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Synthesize neuron with a simple diameter modelΒΆ
This example shows how to synthesize a cell with one of the simple provided diameter models.
25 import json
26 from pathlib import Path
27
28 import neurots
29 from neurots import extract_input
30
31
32 def run(output_dir, data_dir):
33 """Run the example for generating a cell with a simple diameter model."""
34 # Extract distributions with diameters
35 distr = extract_input.distributions(
36 data_dir / "neurons", feature="path_distances", diameter_model="M5"
37 )
38
39 # Load default parameters dictionary
40 with open(data_dir / "bio_params.json", "r", encoding="utf-8") as F:
41 params = json.load(F)
42
43 # Set the diameter method
44 params["diameter_params"]["method"] = "M5"
45
46 # Initialize a neuron
47 N = neurots.NeuronGrower(input_distributions=distr, input_parameters=params)
48
49 # Grow the neuron
50 neuron = N.grow()
51
52 # Export the synthesized cell
53 neuron.write(output_dir / "generated_cell.asc")
54 neuron.write(output_dir / "generated_cell.swc")
55 neuron.write(output_dir / "generated_cell.h5")
56
57
58 if __name__ == "__main__":
59 result_dir = Path("results_neuron_with_diameters")
60 result_dir.mkdir(parents=True, exist_ok=True)
61
62 run(result_dir, Path("data"))