Warning
The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization. Future development will take place at: https://github.com/openbraininstitute/synthesis-workflow
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.
To install:
pip install 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.
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
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