A student’s guide to neural circuit tracing

Christine Saleeba, Bowen Dempsey, Sheng Le, Ann Goodchild, Simon McMullan*

*Corresponding author for this work

    Research output: Contribution to journalReview articlepeer-review

    79 Citations (Scopus)
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    The mammalian nervous system is comprised of a seemingly infinitely complex network of specialized synaptic connections that coordinate the flow of information through it. The field of connectomics seeks to map the structure that underlies brain function at resolutions that range from the ultrastructural, which examines the organization of individual synapses that impinge upon a neuron, to the macroscopic, which examines gross connectivity between large brain regions. At the mesoscopic level, distant and local connections between neuronal populations are identified, providing insights into circuit-level architecture. Although neural tract tracing techniques have been available to experimental neuroscientists for many decades, considerable methodological advances have been made in the last 20 years due to synergies between the fields of molecular biology, virology, microscopy, computer science and genetics. As a consequence, investigators now enjoy an unprecedented toolbox of reagents that can be directed against selected subpopulations of neurons to identify their efferent and afferent connectomes. Unfortunately, the intersectional nature of this progress presents newcomers to the field with a daunting array of technologies that have emerged from disciplines they may not be familiar with. This review outlines the current state of mesoscale connectomic approaches, from data collection to analysis, written for the novice to this field. A brief history of neuroanatomy is followed by an assessment of the techniques used by contemporary neuroscientists to resolve mesoscale organization, such as conventional and viral tracers, and methods of selecting for sub-populations of neurons. We consider some weaknesses and bottlenecks of the most widely used approaches for the analysis and dissemination of tracing data and explore the trajectories that rapidly developing neuroanatomy technologies are likely to take.

    Original languageEnglish
    Article number897
    Pages (from-to)1-19
    Number of pages19
    JournalFrontiers in Neuroscience
    Issue numberAUG
    Publication statusPublished - 27 Aug 2019

    Bibliographical note

    Copyright the Author(s) 2019. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

    A corrigendum exists for this article and can be found in Frontiers in Neuroscience (2020) Vol. 14 Article 177 at doi: 10.3389/fnins.2020.00177


    • anterograde tracer
    • connectome analysis
    • neuroanatomy
    • retrograde tracers
    • synaptic contacts
    • viral tracers


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