Workflow used for synthesis and its validation.
Project description
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-workflowUsage
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> --helpYou 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]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-compareYou can get help and complete parameter description with the following command:
morph_validation --helpFunding & 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
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