A tool to create 2D morphology collage plots based on matplotlib.
Project description
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 sonatacircuit_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, theatlas-path
parameter of the CLI corresponds to thepath
parameter of theatlas
section in the configuration file.
Outputs
This package contains three main functions:
get_layer_annotation
: can generate annotation of layers for plotting or other usescreate_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 formeratlas_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
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