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A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale
Jason W. Bohland, Caizhi Wu, Helen Barbas, Hemant Bokil, Mihail Bota, Hans C. Breiter, Hollis T. Cline, John C. Doyle, Peter J. Freed, Ralph J. Greenspan, Suzanne N. Haber, Michael Hawrylycz, Daniel G. Herrera, Claus C. Hilgetag, Z. Josh Huang, Allan Jones, Edward G. Jones, Harvey J. Karten, David Kleinfeld, Rolf Kotter, Henry A. Lester, John M. Lin, Brett D. Mensh, Shawn Mikula, Jaak Panksepp, Joseph L. Price, Joseph Safdieh, Clifford B. Saper, Nicholas D. Schiff, Jeremy D. Schmahmann, Bruce W. Stillman, Karel Svoboda, Larry W. Swanson, Arthur W. Toga, David C. Van Essen, James D. Watson, Partha P. Mitra
TL;DR
Neuroanatomical connectivity remains a major gap despite complete genomes and its importance for understanding brain function and disease. The paper proposes standardized, experimental mesoscopic mapping across model organisms, beginning with a comprehensive mouse project and extending through macaque data curation and human technique development. It argues that open, brainwide connectivity maps are feasible at this scale and would provide a foundation for broader anatomical and genomic research.
Problem
Empirical knowledge of neuroanatomical connectivity is sparse, although connectivity underlies nervous-system function and links genotype with behavioral phenotype.
Method
The paper proposes standardized, high-throughput brainwide mesoscopic mapping using tracer injections and viral gene transfer, with open data and complementary macaque and human efforts.
Results
The proposal identifies a tractable mouse-first program based on existing methods, with additional macaque curation and targeted experiments and human technique development.
Takeaways & Limitations
Comprehensive mesoscopic connectivity maps would provide scaffolding for anatomical projects and support research spanning neuroscience, genomics, comparative biology, and medicine.
Takeaways & Limitations
High-throughput primate mapping at the proposed mouse scale is not feasible, while precise human connectivity mapping requires further technological development.
Abstract
from arXiv · showhide
In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is however critical both for basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brain-wide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brain-wide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open access data repository; compatibility with existing resources, and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.
Introduction
Neuroanatomical connectivity remains sparsely documented despite its central role in nervous-system function. The paper argues that a coordinated, brainwide effort is timely and feasible for model organisms.
- Only about 10% of possible long-range projections between roughly 500 rat brain regions are documented in curated literature.Existing presentations are also largely qualitative, leaving many projections unstudied with modern tracing methods.
- The paper proposes coordinated community-wide mapping of neuroanatomical connectivity across mouse, macaque, and eventually human brains.It outlines rationale, resolution, techniques, experimental planning, and informatics requirements.
- Brainwide connectivity projects are presented as timely because standardized neuroanatomical approaches have already demonstrated scalable, brainwide feasibility.The Allen Brain Atlas is cited as evidence that standardized techniques can be scaled in neuroanatomical research.
The mesoscopic level of resolution
Mesoscopic connectivity maps would provide tractable, brainwide descriptions of circuit organization that complement finer-scale cellular data and support neuroscience, comparative biology, and biomedicine. Connectivity is especially valuable because it links structure and function, genotype and behavioral phenotype, and can revise interpretations based on morphology alone.
- Scientific rationale: Mesoscopic wiring diagrams would provide a brainwide circuit scaffold that complements finer-scale descriptions of neurons and cortical columns.The proposed scale is intended to capture representative connectivity without requiring individually resolved neuronal wiring.
- Scientific rationale: Connectivity supplies a missing link between genotype and behavioral phenotype alongside comprehensive genomic information.The paper identifies the connectivity phenotype as a critical intermediate level of biological organization.
- Scientific rationale: Explicit connectivity information improves interpretation of physiological activity, microstimulation, attention-related dynamics, and neural network models.Many experimental and theoretical claims depend on anatomical constraints that remain deficient.
- Comparative and evolutionary rationale: Connectivity comparisons across model organisms can advance evolutionary neuroanatomy beyond analyses based mainly on morphology and regional size.The paper describes avian–mammalian comparisons as an example of this benefit.
- Comparative and evolutionary rationale: Connectivity evidence overturned homology assignments based on the presence of a layered cortex and led to revised avian brain nomenclature.Structural similarities alone had linked avian telencephalic structures incorrectly with mammalian basal ganglia.
- Biomedical rationale: Circuit-level knowledge is relevant to disorders including depression, anxiety, obsessive-compulsive disorder, addiction, schizophrenia, autism, and dyslexia.The paper emphasizes affective circuitry and aberrant wiring as important but incompletely characterized disease-related features.
What is being proposed?
