neurocollage 0.3.6

A tool to create 2D morphology collage plots based on matplotlib.

NeuroCollage

A tool to create 2D morphology collage plots based on matplotlib.

Installation

It is recommended to install NeuroCollage using pip:

pip install neurocollage

Usage

This package provides only one command that aims at building figures of morphologies in atlas planes (i.e. collage plots).

Inputs

The collage requires the following inputs:

• the path to a standard CircuitConfig, or the path to a sonata circuit_config.json file of a SONATA circuit and the path to an Atlas directory that can be read by Voxcell.
• [optional] a configuration file containing the default values used for the CLI arguments (all these values are overridden by the ones passed to the CLI). The config file is a INI file divided in sections. These sections correspond to the first part of the CLI parameter names. For example, the atlas-path parameter of the CLI corresponds to the path parameter of the atlas section in the configuration file.

Outputs

This package contains three main functions:

• get_layer_annotation: can generate annotation of layers for plotting or other uses
• create_planes: defines a set of planes to create collage plots, with various algorithms. Planes are sampled along a centerline, which can be straight aligned or not with world coordinates or curved using an algorithm from former atlas_analysis package. The first and last point of the centerline can be defined manually, or estimated internally to span the given region best.
• plot_collage: make the collage plot, see API for possible arguments.

Command

This package provides a CLI whose parameters are described in the Command Line Interface page of this documentation. It is also possible to get help from the command:

neuro-collage --help

If all the arguments are provided in the configuration file, the command is just:

neuro-collage -c <config-file>

Any argument from the configuration file can be overridden through the CLI:

neuro-collage -c <config-file> --cells-sample 20 --collage-pdf-filename custom_collage_name.pdf

Note that the parameter names of the CLI use the section in the configuration file as prefix. In the previous example, the --cells-sample overrides the sample parameter of the cells section of the configuration file.

Examples

The examples folder contains a simple example on S1 region of SSCx with L5_TPC:A morphologies. It also provides examples of programmatic use of the NeuroCollage API with both types of circuit formats.

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