brainrender

A Python package to visualise neuroanatomical data in atlas space

https://github.com/brainglobe/brainrender

Science Score: 67.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 7 DOI reference(s) in README
○
Academic publication links
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Committers with academic emails
3 of 20 committers (15.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (13.0%) to scientific vocabulary

Keywords

anatomy neuroscience python visualization

Keywords from Contributors

microscopy atlases brain registration visualisation image-analysis cell-detection imaging neuroanatomy animal

Last synced: 4 months ago · JSON representation ·

Repository

A Python package to visualise neuroanatomical data in atlas space

Basic Info

Host: GitHub
Owner: brainglobe
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://brainglobe.info/documentation/brainrender/index.html
Size: 271 MB

Statistics

Stars: 590
Watchers: 16
Forks: 90
Open Issues: 11
Releases: 21

Topics

anatomy neuroscience python visualization

Created over 6 years ago · Last pushed 6 months ago

Metadata Files

Readme License Citation

brainrender

A user-friendly python library to create high-quality, 3D neuro-anatomical renderings combining data from publicly available brain atlases with user-generated experimental data.

Example gallery

From: Claudi et al. (2021) Visualizing anatomically registered data with brainrender. eLife

Documentation

brainrender is a project of the BrainGlobe Initiative, which is a collaborative effort to develop a suite of Python-based software tools for computational neuroanatomy. A comprehensive online documentation for brainrender can be found on the BrainGlobe website here.

Furthermore, an open-access journal article describing BrainRender has been published in eLife, available here.

Installation

From PyPI:

pip install brainrender

Quickstart

``` python import random

import numpy as np

from brainrender import Scene from brainrender.actors import Points

def getnrandompointsin_region(region, N): """ Gets N random points inside (or on the surface) of a mesh """

region_bounds = region.mesh.bounds()
X = np.random.randint(region_bounds[0], region_bounds[1], size=10000)
Y = np.random.randint(region_bounds[2], region_bounds[3], size=10000)
Z = np.random.randint(region_bounds[4], region_bounds[5], size=10000)
pts = [[x, y, z] for x, y, z in zip(X, Y, Z)]

ipts = region.mesh.inside_points(pts).coordinates
return np.vstack(random.choices(ipts, k=N))

Display the Allen Brain mouse atlas.

scene = Scene(atlasname="allenmouse_25um", title="Cells in primary visual cortex")

Display a brain region

primaryvisual = scene.addbrain_region("VISp", alpha=0.2)

Get a numpy array with (fake) coordinates of some labelled cells

coordinates = getnrandompointsinregion(primaryvisual, 2000)

Create a Points actor

cells = Points(coordinates)

Add to scene

scene.add(cells)

Add label to the brain region

scene.addlabel(primaryvisual, "Primary visual cortex")

Display the figure.

scene.render()

```

Seeking help or contributing

We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the contact page of our website.

Citing brainrender

If you use brainrender in your scientific work, please cite: Claudi, F., Tyson, A. L., Petrucco, L., Margrie, T.W., Portugues, R., Branco, T. (2021) "Visualizing anatomically registered data with Brainrender" <i>eLife</i> 2021;10:e65751 [doi.org/10.7554/eLife.65751](https://doi.org/10.7554/eLife.65751)

BibTeX:

``` bibtex @article{Claudi2021, author = {Claudi, Federico and Tyson, Adam L. and Petrucco, Luigi and Margrie, Troy W. and Portugues, Ruben and Branco, Tiago}, doi = {10.7554/eLife.65751}, issn = {2050084X}, journal = {eLife}, pages = {1--16}, pmid = {33739286}, title = {{Visualizing anatomically registered data with brainrender}}, volume = {10}, year = {2021} }

```

Owner

Name: BrainGlobe
Login: brainglobe
Kind: organization
Location: London/Munich

Website: https://brainglobe.info/
Twitter: brain_globe
Repositories: 28
Profile: https://github.com/brainglobe

Open python tools for morphological analyses in systems neuroscience

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: brainrender
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Federico
    family-names: Claudi
  - given-names: Adam
    family-names: Tyson
    email: hello@brainglobe.info
  - given-names: Luigi
    family-names: Petrucco
  - given-names: BrainGlobe
    family-names: Developers
    email: hello@brainglobe.info
repository-code: 'https://github.com/brainglobe/brainrender'
url: 'https://brainglobe.info'
abstract: >-
  Visualisation and exploration of brain atlases and other
  anatomical data.
license: BSD-3-Clause
date-released: '2024-01-25'
year: 2024
preferred-citation:
  type: article
  title: "Visualizing anatomically registered data with brainrender"
  authors:
  - given-names: Federico
    family-names: Claudi
  - given-names: Adam
    family-names: Tyson
  - given-names: Luigi
    family-names: Petrucco
  - given-names: Troy W.
    family-names: Margrie
  - given-names: Ruben
    family-names: Portugues
  - given-names: Tiago
    family-names: Branco
  year: 2021
  month: 3
  doi: 10.7554/eLife.65751
  url: https://doi.org/10.7554/eLife.65751
  journal: eLife
  volume: 10
  issn: "2050-084X"
  pages: e65761