The paper proposes a coordinated, brainwide effort to map mesoscale neuronal connectivity in model organisms using standardized experimental methods and open data. It outlines essential project attributes, reviews current limitations and techniques, and describes staged plans for mouse, macaque, and human studies.
- Core proposal: The primary objective is a standardized, high-throughput mouse connectivity map, with macaque curation and targeted experiments, plus human technique development.The proposal uses existing tracers and viral gene transfer and calls for public access to results and digitized primary data.
- Project requirements: Required project attributes include brainwide mesoscopic coverage, validated extensible techniques, a centralized open-access repository, and compatibility with existing resources.The methods should support stereotyped, low-complexity steps and high-throughput sample preparation, detection, and analysis.
- Current knowledge: Existing connectivity knowledge remains difficult to assess because studies vary in animals, methods, nomenclature, and result presentation, while primary materials are often unavailable.Current repositories also remain sparse and uncertain because they reconcile heterogeneous reports across parcellation schemes and nomenclatures.
- Techniques: The proposed experimental toolkit includes conventional tracers and neurotropic viruses, which differ in transport properties and in whether they cross synapses.Viral spread can make weak first-order and strong second-order projections difficult to distinguish because its time course varies with projection strength.
- Implementation across species: The mouse project is estimated to take 5 years and cost less than 20 million dollars, while primate-scale high-throughput mapping is not feasible.The macaque plan therefore emphasizes literature curation, slide digitization, and targeted standardized experiments; human mapping requires further technological development.
Supporting Text 1: Survey of methods relevant for determining neuronal connectivity
The survey reviews anatomical, imaging, tracer, viral, transgenic, and microscopy methods for determining neuronal connectivity, emphasizing their distinct capabilities and limitations. It presents neuronal tracers and light microscopy as important components of scalable connectivity mapping while noting limits of inferential imaging and some tracer classes.
- Classical dissection and degeneration methods provided foundational fiber-pathway knowledge but have limited selectivity.
- Diffusion and functional imaging offer non-invasive connectivity measures, but anatomical inference from task-based functional data remains tenuous.
- Axonal-transport tracers label projections within intact neurons after injection, tissue processing, histochemistry, and microscopy.
- PHA-L provides nearly exclusive anterograde transport, whereas BDA can show both directional transport and introduce interpretive ambiguity.
- Multi-tracer protocols can combine anterograde and retrograde labeling, with CTB and Fluoro-gold identified as candidate tracers.
- Viral vectors and transgenic methods enable selected-cell targeting, while Brainbow supports distinguishing adjacent neurons through combinatorial fluorescent labeling.
- Light microscopy remains the most viable high-throughput imaging option, and automation has been demonstrated in the Allen Institute gene-expression atlas project.
mesoscopic scale: Supporting information
The supporting information describes the proposed connectivity experiment as a pipeline in which tracer or viral-vector injections produce tissue and image data that move through experimental and software stages. It also introduces a five-year project timeline organized by components, milestones, and completion curves.
- The single-experiment workflow begins with conventional-tracer or viral-vector injections and carries tissue and images through experimental and software stages.
- Square boxes represent stages requiring primarily experimental apparatus, whereas rounded boxes represent stages implemented primarily in software.
- Red, blue, and purple arrows distinguish viral-tracer, conventional-tracer, and shared material flows, respectively.
- The proposed project timeline divides work into colored horizontal bands whose thickness indicates relative resource distribution.
- Milestones appear as circles, subprojects as horizontal bars, and background curves represent expected completion across the proposed five-year span.
Supporting Text 3: Brief proposal for primate connectivity project
The primate proposal combines literature curation, legacy-slide digitization, targeted new experiments, and standardized protocols rather than attempting mouse-scale high-throughput mapping. It emphasizes filling knowledge gaps while adapting imaging, injection, tracer, and registration procedures to macaque brains.
- Mouse-scale high-throughput connectivity mapping is not currently feasible in primates because primate experiments are costlier and brains are larger, more complex, and more variable.
- The primate effort should curate existing macaque findings, digitize available slides, preserve physical slide libraries, and conduct new studies to fill key gaps.
- A substantial portion of legacy fluorescent-tracer data may no longer be visible because of degradation over time.
- Legacy image data would improve geographic interpretation by enabling computational registration to a common geometric template.
- New macaque experiments should target knowledge deficits and scientifically or biomedically important circuits while using standardized protocols where possible.
- Each experimental subject should receive a T1-weighted MRI scan with 1 cubic millimeter or less voxel size before injection.
- Macaque protocols require controlled air-pressure injections instead of iontophoresis, potentially additional tracers or injection sites, and altered survival periods.
- Available BrainMaps.org data provide online sub-micron images from primate tracer experiments and are expected to support a multi-terabyte virtual-slide database.