# Region Grower
Synthesize neuronal morphologies in a given spatial context provided by an atlas.
## Introduction
This package provides a general tools to synthesize cells in a given spatial context (a brain Atlas)
with embarrassingly parallel computation (with distributed computing via dask-mpi).
This package is difficult to use on its own, as it requires several specific inputs from atlas and
synthesis. It is advised to use it via [synthesis-workflow](https://github.com/BlueBrain/synthesis-workflow),
which is a workflow generating most of the inputs of region-grower.
## Installation
This package should be installed using pip:
```bash
pip install region-grower
```
## Usage
This package provides one main command which provides several tools.
Two tools to generate input parameters and input distributions and another to synthesize the cells.
### Generate distributions
Generate the TMD distribution file:
```bash
region-grower generate-distributions --help
```
#### Input data
The command ``region-grower generate-distributions`` needs the following inputs:
* a folder containing the cells which are used to generate the parameters (see the ``input_folder`` and ``--ext`` parameters).
* a ``dat`` file (see the ``dat_file`` parameter) with 3 columns:
* morphology names,
* any integer value (this column is not used by ``region-grower``)
* mtypes.
* optionally a ``JSON`` file containing the specific parameters used for diametrization (see the ``--diametrizer-config`` parameter).
#### Output data
The command ``region-grower generate-distributions`` will create the following outputs:
* a ``JSON`` file containing the formatted distributions (see the ``--parameter-filename`` parameter).
### Generate parameters
Generate the TMD parameter file:
```bash
region-grower generate-parameters --help
```
#### Input data
The command ``region-grower generate-parameters`` needs the following inputs:
* a folder containing the cells which are used to generate the parameters (see the ``input_folder`` and ``--ext`` parameters).
* a ``dat`` file (see the ``dat_file`` parameter) with 3 columns:
* morphology names,
* any integer value (this column is not used by ``region-grower``)
* mtypes.
* optionally a ``JSON`` file containing the specific parameters used for diametrization (see the ``--diametrizer-config`` parameter).
#### Output data
The command ``region-grower generate-parameters`` will create the following outputs:
* a ``JSON`` file containing the formatted parameters (see the ``--parameter-filename`` parameter).
### Synthesize cells
Synthesize morphologies into an given atlas according to the given TMD parameters and distributions:
```bash
region-grower synthesize-morphologies --help
```
#### Input data
The command ``region-grower synthesize-morphologies`` needs the following inputs:
* a ``sonata`` file containing the positions of the cells that must be synthesized.
* a ``JSON`` file containing the parameters used to synthesize the cells (see the ``--tmd-parameters`` parameter). This file should follow the schema given in :ref:`Parameters`.
* a ``JSON`` file containing the distributions used to synthesize the cells (see the ``--tmd-distributions`` parameter). This file should follow the schema given in :ref:`Parameters`.
* a ``TSV`` file giving which morphology should be used for axon grafting and the optional scaling factor (see the ``--morph-axon`` parameter). The morphologies referenced in this file should exist in the directory given with the ``--base-morph-dir`` parameter.
* a directory containing an Atlas.
#### Output data
The command ``region-grower synthesize-morphologies`` will create the following outputs:
* a ``sonata`` file containing all the positions and orientations of the synthesized cells (see ``--out-cells`` parameter).
* a directory containing all the synthesized morphologies (see ``--out-morph-dir`` and ``--out-morph-ext`` parameters).
* a ``YAML`` file containing the apical point positions (see ``--out-apical`` parameter).
* a ``YAML`` file containing the Neuron IDs of the sections containing the apical points (see ``--out-apical-nrn-sections`` parameter).
