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A Digital Atlas to Unlock the Potential of Brain Biorepository Tissue for Interdisciplinary Research

Poster No:

1809

Submission Type:

Late-Breaking Abstract Submission

Authors:

Jason Webster¹, Ali Shojaie¹, Yiqin Shen¹, Tung Le², Emily Ragaglia¹, Marika Bogdani¹, Amanda Kirkland¹, Christine Mac Donald¹, Caitlin Latimer¹, C. Dirk Keene¹, Thomas Grabowski¹

Institutions:

¹University of Washington, Seattle, WA, ²ADRC, Seattle, WA

First Author:

Jason Webster
University of Washington
Seattle, WA

Co-Author(s):

Ali Shojaie
University of Washington
Seattle, WA

Yiqin Shen
University of Washington
Seattle, WA

Tung Le
ADRC
Seattle, WA

Emily Ragaglia
University of Washington
Seattle, WA

Marika Bogdani
University of Washington
Seattle, WA

Amanda Kirkland
University of Washington
Seattle, WA

Christine Mac Donald
University of Washington
Seattle, WA

Caitlin Latimer
University of Washington
Seattle, WA

C. Dirk Keene
University of Washington
Seattle, WA

Thomas Grabowski
University of Washington
Seattle, WA

Late Breaking Reviewer(s):

Fernando Barrios, Ph.D.
Universidad Nacional Autónoma de México
Querétaro, Querétaro

Stephanie Forkel, PhD
Donders Institute for Brain, Cognition, and Behaviour
Nijmegen, Gelderland

Casey Paquola
Institute for Neuroscience and Medicine, INM-7, Forschungszentrum Jülich
Jülich, NA

Anna Roe, Phd
Zhejiang University
Hangzhou, Zhejiang

Introduction:

The structural, cellular, and biomolecular research necessary for a mechanistic understanding of neuroscience relies on brain tissue collected according to a brain sampling protocol (BSP) and preserved in biorepositories. These analyses are crucial for assessing the validity of research in Alzheimer's Disease and Related Dementias. The University of Washington BioRepository and Integrated Neuropathology (BRaIN) Laboratory has developed an extensive BSP for brain preparation, sampling, characterization, and storage. The digital BSP atlas uses a neuroimaging framework to create a 3D representation of this BSP to advance the tissue request process, augment biorepository workflows, generate scientific visualizations, and provide a link to neuroimaging data and analysis methods.

Methods:

Virtual neuropathology was performed according to the BRaIN lab BSP using the Montreal Neurological Institute and International Consortium on Brain Mapping 2009b Nonlinear Asymmetric Brain Template. Brain extraction, segmentation, and slicing were precisely replicated using FreeSurfer, FMRIB's Software Library (FSL), and custom Python/R scripts. Virtual tissue sampling was performed by the Lead Tissue Procurement Technician and a board-certified neuropathologist in Figma, a collaborative cloud-based platform with an intuitive dynamic interface. Data were exported in Scalable Vector Graphics (SVG) format and processed in Python to create the 3D digital BSP atlas.

Results:

The Digital BSP Atlas provides volumetric labels for all routinely collected fixed-tissue samples in the BRaIN lab BSP and incorporates standard neuroinformatics conventions for compatibility with freely available software including FSL, MRICroGL, and FreeSurfer.

Conclusions:

The digital BSP atlas provides an explicit spatial representation of the BSP, enabling researchers to more efficiently locate, reference, and utilize postmortem samples. Implementing the BSP with modern neuroinformatics conventions provides a highly portable, quantitative reference that facilitates interdisciplinary collaboration, dynamic visualization, figure generation, protocol optimization, and integration with in-vivo neuroimaging. Ongoing extensions of this work include the development of neuropathology sampling training software and a flexible interface to identify corresponding samples from free-form neuroscience terms.

Modeling and Analysis Methods:

Methods Development ²

Neuroinformatics and Data Sharing:

Brain Atlases ¹

Novel Imaging Acquisition Methods:

Anatomical MRI

Keywords:

Atlasing

Brainstem

Cerebellum

Cortex

Informatics

MRI

Segmentation

STRUCTURAL MRI

^1|2Indicates the priority used for review

Abstract Information

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Please indicate below if your study was a "resting state" or "task-activation” study.

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Healthy subjects

Was this research conducted in the United States?

Yes

Are you Internal Review Board (IRB) certified? Please note: Failure to have IRB, if applicable will lead to automatic rejection of abstract.

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Were any human subjects research approved by the relevant Institutional Review Board or ethics panel? NOTE: Any human subjects studies without IRB approval will be automatically rejected.

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Were any animal research approved by the relevant IACUC or other animal research panel? NOTE: Any animal studies without IACUC approval will be automatically rejected.

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Please indicate which methods were used in your research:

Structural MRI

Postmortem anatomy

Which processing packages did you use for your study?

FSL

Free Surfer

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