ArticleNeuroinformatics2021
DeepMapi: a Fully Automatic Registration Method for Mesoscopic Optical Brain Images Using Convolutional Neural Networks.
Article in Neuroinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Article
- The External Globus Pallidus is a Basal Ganglia Output Hub with Action-Specific Circuits.bioRxiv : the preprint server for biology · 2026Article
- SlicesMapi: An Interactive Three-Dimensional Registration Method for Serial Histological Brain Slices.Neuroinformatics · 2025Article
- Connecto-informatics at the mesoscale: current advances in image processing and analysis for mapping the brain connectivity.Brain informatics · 2024Review
- Detecting the effect of genetic diversity on brain composition in an Alzheimer's disease mouse model.Communications biology · 2024Article
- Subregion preference in the long-range connectome of pyramidal neurons in the medial prefrontal cortex.BMC biology · 2024Article
- Connecting single-cell transcriptomes to projectomes in mouse visual cortex.bioRxiv : the preprint server for biology · 2023Article
- D-LMBmap: a fully automated deep-learning pipeline for whole-brain profiling of neural circuitry.Nature methods · 2023Article
- DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas.Nature communications · 2023Article
- Detecting the effect of genetic diversity on brain composition in an Alzheimer's disease mouse model.bioRxiv : the preprint server for biology · 2023Article
- Three-dimensional mapping in multi-samples with large-scale imaging and multiplexed post staining.Communications biology · 2023Article
- Progressive 3D biomedical image registration network based on deep self-calibration.Frontiers in neuroinformatics · 2022Article
- Mesoscale microscopy and image analysis tools for understanding the brain.Progress in biophysics and molecular biology · 2022Review
- High-Throughput Strategy for Profiling Sequential Section With Multiplex Staining of Mouse Brain.Frontiers in neuroanatomy · 2021Article
- SMART: An Open-Source Extension of WholeBrain for Intact Mouse Brain Registration and Segmentation.eNeuroArticle
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13 authors.
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Abstract
The extreme complexity of mammalian brains requires a comprehensive deconstruction of neuroanatomical structures. Scientists normally use a brain stereotactic atlas to determine the locations of neurons and neuronal circuits. However, different brain images are normally not naturally aligned even when they are imaged with the same setup, let alone under the differing resolutions and dataset sizes used in mesoscopic imaging. As a result, it is difficult to achieve high-throughput automatic registration without manual intervention. Here, we propose a deep learning-based registration method called DeepMapi to predict a deformation field used to register mesoscopic optical images to an atlas. We use a self-feedback strategy to address the problem of imbalanced training sets (sampling at a fixed step size in nonuniform brains of structures and deformations) and use a dual-hierarchical network to capture the large and small deformations. By comparing DeepMapi with other registration methods, we demonstrate its superiority over a set of ground truth images, including both optical and MRI images. DeepMapi achieves fully automatic registration of mesoscopic micro-optical images, even macroscopic MRI datasets, in minutes, with an accuracy comparable to those of manual annotations by anatomists.
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