Axon Synthesis¶

A package to synthesize artificial axons.

The main documentation, is available here: https://axon-synthesis.readthedocs.io

Installation¶

It is recommended to install axon-synthesis using pip:

pip install axon-synthesis

Examples¶

An example can be found in the examples directory. This example contains a small input dataset and a run.sh script that will execute the code. The inputs can be reviewed and modified for testing.

Citation¶

When you use the axon-synthesis software or method for your research, we ask you to cite the publication associated to this repository (use the Cite this repository button on the main page of the code).

Funding & Acknowledgment¶

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

For license and authors, see LICENSE.txt and AUTHORS.md respectively.

Workflows¶

The axon-synthesis tool contains 2 main workflows:

one to create and format the inputs required to actually synthesizing long-range axons.
one to synthesize the long-range axons.

Create inputs workflow¶

digraph {
"Atlas" -> "Brain region masks";
"White Matter Recipe" -> "Probabilities";
"Morphologies" -> "Clustering";
"Clustering" -> "Tuft properties";
"Clustering" -> "Main trunk properties";
"Tuft properties" -> "Synthesis inputs"
"Main trunk properties" -> "Synthesis inputs"
"Brain region masks" -> "Synthesis inputs"
"Probabilities" -> "Synthesis inputs"
}

Synthesize axons workflow¶

digraph {
"Inputs" -> "Source points";
"Inputs" -> "Target points";
"Source points" -> "3D graph";
"Target points" -> "3D graph";
"3D graph" -> "Steiner tree";
"Steiner tree" -> "Main trunk";
"Inputs" -> "Tufts";
"Main trunk" -> "Tufts";
"Tufts" -> "Morphology";
}

See the CLI page for details on how to run each workflow.