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Open Source Science

https://github.com/bluebrain/neurocollage

https://github.com/bluebrain/neurocollage

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 3 committers (66.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.8%) to scientific vocabulary

Keywords from Contributors

neuron interactive projection morphology generic sequences archival embedded genomics observability
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: BlueBrain
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Size: 639 KB
Statistics
  • Stars: 1
  • Watchers: 3
  • Forks: 1
  • Open Issues: 1
  • Releases: 2
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License Authors

README.md

NeuroCollage

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

Installation

It is recommended to install NeuroCollage using pip:

bash 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:

bash neuro-collage --help

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

bash neuro-collage -c <config-file>

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

bash 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

Owner

  • Name: The Blue Brain Project
  • Login: BlueBrain
  • Kind: organization
  • Email: bbp.opensource@epfl.ch
  • Location: Geneva, Switzerland

Open Source Software produced and used by the Blue Brain Project

GitHub Events

Total
  • Release event: 2
  • Watch event: 1
  • Delete event: 6
  • Push event: 9
  • Public event: 1
  • Pull request event: 14
  • Fork event: 1
  • Create event: 9
Last Year
  • Release event: 2
  • Watch event: 1
  • Delete event: 6
  • Push event: 9
  • Public event: 1
  • Pull request event: 14
  • Fork event: 1
  • Create event: 9

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 81
  • Total Committers: 3
  • Avg Commits per committer: 27.0
  • Development Distribution Score (DDS): 0.494
Past Year
  • Commits: 17
  • Committers: 3
  • Avg Commits per committer: 5.667
  • Development Distribution Score (DDS): 0.412
Top Committers
Name Email Commits
Adrien Berchet a****t@e****h 41
Alexis Arnaudon a****n@e****h 38
dependabot[bot] 4****] 2
Committer Domains (Top 20 + Academic)
epfl.ch: 2

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 15
  • Average time to close issues: N/A
  • Average time to close pull requests: about 21 hours
  • Total issue authors: 0
  • Total pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 6
Past Year
  • Issues: 0
  • Pull requests: 15
  • Average time to close issues: N/A
  • Average time to close pull requests: about 21 hours
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 6
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • dependabot[bot] (6)
  • adrien-berchet (5)
  • arnaudon (4)
Top Labels
Issue Labels
Pull Request Labels
dependencies (6) github_actions (3)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 25 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 3
pypi.org: neurocollage

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

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 25 Last month
Rankings
Dependent packages count: 10.1%
Average: 33.4%
Dependent repos count: 56.6%
Maintainers (3)
bbp.opensource adrien-berchet obi.maintainer
Last synced: 11 months ago

Dependencies

.github/workflows/commitlint.yml actions
  • actions/checkout v4 composite
  • actions/setup-node v4 composite
.github/workflows/publish-sdist.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/run-tox.yml actions
  • actions/cache v4 composite
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • actions/upload-artifact v4 composite
  • awalsh128/cache-apt-pkgs-action latest composite
  • codecov/codecov-action v4 composite
  • mikepenz/action-junit-report v5 composite
package.json npm
pyproject.toml pypi
setup.py pypi