ArticleScientific reports2020
A multimodal computational pipeline for 3D histology of the human brain.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Review
- SKUF Protocol: Slice, Keep, Unwrap, Fuse-A Pilot Multimodal Approach to Cardiac Innervation Mapping.Diagnostics (Basel, Switzerland) · 2026Article
- A unified 3D reconstruction of microscopy and MRI in a brain showing Alzheimer's disease-related neuropathology.Brain pathology (Zurich, Switzerland) · 2026Article
- Article
- Brainbuilder: a software pipeline for 3D reconstruction of cortical maps from multi-modal 2D data sets.Communications biology · 2025Article
- Precise MRI-Histology Coregistration of Paraffin-Embedded Tissue with Blockface Imaging.bioRxiv : the preprint server for biology · 2025Article
- Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3-Ex vivo imaging: Data processing, comparisons with microscopy, and tractography.Magnetic resonance in medicine · 2025Review
- Operationalizing postmortem pathology-MRI association studies in Alzheimer's disease and related disorders with MRI-guided histology sampling.Acta neuropathologica communications · 2025Article
- Precise MRI-histology coregistration of paraffin-embedded tissue with blockface imaging.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Automated deep learning segmentation of high-resolution 7 Tesla postmortem MRI for quantitative analysis of structure-pathology correlations in neurodegenerative diseases.Imaging neuroscience (Cambridge, Mass.) · 2024Article
- Three-dimensional histology reveals dissociable human hippocampal long-axis gradients of Alzheimer's pathology.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024Article
- Three-dimensional histology reveals dissociable human hippocampal long axis gradients of Alzheimer's pathology.bioRxiv : the preprint server for biology · 2023Article
- 3D reconstruction of skin and spatial mapping of immune cell density, vascular distance and effects of sun exposure and aging.Communications biology · 2023Article
- giRAff: an automated atlas segmentation tool adapted to single histological slices.Frontiers in neuroscience · 2023Article
- A technology platform for standardized cryoprotection and freezing of large-volume brain tissues for high-resolution histology.Frontiers in neuroanatomy · 2023Article
- High-resolution atlasing and segmentation of the subcortex: Review and perspective on challenges and opportunities created by machine learning.NeuroImage · 2022Review
- Deep active learning for suggestive segmentation of biomedical image stacks via optimisation of Dice scores and traced boundary length.Medical image analysis · 2022Article
- Current Approaches for Image Fusion of Histological Data with Computed Tomography and Magnetic Resonance Imaging.Radiology research and practice · 2022Review
- Micro-CT-Based Bone Microarchitecture Analysis of the Murine Skull.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas.Medical image analysis · 2022Article
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9 authors.
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Abstract
Ex vivo imaging enables analysis of the human brain at a level of detail that is not possible in vivo with MRI. In particular, histology can be used to study brain tissue at the microscopic level, using a wide array of different stains that highlight different microanatomical features. Complementing MRI with histology has important applications in ex vivo atlas building and in modeling the link between microstructure and macroscopic MR signal. However, histology requires sectioning tissue, hence distorting its 3D structure, particularly in larger human samples. Here, we present an open-source computational pipeline to produce 3D consistent histology reconstructions of the human brain. The pipeline relies on a volumetric MRI scan that serves as undistorted reference, and on an intermediate imaging modality (blockface photography) that bridges the gap between MRI and histology. We present results on 3D histology reconstruction of whole human hemispheres from two donors.
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