The Infant Brainstem - A Multimodal Multiscale Postmortem Imaging Pipeline
- 1Martinos Center for Biomedical Imaging / Massachusetts General Hospital
Abstract
Brainstem disorders in human infants - including sudden infant death syndrome (SIDS), the leading cause of postnatal infant mortality in the United States - are characterized by cellular and molecular abnormalities that conventional neuroimaging cannot detect. A substantial challenge arises from the fact that the immature myelination of the infant brain severely degrades MRI contrast, leaving the discrete nuclei and white matter tracts of the brainstem poorly resolved at the scale where pathology occurs. We introduce a postmortem imaging pipeline that bridges this gap by integrating four spatially registered modalities: whole-brain magnetic resonance imaging (MRI) (550 m), brainstem-specific MRI (150 m), polarization-sensitive optical coherence tomography (PSOCT, 10 m), and histology with immunohistochemistry (1.88 m). Our central finding is that PSOCT provides excellent tissue contrast independent of myelination state - directly overcoming the principal limitation of MRI in the infant brain -while enabling three-dimensional visualization of nuclei and tracts at resolutions 15 to 55 times finer than MRI alone. Histology provides cellular-level ground truth and validates the optical contrasts. Applied here to a normative 34-day-old infant brainstem, this pipeline establishes a generalizable framework for studying infant brainstem neuroanatomy in three dimensions, with particular relevance to disorders such as SIDS where gross anatomy is intact but cellular abnormalities remain the target of investigation.
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BibTeX
@misc{magnain2026infant,
title = {{The Infant Brainstem - A Multimodal Multiscale Postmortem Imaging Pipeline}},
author = {C. Magnain and J. Augustinack and C. Clickner and W. Ammon and N. Ngo and A. van der Kouwe and B. Edlow and R. Haynes and L. F. Ferraz da Silva and H. Kinney and L. Zöllei},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.28.744504},
url = {https://www.biorxiv.org/content/10.64898/2026.08.28.744504v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - The Infant Brainstem - A Multimodal Multiscale Postmortem Imaging Pipeline
AU - C. Magnain
AU - J. Augustinack
AU - C. Clickner
AU - W. Ammon
AU - N. Ngo
AU - A. van der Kouwe
AU - B. Edlow
AU - R. Haynes
AU - L. F. Ferraz da Silva
AU - H. Kinney
AU - L. Zöllei
PY - 2026
DA - 2026/08/28
PB - bioRxiv
DO - 10.64898/2026.08.28.744504
UR - https://www.biorxiv.org/content/10.64898/2026.08.28.744504v1
AB - Brainstem disorders in human infants - including sudden infant death syndrome (SIDS), the leading cause of postnatal infant mortality in the United States - are characterized by cellular and molecular abnormalities that conventional neuroimaging cannot detect. A substantial challenge arises from the fact that the immature myelination of the infant brain severely degrades MRI contrast, leaving the discrete nuclei and white matter tracts of the brainstem poorly resolved at the scale where pathology occurs. We introduce a postmortem imaging pipeline that bridges this gap by integrating four spatially registered modalities: whole-brain magnetic resonance imaging (MRI) (550 m), brainstem-specific MRI (150 m), polarization-sensitive optical coherence tomography (PSOCT, 10 m), and histology with immunohistochemistry (1.88 m). Our central finding is that PSOCT provides excellent tissue contrast independent of myelination state - directly overcoming the principal limitation of MRI in the infant brain -while enabling three-dimensional visualization of nuclei and tracts at resolutions 15 to 55 times finer than MRI alone. Histology provides cellular-level ground truth and validates the optical contrasts. Applied here to a normative 34-day-old infant brainstem, this pipeline establishes a generalizable framework for studying infant brainstem neuroanatomy in three dimensions, with particular relevance to disorders such as SIDS where gross anatomy is intact but cellular abnormalities remain the target of investigation.
ER -