ArticleNature communications2025
The ANTsX ecosystem for mapping the mouse brain.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Advances in the Comprehensive Tree Shrew Brain Atlas.Biomolecules · 2026Review
- Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis.bioRxiv : the preprint server for biology · 2026Article
- Adaptive Riemannian optimization for multi-scale diffeomorphic matching.Nature communications · 2026Article
- Deep Computational Anatomy via Latent-Aligned Multiview Normalizing Flows.bioRxiv : the preprint server for biology · 2026Article
- Anatomy-aware, label-informed approach improves image registration for challenging datasets.PloS one · 2026Article
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13 authors.
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Abstract
Large-scale efforts by the BRAIN Initiative Cell Census Network (BICCN) are generating a comprehensive reference atlas of cell types in the mouse brain. A key challenge in this effort is mapping diverse datasets, acquired with varied imaging, tissue processing, and profiling methods, into shared coordinate frameworks. Here, we present mouse brain mapping pipelines developed using the Advanced Normalization Tools Ecosystem (ANTsX) to align MERFISH spatial transcriptomics and high-resolution fMOST morphology data to the Allen Common Coordinate Framework (CCFv3), and developmental MRI and LSFM data to the Developmental CCF (DevCCF). Simultaneously, we introduce two novel methods: 1) a velocity field-based approach for continuous interpolation across developmental timepoints, and 2) a deep learning framework for automated brain parcellation using minimally annotated and publicly available data. All workflows are open-source and reproducible. We also provide general guidance for selecting appropriate strategies across modalities, enabling researchers to adapt these tools to new data.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.