immediate fix for this but in the future we should be able to implement something in navis-fastcore that will solve this.

schlegelp commented 10 months ago

Another quick update: I had a crack at this but implemented in rust as part of an experiment in fastcore-rs.

With that I can calculate the synapse flow (which is what failed previously) in ~30s for the hemibrain APL:

Screenshot 2024-01-16 at 12 12 19

(Brighter = higher synapse flow)

Making an axon-dendrite split based off that currently still needs a bit of tinkering to get to work but if I cut some corners, we get something that doesn't look half bad:

Screenshot 2024-01-16 at 14 31 40

(dark blue = dendrites; cyan = axon)

I always assumed the APL simply goes calyx (CA) -> peduncle -> lobes but if that skeleton is topologically correct, then the CA + peduncle are actually isolated from the lobes and it's actually CA + peduncle -> lobes.