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.

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.

Scientific methodology for synthesis¶

The Synthesis methodology page contains detailed documentation of the methodology on which this package is based.

Workflows¶

The package synthesis_workflow contains many tasks that are organized in workflows. The two main workflows are the following:

tasks.workflows.ValidateVacuumSynthesis: this workflow generates cells in vacuum (e.g. with no atlas information) and compute some simple validation features.
tasks.workflows.ValidateSynthesis: this workflow generates cells in a given atlas and compute many validation features.

All workflows need configuration files. Some examples are given in Configuration files.

More details on these workflows and their tasks can be found in the API Reference.

API Reference¶

The API Reference page contains detailed documentation of:

Note

tasks appears as a package in this documentation but it is actually a subpackage of the synthesis_workflow package.