synthesis-workflow 1.2.3

Workflow used for synthesis and its validation.

This project contains several workflows used for neuron synthesis and the validation of this process. It is divided into two packages:

• synthesis-workflow, which contains the workflow tasks and tools.

• MorphVal, which is a library used for morphology validation and can be used as a standalone.

Installation

To install:

pip install synthesis-workflow

Usage

Synthesis workflow

The usual command is the following:

synthesis-workflow <workflow>

You can get help and complete parameter description with the following commands:

synthesis-workflow --help
synthesis-workflow <workflow> --help

You can also run a complete luigi command in order to fine-control task parameters:

luigi --module synthesis_workflow.tasks.workflows --help
luigi --module synthesis_workflow.tasks.workflows <workflow> --help
luigi --module synthesis_workflow.tasks.workflows <workflow> [specific arguments]

Note

The synthesis-workflow command (or the complete luigi command) must be executed from a directory containing a luigi.cfg file. A simple example of such file is given in the examples directory.

Morphology validation

The usual command is the following:

morph-validation -t <path to reference data> -r <path to test data> -o <output path> -c <YAML config file> --bio-compare

You can get help and complete parameter description with the following command:

morph-validation --help

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.

Copyright (c) 2022-2024 Blue Brain Project/EPFL