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In polar coordinates, the motion of a particle follows a curvilinear path. The radial coordinate symbolized as 'r,' extends outward from a fixed origin to the particle, while the angular coordinate, 'θ,' measured in radians, represents the counterclockwise angle between a fixed reference line and the radial line connecting the origin to the particle.
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A curvilinear coordinate flatmap for visualizing hippocampal structure and development.

Ashwin A Bhandiwad1, Fae N Kronman2, Josephine Liwang2

  • 1Allen Institute for Brain Science, Seattle, WA.

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|February 9, 2026
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Summary
This summary is machine-generated.

We developed a computational method to flatten the complex hippocampus into an accessible map. This new hippocampal flatmap visualization tool aids in studying brain development and diseases like Alzheimer's.

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Area of Science:

  • Neuroscience
  • Computational Biology
  • Neuroanatomy

Background:

  • The hippocampus, a complex brain structure, poses challenges for detailed analysis due to its intricate geometry.
  • Understanding subregional, laminar, and connectivity patterns is crucial for neuroscience research.

Purpose of the Study:

  • To present a novel computational workflow for generating curvilinear-coordinate flatmaps of the hippocampal formation.
  • To overcome the limitations of the Common Coordinate Framework (CCF) in visualizing hippocampal topography.

Main Methods:

  • Solving the Laplacian equation to derive geodesic streamlines for creating flatmaps.
  • Transforming the hippocampus into a planar slab with defined radial and surface boundaries.
  • Applying the flatmap transformation to diverse datasets including image volumes, neuron reconstructions, and spatial transcriptomic data.

Main Results:

  • Revealed obscured topographic variations along dorsoventral and radial axes within the hippocampus.
  • Demonstrated the utility of flatmaps in identifying connectivity loss in an Alzheimer's disease mouse model.
  • Tracked the developmental distribution of microglia in the hippocampus using the flatmap approach.

Conclusions:

  • The developed hippocampal flatmap provides an efficient and accessible resource for visualizing brain organization.
  • This method facilitates the study of hippocampal structure and function across development and disease states.
  • Offers new avenues for interrogating the hippocampus in conditions like Alzheimer's disease.