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Updated: Aug 14, 2025

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Histological E-data Registration in rodent Brain Spaces.

Jingyi Guo Fuglstad1, Pearl Saldanha1, Jacopo Paglia1

  • 1Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.

Elife
|January 13, 2023
PubMed
Summary
This summary is machine-generated.

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HERBS (Histological E-data Registration in rodent Brain Spaces) is a new, user-friendly tool for rodent brain research. It aids in planning experiments and registering histological data, simplifying anatomical analysis for neuroscience.

Area of Science:

  • Neuroscience
  • Computational Biology
  • Bioinformatics

Background:

  • Recent advances in rodent neural recording technologies allow simultaneous sampling of thousands of neurons.
  • This necessitates advanced digital tools for curating anatomical data.
  • Existing tools often have limited functionality or require coding expertise.

Purpose of the Study:

  • To introduce HERBS (Histological E-data Registration in rodent Brain Spaces), a comprehensive, user-friendly software tool.
  • To provide researchers with a graphical interface for planning and analyzing rodent brain anatomy.
  • To address the limitations of current anatomical data curation tools.

Main Methods:

  • HERBS utilizes a graphical user interface for planning electrode implantation and viral tracing.
Keywords:
GUIanatomicalatlasbrainmouseneurosciencerat

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  • It enables registration of recording sites, viral expression, and other anatomical features post-experiment.
  • The tool integrates with 3D brain atlases (e.g., Waxholm Space, Allen Mouse Brain Atlas) and supports custom slice cuts and transformations.

    • Main Results:

    • HERBS facilitates pre-experimental planning of electrode placement and injections.
    • Post-experiment, it allows accurate registration of neural recordings and anatomical features.
    • The software can delineate multi-injection labeling, perform cell counts, and reconstruct 3D brain meshes.

    Conclusions:

    • HERBS offers a powerful, accessible solution for rodent brain anatomical data management.
    • Its user-friendly interface democratizes advanced histological data analysis.
    • As an open-source Python package, HERBS is broadly accessible and adaptable for various neuroscience research needs.