Contact information
Collaborators
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Karla Miller
Professor of Biomedical Engineering
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Saad Jbabdi
Professor of Biomedical Engineering
Websites
- FMRIB Physics Research
- FMRIB Analysis Research
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Oxford-Nottingham Biomedical Imaging (ONBI)
Centre for Doctoral Training
Research groups
Amy Howard
Postdoctoral Researcher
Combining diffusion MRI and microscopy to probe tissue microstructure
What can we learn from highly detailed microscopy images that can help us infer brain connectivity in vivo? My research considers different ways in which we can combine complementary data from both microscopy and diffusion MRI, to both validate and drive biophysical modelling of the brain tissue microstructure.
Recently, our focus has been on collecting an extensive dataset, the BigMac dataset, which combines in vivo MRI, extensive postmortem MRI and microscopy (polarised light imaging and histology) data from the same, single brain. This dataset provides an open access platform to interconnect microstructural features with MR signals throughout the brain. More details can be found in this manuscript detailing the first release of the data.
At FMRIB, my research spans both the physics and analysis groups and is co-supervised by Profs Karla Miller & Saad Jbabdi.
Interests include:
- In vivo & postmortem MRI
- Diffusion MRI connectivity & microstructure imaging
- Biophysical modelling & model validation
- Light microscopy: polarised light imaging & histological staining
- Quantitative analysis of histology (structure tensor analysis & cell segmentation)
- MRI-microscopy co-registration
- Data fusion / joint analysis of MRI and microscopy (e.g. hybrid tractography)
- Open data
Key publications
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An open resource combining multi-contrast MRI and microscopy in the macaque brain
Journal article
Howard AFD. et al, (2023), Nature Communications, 14
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Joint modelling of diffusion MRI and microscopy
Journal article
Howard A. et al, (2019), NeuroImage
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Estimating axial diffusivity in the NODDI model
Journal article
Howard AFD. et al, (2022), NeuroImage, 262, 119535 - 119535
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An automated pipeline for extracting histological stain area fraction for voxelwise quantitative MRI-histology comparisons
Journal article
Kor DZL. et al, (2022), NeuroImage, 264, 119726 - 119726
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Post mortem mapping of connectional anatomy for the validation of diffusion MRI.
Journal article
Yendiki A. et al, (2022), Neuroimage, 256
Recent publications
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Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 2—Ex vivo imaging: Added value and acquisition
Journal article
Schilling KG. et al, (2025), Magnetic Resonance in Medicine
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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
Journal article
Schilling KG. et al, (2025), Magnetic Resonance in Medicine
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Imaging the structural connectome with hybrid MRI-microscopy tractography.
Journal article
Zhu S. et al, (2025), Med Image Anal, 102
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Linking microscopy to diffusion MRI with degenerate biophysical models: an application of the Bayesian EstimatioN of CHange (BENCH) framework
Preprint
Kor DZL. et al, (2024)
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High resolution diffusion imaging in the unfixed post-mortem infant brain at 7T
Journal article
Wu W. et al, (2024), Imaging Neuroscience