## 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
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"description": "# Region Grower\n\nSynthesize neuronal morphologies in a given spatial context provided by an atlas.\n\n\n## Introduction\n\nThis package provides a general tools to synthesize cells in a given spatial context (a brain Atlas)\nwith embarrassingly parallel computation (with distributed computing via dask-mpi).\nThis package is difficult to use on its own, as it requires several specific inputs from atlas and\nsynthesis. It is advised to use it via [synthesis-workflow](https://github.com/BlueBrain/synthesis-workflow),\nwhich is a workflow generating most of the inputs of region-grower.\n\n\n## Installation\n\nThis package should be installed using pip:\n\n```bash\npip install region-grower\n```\n\n\n## Usage\n\nThis package provides one main command which provides several tools.\nTwo tools to generate input parameters and input distributions and another to synthesize the cells.\n\n### Generate distributions\n\nGenerate the TMD distribution file:\n\n```bash\nregion-grower generate-distributions --help\n```\n\n#### Input data\n\nThe command ``region-grower generate-distributions`` needs the following inputs:\n\n* a folder containing the cells which are used to generate the parameters (see the ``input_folder`` and ``--ext`` parameters).\n* a ``dat`` file (see the ``dat_file`` parameter) with 3 columns:\n\t* morphology names,\n\t* any integer value (this column is not used by ``region-grower``)\n\t* mtypes.\n* optionally a ``JSON`` file containing the specific parameters used for diametrization (see the ``--diametrizer-config`` parameter).\n\n#### Output data\n\nThe command ``region-grower generate-distributions`` will create the following outputs:\n\n* a ``JSON`` file containing the formatted distributions (see the ``--parameter-filename`` parameter).\n\n### Generate parameters\n\nGenerate the TMD parameter file:\n\n```bash\nregion-grower generate-parameters --help\n```\n\n#### Input data\n\nThe command ``region-grower generate-parameters`` needs the following inputs:\n\n* a folder containing the cells which are used to generate the parameters (see the ``input_folder`` and ``--ext`` parameters).\n* a ``dat`` file (see the ``dat_file`` parameter) with 3 columns:\n\t* morphology names,\n\t* any integer value (this column is not used by ``region-grower``)\n\t* mtypes.\n* optionally a ``JSON`` file containing the specific parameters used for diametrization (see the ``--diametrizer-config`` parameter).\n\n#### Output data\n\nThe command ``region-grower generate-parameters`` will create the following outputs:\n\n* a ``JSON`` file containing the formatted parameters (see the ``--parameter-filename`` parameter).\n\n### Synthesize cells\n\nSynthesize morphologies into an given atlas according to the given TMD parameters and distributions:\n\n```bash\nregion-grower synthesize-morphologies --help\n```\n\n#### Input data\n\nThe command ``region-grower synthesize-morphologies`` needs the following inputs:\n\n* a ``sonata`` file containing the positions of the cells that must be synthesized.\n* a ``JSON`` file containing the parameters used to synthesize the cells (see the ``--tmd-parameters`` parameter). This file should follow the schema given in :ref:`Parameters`.\n* a ``JSON`` file containing the distributions used to synthesize the cells (see the ``--tmd-distributions`` parameter). This file should follow the schema given in :ref:`Parameters`.\n* a ``TSV`` file giving which morphology should be used for axon grafting and the optional scaling factor (see the ``--morph-axon`` parameter). The morphologies referenced in this file should exist in the directory given with the ``--base-morph-dir`` parameter.\n* a directory containing an Atlas.\n\n#### Output data\n\nThe command ``region-grower synthesize-morphologies`` will create the following outputs:\n\n* a ``sonata`` file containing all the positions and orientations of the synthesized cells (see ``--out-cells`` parameter).\n* a directory containing all the synthesized morphologies (see ``--out-morph-dir`` and ``--out-morph-ext`` parameters).\n* a ``YAML`` file containing the apical point positions (see ``--out-apical`` parameter).\n* a ``YAML`` file containing the Neuron IDs of the sections containing the apical points (see ``--out-apical-nrn-sections`` parameter).\n\n## Funding & Acknowledgment\n\nThe development of this software was supported by funding to the Blue Brain Project,\na research center of the \u00c9cole polytechnique f\u00e9d\u00e9rale de Lausanne (EPFL),\nfrom the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.\n\nCopyright (c) 2022-2024 Blue Brain Project/EPFL\n",
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