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).

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

  • 2,421
    views
  • 214
    downloads
  • 5
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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

Share this article

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

Further reading

    1. Neuroscience
    2. Structural Biology and Molecular Biophysics
    Amy N Shore, Keyong Li ... Matthew C Weston
    Research Article

    More than 20 recurrent missense gain-of-function (GOF) mutations have been identified in the sodium-activated potassium (KNa) channel gene KCNT1 in patients with severe developmental and epileptic encephalopathies (DEEs), most of which are resistant to current therapies. Defining the neuron types most vulnerable to KCNT1 GOF will advance our understanding of disease mechanisms and provide refined targets for precision therapy efforts. Here, we assessed the effects of heterozygous expression of a Kcnt1 GOF variant (Kcnt1Y777H) on KNa currents and neuronal physiology among cortical glutamatergic and GABAergic neurons in mice, including those expressing vasoactive intestinal polypeptide (VIP), somatostatin (SST), and parvalbumin (PV), to identify and model the pathogenic mechanisms of autosomal dominant KCNT1 GOF variants in DEEs. Although the Kcnt1Y777H variant had no effects on glutamatergic or VIP neuron function, it increased subthreshold KNa currents in both SST and PV neurons but with opposite effects on neuronal output; SST neurons became hypoexcitable with a higher rheobase current and lower action potential (AP) firing frequency, whereas PV neurons became hyperexcitable with a lower rheobase current and higher AP firing frequency. Further neurophysiological and computational modeling experiments showed that the differential effects of the Kcnt1Y777H variant on SST and PV neurons are not likely due to inherent differences in these neuron types, but to an increased persistent sodium current in PV, but not SST, neurons. The Kcnt1Y777H variant also increased excitatory input onto, and chemical and electrical synaptic connectivity between, SST neurons. Together, these data suggest differential pathogenic mechanisms, both direct and compensatory, contribute to disease phenotypes, and provide a salient example of how a pathogenic ion channel variant can cause opposite functional effects in closely related neuron subtypes due to interactions with other ionic conductances.

    1. Neuroscience
    Jun Yang, Hanqi Zhang, Sukbin Lim
    Research Article

    Errors in stimulus estimation reveal how stimulus representation changes during cognitive processes. Repulsive bias and minimum variance observed near cardinal axes are well-known error patterns typically associated with visual orientation perception. Recent experiments suggest that these errors continuously evolve during working memory, posing a challenge that neither static sensory models nor traditional memory models can address. Here, we demonstrate that these evolving errors, maintaining characteristic shapes, require network interaction between two distinct modules. Each module fulfills efficient sensory encoding and memory maintenance, which cannot be achieved simultaneously in a single-module network. The sensory module exhibits heterogeneous tuning with strong inhibitory modulation reflecting natural orientation statistics. While the memory module, operating alone, supports homogeneous representation via continuous attractor dynamics, the fully connected network forms discrete attractors with moderate drift speed and nonuniform diffusion processes. Together, our work underscores the significance of sensory-memory interaction in continuously shaping stimulus representation during working memory.