Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Brainrender: a python-based software for visualizing anatomically registered data

View ORCID ProfileF. Claudi, View ORCID ProfileA. L. Tyson, View ORCID ProfileL. Petrucco, View ORCID ProfileT.W. Margrie, View ORCID ProfileR. Portugues, T. Branco
doi: https://doi.org/10.1101/2020.02.23.961748
F. Claudi
1UCL Sainsbury Wellcome Centre, London, U.K.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for F. Claudi
  • For correspondence: federico.claudi.17@ucl.ac.uk
A. L. Tyson
1UCL Sainsbury Wellcome Centre, London, U.K.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for A. L. Tyson
L. Petrucco
2Institute of Neuroscience, Technical University of Munich, Munich, Germany
3Max Planck Institute of Neurobiology, ResearchGroup of Sensorimotor Control, Martinsried, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for L. Petrucco
T.W. Margrie
1UCL Sainsbury Wellcome Centre, London, U.K.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for T.W. Margrie
R. Portugues
2Institute of Neuroscience, Technical University of Munich, Munich, Germany
3Max Planck Institute of Neurobiology, ResearchGroup of Sensorimotor Control, Martinsried, Germany
4Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for R. Portugues
T. Branco
1UCL Sainsbury Wellcome Centre, London, U.K.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

Abstract

The recent development of high-resolution three-dimensional (3D) digital brain atlases and high-throughput brain wide imaging techniques has fueled the generation of large datasets that can be registered to a common reference frame. This registration facilitates integrating data from different sources and resolutions to assemble rich multidimensional datasets. Generating insights from these new types of datasets depends critically on the ability to easily visualize and explore the data in an interactive manner. This is, however, a challenging task. Currently available software is dedicated to single atlases, model species or data types, and generating 3D renderings that merge anatomically registered data from diverse sources requires extensive development and programming skills. To address this challenge, we have developed brainrender: a generic, open-source Python package for simultaneous and interactive visualization of multidimensional datasets registered to brain atlases. Brainrender has been designed to facilitate the creation of complex custom renderings and can be used programmatically or through a graphical user interface. It can easily render different data types in the same visualization, including user-generated data, and enables seamless use of different brain atlases using the same code base. In addition, brainrender generates high-quality visualizations that can be used interactively and exported as high-resolution figures and animated videos. By facilitating the visualization of anatomically registered data, brainrender should accelerate the analysis, interpretation, and dissemination of brain-wide multidimensional data.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Updated manuscript to describe the new brainrender 2.0. In particular the integration between brainrender and brainglobe's AtlasAPI is described in detail

  • https://github.com/brainglobe/brainrender

  • https://figshare.com/articles/media/Claudi_et_al_2020_-_Brainrender_videos/13359785

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted December 11, 2020.
Download PDF
Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Brainrender: a python-based software for visualizing anatomically registered data
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Brainrender: a python-based software for visualizing anatomically registered data
F. Claudi, A. L. Tyson, L. Petrucco, T.W. Margrie, R. Portugues, T. Branco
bioRxiv 2020.02.23.961748; doi: https://doi.org/10.1101/2020.02.23.961748
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Brainrender: a python-based software for visualizing anatomically registered data
F. Claudi, A. L. Tyson, L. Petrucco, T.W. Margrie, R. Portugues, T. Branco
bioRxiv 2020.02.23.961748; doi: https://doi.org/10.1101/2020.02.23.961748

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Neuroscience
Subject Areas
All Articles
  • Animal Behavior and Cognition (3514)
  • Biochemistry (7371)
  • Bioengineering (5347)
  • Bioinformatics (20329)
  • Biophysics (10048)
  • Cancer Biology (7781)
  • Cell Biology (11353)
  • Clinical Trials (138)
  • Developmental Biology (6454)
  • Ecology (9985)
  • Epidemiology (2065)
  • Evolutionary Biology (13361)
  • Genetics (9377)
  • Genomics (12616)
  • Immunology (7729)
  • Microbiology (19119)
  • Molecular Biology (7478)
  • Neuroscience (41163)
  • Paleontology (301)
  • Pathology (1235)
  • Pharmacology and Toxicology (2142)
  • Physiology (3183)
  • Plant Biology (6885)
  • Scientific Communication and Education (1276)
  • Synthetic Biology (1900)
  • Systems Biology (5329)
  • Zoology (1091)