ANTsX pipelines for mapping the mouse brain

November 22, 2025 October 22, 2026

The BRAIN Initiative Cell Census Network (BICCN) is building a comprehensive reference atlas of cell types in the mouse brain. A central challenge is bringing very different datasets, acquired with different imaging, tissue processing and profiling methods, into shared coordinate frameworks.

In a paper in Nature Communications, Nicholas Tustison, Min Chen, Jeffrey Duda, Jim Gee and colleagues present mouse brain mapping pipelines built on the Advanced Normalization Tools Ecosystem (ANTsX). The pipelines align:

MERFISH spatial transcriptomics and high-resolution fMOST morphology data to the Allen Common Coordinate Framework (CCFv3).
Developmental MRI and light-sheet fluorescence microscopy data to the Developmental CCF (DevCCF).

The paper also introduces two new methods: a velocity field approach for continuous interpolation between developmental time points, and a deep learning framework for automatic brain parcellation trained on minimally annotated, publicly available data. All workflows are open-source and reproducible, and the paper gives practical guidance for choosing a strategy for new types of data.

Developmental mouse brain templates warped across time points with the DevCCF velocity flow model. Figure 5 from Tustison et al., Nature Communications 2025 , CC BY 4.0 https: creativecommons.org licenses by 4.0 . — Developmental mouse brain templates warped across time points with the DevCCF velocity flow model. Figure 5 from Tustison et al., *Nature Communications* (2025), CC BY 4.0.

Reference: Tustison NJ, Chen M, Kronman FN, Duda JT, et al., Gee JC. The ANTsX ecosystem for mapping the mouse brain. Nature Communications. 2025. doi:10.1038/s41467-025-66741-5