Clinical and Translational Scientist Seminar Series

LEARN'd Conference

Dashboard and Mobile Health Application

Ohio Equity Initiative

Available per PI request
A set of dashboards hosted by the Ohio Department of Medicaid to display health outcomes on infant mortality among high-risk pregnant women across the state of Ohio.
Reference: PMID: 34974826
Contact: Naleef Fareed
Achieve Study

Available per PI request.
A clinical dashboard embedded in EPIC for the maternal fetal medicine and endocrinology care team to use for monitoring health and social needs progress among pregnant individuals living with T2D.
Reference: PMID: 37164461
Contact: Naleef Fareed
HEALing Communities Study

Available per PI request.
A NIH funded dashboard that provided user-based access to opioid use health outcomes across the state of Ohio to community and study end-users involved in the HEALing Communities Study. The dashboard provides information to base decisions on selection of evidence-based practices within a community.
Reference: PMID: 33070058
Contact: Naleef Fareed
Integrated Behavioral Health

A dashboard hosted by the state of Ohio displaying opioid and substance abuse related health outcomes across all 88 counties in the state.
Contact: Naleef Fareed
Ohio Opportunity Index

A dashboard displaying area deprivation information across all census tracts in the state of Ohio; used by the state department of Medicaid for resource allocation
Reference: PMID: 32757202
Contact: Naleef Fareed
Ohio Children's Opportunity Index

A dashboard displaying area deprivation information across all census tracts in the state of Ohio; used by the state department of Medicaid for resource allocation focused on children's health outcomes.
Reference: PMID: 35081656
Contact: Naleef Fareed
Github Repository Ohio Opportunity Index

A repository containing R scripts and teaching material to develop area deprivation indices and build dashbaords in Tableau.
Reference: PMID: 35942261
Contact: Naleef Fareed
Github Repository HEALing Communities Study

A repository containing software scripts (R, Drupal) and teaching material to develop substance use measures and build dashboards in various softwares.
Contact: Naleef Fareed
Achieve Study

Available per PI request.
A mobile health application used by pregnant individuals living with T2D to report continous glucose values (via a Dexcom device) and report momentary ecological assessments on social needs, diabetes distress and related health outcomes.
Reference: PMID: 36644662
Contact: Naleef Fareed

Image Data Analytics

ITK-SNAP

ITK-SNAP is an open-source software application for medical image segmentation. It features manual, semi-automatic and automatic tools for delineating anatomical structures in 3D imaging data.
Reference: https://doi.org/10.1016/j.neuroimage.2006.01.015
Contact: Yuan Xue
ANTs

ANTs is a suite of image processing tools for medical image analysis, including image registration, segmentation and statistical analysis. It is widely used for brain imaging studies and other biomedical applications.
Reference: https://doi.org/10.1038/s41598-021-87564-6
Contact: Yuan Xue
3D Slicer

3D Slicer is a free, open-source software platform for the analysis and visualization of medical images. It supports a variety of image processing tasks, including segmentation, registration and 3D reconstruction.
Reference: PMID: 22770690
Contact: Yuan Xue
Segment Anything Model 2 (SAM 2)

SAM 2 is a general-purpose, promptable segmentation model that can be used to segment objects in images and videos. Developed by Meta AI, it is designed to handle a wide variety of image types and segmentation tasks with minimal manual annotation.
Reference: ArXiv: 2408.00714
Contact: Yuan Xue
QuPath

QuPath is an open-source software for digital pathology image analysis. It provides tools for the visualization, annotation, and analysis of whole slide images, with a focus on machine learning-based methods for tissue and cell classification.
Reference: https://doi.org/10.1038/s41598-017-17204-5
Contact: Yuan Xue
ImageJ

ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health (NIH). It is widely used for scientific image analysis and supports a wide range of plugins for various types of image processing tasks.
Referenece: https://doi.org/10.1186/s12859-017-1934-z
Contact: Yuan Xue
MONAI (Medical Open Network for AI)

MONAI is an open-source framework designed for deep learning in healthcare imaging. It provides domain-optimized foundational capabilities for developing AI models, including pre-built pipelines for segmentation, classification and other image analysis tasks.
Reference: ArXiv: 2211.02701
Contact: Yuan Xue
nnU-Net

nnU-Net is a self-adapting framework for biomedical image segmentation. It automatically configures itself to a given dataset, optimizing the architecture, preprocessing and training pipelines. It has been highly successful in various biomedical image segmentation challenges.
Reference: https://doi.org/10.1038/s41592-020-01008-z
Contact: Yuan Xue

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