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Caroline Magnain, PhD




Assistant Professor




Assistant Investigator




Caroline Magnain*, Erendira Garcia Pallares, Sam Blackman, Seoyoon Kim, Ream Gebrekidan, Brian L. Edlow, Robin L. Haynes, Hannah C. Kinney and Lilla Zöllei

The infant brainstem: postmortem multimodal and multiscale imaging of structure and connectivity

I am relatively new to the research involving infant imaging, developing brain, and its pathologies. I develop and use Optical Coherence Tomography which is not yet widely known and applied by the neuroimaging community. OCT can provide high resolution and volumetric reconstruction of postmortem brain tissue. I would love to promote OCT and its applications. I have been involved in promoting Equity and Diversity at the Martinos Center and have been a member of Women In Science since its foundation in 2018. I thought important of participating, as a new assistant professor, a women in science and an activist.


Sudden infant death syndrome is the leading cause of postneonatal infant mortality in industrialized nations. A subset of SIDS may be the result of an intrinsic defect in brain anatomy, in particular of the subcortical ascending arousal network, whose arousal pathways originate in the brainstem.


We use a multimodal and multiscale imaging approach to study the structure and connectivity of the postmortem infant brainstem in a control subject. We used whole brain and brainstem structural and diffusion MRI at various resolution. However, even at high resolution, ex vivo MRI is unable to provide sufficient contrast to segment the brainstem nuclei and tracts due to their size and the lack of myelination. We turned to Optical Coherence Tomography, which rely on intrinsic optical properties at an isotropic resolution of 3.5 µm and validate our results using histology.


A brainstem is imaged via the entire pipeline, the OCT data set is segmented and all the modalities are registered into the same space for comparison and analysis.


This work lays the foundation to compare the brainstem connectivity between SIDS cases and controls, with the potential to identify biomarkers and abnormalities of the disease not detectable by standard histopathological techniques.