The Stroke Neuro-Imaging Phenotype Repository: An Open Data Science Platform for Stroke Research

Abstract

Stroke is one of the leading causes of death and disability worldwide. Reducing this disease burden through drug discovery and evaluation of stroke patient outcomes requires broader characterization of stroke pathophysiology, yet the underlying biologic and genetic factors contributing to outcomes are largely unknown. Remedying this critical knowledge gap requires deeper phenotyping, including large-scale integration of demographic, clinical, genomic, and imaging features. Such big data approaches will be facilitated by developing and running processing pipelines to extract stroke-related phenotypes at large scale. Millions of stroke patients undergo routine brain imaging each year, capturing a rich set of data on stroke-related injury and outcomes. The Stroke Neuroimaging Phenotype Repository (SNIPR) was developed as a multi-center centralized imaging repository of clinical computed tomography (CT) and magnetic resonance imaging (MRI) scans from stroke patients worldwide, based on the open source XNAT imaging informatics platform. The aims of this repository are to: (i) store, manage, process, and facilitate sharing of high-value stroke imaging data sets, (ii) implement containerized automated computational methods to extract image characteristics and disease-specific features from contributed images, (iii) facilitate integration of imaging, genomic, and clinical data to perform large-scale analysis of complications after stroke; and (iv) develop SNIPR as a collaborative platform aimed at both data scientists and clinical investigators. Currently, SNIPR hosts research projects encompassing ischemic and hemorrhagic stroke, with data from 2,246 subjects, and 6,149 imaging sessions from Washington University’s clinical image archive as well as contributions from collaborators in different countries, including Finland, Poland, and Spain. Moreover, we have extended the XNAT data model to include relevant clinical features, including subject demographics, stroke severity (NIH Stroke Scale), stroke subtype (using TOAST classification), and outcome [modified Rankin Scale (mRS)]. Image processing pipelines are deployed on SNIPR using containerized modules, which facilitate replicability at a large scale. The first such pipeline identifies axial brain CT scans from DICOM header data and image data using a meta deep learning scan classifier, registers serial scans to an atlas, segments tissue compartments, and calculates CSF volume. The resulting volume can be used to quantify the progression of cerebral edema after ischemic stroke. SNIPR thus enables the development and validation of pipelines to automatically extract imaging phenotypes and couple them with clinical data with the overarching aim of enabling a broad understanding of stroke progression and outcomes.

Imaging biomarkers of cerebral edema automatically extracted from routine CT scans of large vessel occlusion strokes

“…The collection of data for each cohort was approved by the respective institution's human studies review board with a waiver of consent. Imaging data were collected in a central stroke repository 21 . They were analyzed using an image analysis pipeline, described below.…”

Functional near-infrared spectroscopy in pediatric clinical research: Different pathophysiologies and promising clinical applications

“…Such scenarios have been proposed for very common neurological diseases (e.g., Ref. 92), but might also serve the establishment of fNIRS for clinical use in the field of pediatrics. We will not reiterate all the challenges and limitations of the previous sections.…”

Siam-VAE: a hybrid deep learning based anomaly detection framework for automated quality control of head CT scans

“…The Stroke Neuroimaging Phenotype Repository (SNIPR) 16 is a multi-site centralized imaging repository of CT scans and magnetic resonance imaging (MRI) scans from stroke patients worldwide. SNIPR was developed as a collaborative platform to investigate the underlying biological and genetic factors of stroke by coupling imaging analysis with clinical and genetic data.…”