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.

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).

Reviewing Editor

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

Publication history

  1. Received: September 16, 2022
  2. Accepted: January 12, 2023
  3. Accepted Manuscript published: January 13, 2023 (version 1)

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.

Metrics

  • 252
    Page views
  • 53
    Downloads
  • 0
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  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

Further reading

    1. Neuroscience
    2. Physics of Living Systems
    Sabrina A Jones, Jacob H Barfield ... Woodrow L Shew
    Research Article

    Naturally occurring body movements and collective neural activity both exhibit complex dynamics, often with scale-free, fractal spatiotemporal structure. Scale-free dynamics of both brain and behavior are important because each is associated with functional benefits to the organism. Despite their similarities, scale-free brain activity and scale-free behavior have been studied separately, without a unified explanation. Here we show that scale-free dynamics of mouse behavior and neurons in visual cortex are strongly related. Surprisingly, the scale-free neural activity is limited to specific subsets of neurons, and these scale-free subsets exhibit stochastic winner-take-all competition with other neural subsets. This observation is inconsistent with prevailing theories of scale-free dynamics in neural systems, which stem from the criticality hypothesis. We develop a computational model which incorporates known cell-type-specific circuit structure, explaining our findings with a new type of critical dynamics. Our results establish neural underpinnings of scale-free behavior and clear behavioral relevance of scale-free neural activity.

    1. Neuroscience
    Barna Zajzon, David Dahmen ... Renato Duarte
    Research Article

    Information from the sensory periphery is conveyed to the cortex via structured projection pathways that spatially segregate stimulus features, providing a robust and efficient encoding strategy. Beyond sensory encoding, this prominent anatomical feature extends throughout the neocortex. However, the extent to which it influences cortical processing is unclear. In this study, we combine cortical circuit modeling with network theory to demonstrate that the sharpness of topographic projections acts as a bifurcation parameter, controlling the macroscopic dynamics and representational precision across a modular network. By shifting the balance of excitation and inhibition, topographic modularity gradually increases task performance and improves the signal-to-noise ratio across the system. We demonstrate that in biologically constrained networks, such a denoising behavior is contingent on recurrent inhibition. We show that this is a robust and generic structural feature that enables a broad range of behaviorally-relevant operating regimes, and provide an in-depth theoretical analysis unravelling the dynamical principles underlying the mechanism.