Histological E-data registration in rodent brain spaces

  1. Jingyi Guo Fuglstad  Is a corresponding author
  2. Pearl Saldanha
  3. Jacopo Paglia
  4. Jonathan R Whitlock  Is a corresponding author
  1. Norwegian University of Science and Technology, Norway

Abstract

Recording technologies for rodents have seen huge advances in the last decade, allowing users to sample thousands of neurons simultaneously from multiple brain regions. This has prompted the need for digital tool kits to aid in curating anatomical data, however, existing tools either provide limited functionalities or require users to be proficient in coding to use them. To address this we created HERBS (Histological E-data Registration in rodent Brain Spaces), a comprehensive new tool for rodent users that offers a broad range of functionalities through a user-friendly graphical user interface. Prior to experiments, HERBS can be used to plan coordinates for implanting electrodes, targeting viral injections or tracers. After experiments, users can register recording electrode locations (e.g. Neuropixels, tetrodes), viral expression or other anatomical features, and visualize the results in 2D or 3D. Additionally, HERBS can delineate labeling from multiple injections across tissue sections and obtain individual cell counts.Regional delineations in HERBS are based either on annotated 3D volumes from the Waxholm Space Atlas of the Sprague Dawley Rat Brain or the Allen Mouse Brain Atlas, though HERBS can work with compatible volume atlases from any species users wish to install. HERBS allows users to scroll through the digital brain atlases and provides custom-angle slice cuts through the volumes, and supports free-transformation of tissue sections to atlas slices. Furthermore, HERBS allows users to reconstruct a 3D brain mesh with tissue from individual animals. HERBS is a multi-platform open-source Python package that is available on PyPI and GitHub, and is compatible with Windows, macOS and Linux operating systems.

Data availability

The software described in this manuscript is an open-source software written completely in Python 3.8.HERBS is fully supported by Windows, macOS and Linux. Source code, HERBS Cookbook and documentation are available on the Whitlock group Github page: https://github.com/Whitlock-Group/HERBS .The Waxholm Space rat brain atlas files can be found here from the NITRC website: https://www.nitrc.org/projects/whs-sd-atlas.The Allen Mouse Brain Atlas software and wiki are freely available at: https://github.com/cortex-lab/allenCCF.

Article and author information

Author details

  1. Jingyi Guo Fuglstad

    Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
    For correspondence
    jingyi.guo@ntnu.no
    Competing interests
    The authors declare that no competing interests exist.
  2. Pearl Saldanha

    Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6749-8240
  3. Jacopo Paglia

    Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
    Competing interests
    The authors declare that no competing interests exist.
  4. Jonathan R Whitlock

    Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
    For correspondence
    jonathan.whitlock@ntnu.no
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2642-8737

Funding

Norges Forskningsråd (300709)

  • Jonathan R Whitlock

Norges Forskningsråd (223262)

  • Jonathan R Whitlock

Norges Forskningsråd (197467)

  • Jonathan R Whitlock

Kavli Foundation

  • Jonathan R Whitlock

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Mathieu Wolff, CNRS, University of Bordeaux, France

Ethics

Animal experimentation: All experiments were performed in accordance with the Norwegian Animal Welfare Act and the European Convention for the Protection of Vertebrate Animals used for Experimental and Other Scientific Purposes. All procedures were approved by the Norwegian Food Safety Authority (Mattilsynet; protocol IDs 27175 and 25094). All tissue for in-house testing came from adult (>15wk) Long-Evans hooded rats. Detailed steps of the surgical preparation and post-operative care are described in Mimica et al. 2018 (doi:10.1126/science.aau2013).

Version history

  1. Preprint posted: October 3, 2021 (view preprint)
  2. Received: September 16, 2022
  3. Accepted: January 12, 2023
  4. Accepted Manuscript published: January 13, 2023 (version 1)
  5. Version of Record published: February 7, 2023 (version 2)

Copyright

© 2023, Fuglstad et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Jingyi Guo Fuglstad
  2. Pearl Saldanha
  3. Jacopo Paglia
  4. Jonathan R Whitlock
(2023)
Histological E-data registration in rodent brain spaces
eLife 12:e83496.
https://doi.org/10.7554/eLife.83496

Share this article

https://doi.org/10.7554/eLife.83496

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