GitHub Events

Total

Create event: 20
Release event: 3
Issues event: 24
Watch event: 42
Delete event: 17
Issue comment event: 79
Push event: 29
Pull request review event: 23
Pull request review comment event: 3
Pull request event: 45
Fork event: 13

Last Year

Create event: 20
Release event: 3
Issues event: 24
Watch event: 42
Delete event: 17
Issue comment event: 79
Push event: 29
Pull request review event: 23
Pull request review comment event: 3
Pull request event: 45
Fork event: 13

Committers

Last synced: about 2 years ago

All Time

Total Commits: 801
Total Committers: 20
Avg Commits per committer: 40.05
Development Distribution Score (DDS): 0.316

Past Year

Commits: 10
Committers: 6
Avg Commits per committer: 1.667
Development Distribution Score (DDS): 0.7

Top Committers

Name	Email	Commits
FedeClaudi	f**i@p**m	548
federico claudi	f**i@g**m	163
Adam Tyson	a**n@u**k	38
federico claudi	f**i@f**l	23
Roberto DF	3****F	5
pre-commit-ci[bot]	6****]	3
Rob Campbell	g**t@r**m	3
mcol	m**l@p**t	2
Luigi Petrucco	l**o@g**m	2
Paul Brodersen	p**n@g**m	2
federico claudi	f**i@e**k	2
Adam Tyson	c**e@a**m	2
Ben Dichter	b**r@g**m	1
Carter Peene	r**e@g**m	1
marcomusy	m**y@g**m	1
federico claudi	f**i@e**k	1
Sebastian Lammers	3****s	1
Sean Martin	m**7@t**e	1
carlocastoldi	3****i	1
4iar	4****r	1

Committer Domains (Top 20 + Academic)

tcd.ie: 1 eduroam-int-dhcp-97-33-104.ucl.ac.uk: 1 adamltyson.com: 1 eduroam-int-dhcp-97-182-110.ucl.ac.uk: 1 posteo.net: 1 raacampbell.com: 1 ucl.ac.uk: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 153
Total pull requests: 147
Average time to close issues: 3 months
Average time to close pull requests: 4 days
Total issue authors: 83
Total pull request authors: 21
Average comments per issue: 4.2
Average comments per pull request: 1.52
Merged pull requests: 134
Bot issues: 0
Bot pull requests: 36

Past Year

Issues: 15
Pull requests: 40
Average time to close issues: 19 days
Average time to close pull requests: 4 days
Issue authors: 10
Pull request authors: 6
Average comments per issue: 2.47
Average comments per pull request: 1.28
Merged pull requests: 36
Bot issues: 0
Bot pull requests: 18

View more stats

Top Authors

Issue Authors

adamltyson (18)
alessandrofelder (16)
IgorTatarnikov (5)
FedeClaudi (4)
RobertoDF (4)
horsto (3)
orena1 (3)
harshk95 (3)
mkunst23 (3)
vigji (2)
GuillaumeLeGoc (2)
janfpl (2)
Eddymorphling (2)
mabbasi6 (2)
MathieuBo (2)

Pull Request Authors

adamltyson (52)
pre-commit-ci[bot] (46)
IgorTatarnikov (38)
alessandrofelder (19)
willGraham01 (10)
FedeClaudi (9)
RobertoDF (5)
carlocastoldi (4)
paulbrodersen (4)
lochhh (2)
jingjie-li (2)
GuillaumeLeGoc (2)
K-Meech (2)
Spkap (2)
seblammers (1)

Top Labels

Issue Labels

bug (84) enhancement (37) help wanted (2) good first issue (2) Volumetric data (2) GUI (1) question (1) documentation (1)

Pull Request Labels

Packages

Total packages: 2
Total downloads:
- pypi 1,635 last-month

Total dependent packages: 6
(may contain duplicates)
Total dependent repositories: 5
(may contain duplicates)
Total versions: 113
Total maintainers: 2

pypi.org: brainrender

Visualisation and exploration of brain atlases and other anatomical data

Homepage: https://brainglobe.info/
Documentation: https://brainglobe.info/documentation/brainrender/index.html
License: BSD-3-Clause
Latest release: 2.1.17
published 10 months ago

Versions: 95
Dependent Packages: 6
Dependent Repositories: 5
Downloads: 1,635 Last month

Rankings

Dependent packages count: 2.4%

Average: 5.1%

Downloads: 6.5%

Dependent repos count: 6.6%

Maintainers (2)

fede123 alessandrofelder

Last synced: 5 months ago

proxy.golang.org: github.com/brainglobe/brainrender

Documentation: https://pkg.go.dev/github.com/brainglobe/brainrender#section-documentation
License: bsd-3-clause
Latest release: v2.1.17+incompatible
published 10 months ago

Versions: 18
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 9.0%

Average: 9.6%

Dependent repos count: 10.2%

Last synced: 4 months ago

brainrender

Science Score: 67.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

brainrender

Documentation

Installation

Quickstart

Display the Allen Brain mouse atlas.

Display a brain region

Get a numpy array with (fake) coordinates of some labelled cells

Create a Points actor

Add to scene

Add label to the brain region

Display the figure.

Seeking help or contributing

Citing brainrender

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: brainrender

Rankings

Maintainers (2)

proxy.golang.org: github.com/brainglobe/brainrender

Rankings