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The ANTsX ecosystem for mapping the mouse brain.

Nicholas J Tustison1, Min Chen2, Fae N Kronman3

  • 1Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. ntustison@virginia.edu.

Nature Communications
|November 22, 2025
PubMed
Summary
This summary is machine-generated.

Researchers developed open-source mouse brain mapping pipelines using ANTsX to integrate diverse datasets, including spatial transcriptomics and morphology, into common coordinate frameworks for cell atlas creation.

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Area of Science:

  • Neuroscience
  • Bioinformatics
  • Computational Biology

Background:

  • The BRAIN Initiative Cell Census Network (BICCN) aims to create a comprehensive mouse brain cell atlas.
  • Integrating diverse datasets from varied methods (imaging, tissue processing, profiling) into shared coordinate frameworks is a major challenge.

Purpose of the Study:

  • To present novel mouse brain mapping pipelines using the Advanced Normalization Tools Ecosystem (ANTsX).
  • To enable the alignment of diverse neurobiological datasets to common coordinate frameworks.
  • To introduce new computational methods for developmental trajectory interpolation and automated brain parcellation.

Main Methods:

  • Utilized ANTsX for aligning MERFISH spatial transcriptomics and fMOST morphology data to the Allen Common Coordinate Framework (CCFv3).
  • Aligned developmental MRI and LSFM data to the Developmental CCF (DevCCF).
  • Developed a velocity field-based method for continuous interpolation across developmental timepoints.
  • Created a deep learning framework for automated brain parcellation using minimally annotated data.

Main Results:

  • Successfully mapped MERFISH and fMOST data to CCFv3, and developmental MRI/LSFM data to DevCCF.
  • Introduced and validated novel computational methods for developmental interpolation and automated parcellation.
  • All developed workflows are open-source and reproducible.

Conclusions:

  • The presented pipelines and methods facilitate the integration of multi-modal brain data.
  • These tools support the creation of a comprehensive reference atlas of mouse brain cell types.
  • Guidance is provided for adapting these strategies to new datasets and modalities.