3. Helpful tips

Check the Jupyter notebooks for useful examples

load.py

If you want to inspect a network you can use load.pyto get some extra information.

To display neuron names and positions:

Snudda/examples$ python3 ../snudda/utils/load.py networks/test-200/network-synapses.hdf5 --listN
Loading 200 neurons with 24269 synapses and 8 gap junctions
Neurons in network: 
0 : dSPN_0  (x: 0.003538, y: 0.004620, z: 0.005022)
1 : iSPN_0  (x: 0.003548, y: 0.004616, z: 0.005041)
2 : iSPN_3  (x: 0.003554, y: 0.004626, z: 0.005055)
3 : iSPN_3  (x: 0.003555, y: 0.004640, z: 0.005048)```
...

To list the presynaptic neurons to neuron 0:

python3 ../snudda/utils/load.py networks/test-200/network-synapses.hdf5 --listPre 0
Loading 200 neurons with 24269 synapses and 8 gap junctions
List neurons pre-synaptic to neuronID = 0 (dSPN_0)
5 : dSPN_0 (4 synapses)
7 : iSPN_3 (4 synapses)
11 : dSPN_3 (3 synapses)
20 : iSPN_1 (4 synapses)
21 : iSPN_1 (2 synapses)
...

To list postsynaptic neurons to neuron 0:

python3 ../snudda/utils/load.py networks/test-200/network-synapses.hdf5 --listPost 0
Loading 200 neurons with 24269 synapses and 8 gap junctions
List neurons post-synaptic to neuronID = 0 (dSPN_0)
11 : dSPN_3 (3 synapses)
16 : dSPN_2 (3 synapses)
38 : iSPN_0 (3 synapses)
94 : iSPN_1 (3 synapses)
146 : dSPN_2 (2 synapses)

neuron_morphology.py

You can also use neuron_morphology.py to inspect a neuron and show the section ID and section X:

$ python3 ../snudda/neurons/neuron_morphology.py ../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20210212/morphology/21-6-DE-cor-rep-ax-res3.swc  --step 10