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suny-downstate-medical-center / netpyne

A Python package to facilitate the development, parallel simulation, optimization and analysis of multiscale biological neuronal networks in NEURON.
http://www.netpyne.org
MIT License
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Correct dimension for basket cell & OLM in CA3 example? #802

Closed pgleeson closed 2 months ago

pgleeson commented 7 months ago

The CA3 example network looks like a great one to highlight more on OSB (https://github.com/suny-downstate-medical-center/netpyne/tree/development/examples/CA3model_3pops), but the dimensions of the basket (white) and olm cells (green), compared to the more normal looking ca3 pyr cell (purple). Is this intentional @salvadord @vvbragin, i.e. have these cells been given larger dims to compensate for no dends etc? I've reduced the numbers of cells in the network for clarity.

Screenshot 2023-12-15 at 11 46 06
salvadord commented 5 months ago

@urdapile can you have a look at this? I think you implemented this model right?

urdapile commented 5 months ago

yes, sure.

El mié, 24 ene 2024 a las 11:48, Salvador Dura-Bernal (< @.***>) escribió:

@urdapile https://github.com/urdapile can you have a look at this? I think you implemented this model right?

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urdapile commented 5 months ago

@pgleeson @salvadord, the model is the NetPyNE replication of the NEURON model developed by Sam Neymotin et al (https://doi.org/10.1523/JNEUROSCI.0501-11.2011), available at ModelDB (https://modeldb.science/139421). In this model, I don't know the reason, the inhibitory cells were assigned an area of 10000 um2 (diam=sqrt(area), L = diam/pi). I tried reduced dimensions, but the basket cells develop unrealistic voltage traces (no spikes, highly depolarized, probably blocked) and E/I balance get lost. Connectivity weights and external stimulation should be tuned for new dimensions. However, if we reduce ONLY the diameter, the impact is very mild. I tried simulations with diam = 10 and L = 31.831 and look fine (the rhythms seem a bit more disorganized). For visualization, this could be more appealing.

salvadord commented 2 months ago

ok, so @pgleeson for OSB visualization we can have a version with the smaller diameter (diam=10).