Nature CommunicationsNeurosciencePeer-reviewed journal article
DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas
Harry CareyiD, Michael Pegios, Lewis Martin, Christine SaleebaiD, Anita J. TurneriD, Nicholas Adams EverettiD, Ingvild Elise BjerkeiD, Maja Amedjkouh PuchadesiD, Jan Gunnar BjaalieiD, Simon McMullaniD
- Citations
- 62
- FWCI
- 5.53
- Field percentile
- top 3%
Abstract
Registration of data to a common frame of reference is an essential step in the analysis and integration of diverse neuroscientific data modalities. To this end, volumetric brain atlases enable histological datasets to be spatially registered and analysed, yet accurate registration remains expertise-dependent and slow. We have trained a neural network, DeepSlice, to register mouse brain histology to the Allen Brain Atlas, retaining accuracy while improving speed by >1000 fold.
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Deep Learning Based Cross-Modality Histological Brain Section Registration in Multiple Species Using Synthetic Images
Siqi Fang, Daniel Jacob Tward·bioRxiv·Jul 22, 2026
- NeuroAtlas: An Artificial Intelligence-based Framework for Annotation, Segmentation and Registration of Large Scale Biomedical Imaging Data
Hassan Mahmood, Farah Nawar, … Asim Iqbal·International Conference on Digital Image Computing: Techniques and Applications (DICTA)Peer-reviewed·Nov 27, 2024
- Riffle Shuffle: A Supervised, Symmetry-Driven, GUI Toolkit for Mouse Brain Stack Registration and Plane Assignment
Marcelo Cicconet, Daniel R. Hochbaum·bioRxiv·Sep 25, 2019
- Bi-channel Image Registration and Deep-learning Segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain
Xuechun Wang, Weilin Zeng, … Peng Fei·eLifePeer-reviewed·Jan 18, 2021
- Mapping Mouse Brain Slice Sequence to a Reference Brain Without 3D Reconstruction
Jing Xiong, Jing Ren, … Mark Horowitz·Frontiers in NeuroinformaticsPeer-reviewed·Dec 11, 2018
- NeuroFlow: An Integrated, Cross-Platform Workflow for Mouse Brain Atlas Registration and Quantification
Aarushi Rao, Henry Zin Oo, … Guangwei Zhang·bioRxiv·Jul 20, 2026