Joseph Naegele

Curriculum Vitae

Jan 2025 - Now
Remote

Member of the Diagnostic Imaging Team at Microsoft Research - Health Futures
Developing new stream-oriented medical image reconstruction framework and related infrastructure

Oct 2023 - Dec 2024
Remote - Contracted by Aquent

Member of the Biomedical Signal Processing team at Microsoft Research - Health Futures
Contributed major features to Yardl:
- Designed the Schema Evolution feature for stream-oriented data models
- Added full support for MATLAB code generation
Built and released the next generation of the Magnetic Resonance Data (MRD) standard and SDKs

Apr 2020 - Sep 2023
Owings Mills, MD

3-year tenure as member of the senior leadership team, responsible for company-wide operational initiatives and strategy
Secured 6+ US defense contract awards as lead of Origination: Grier’s research, design, and proposal development team
Led teams of software engineers across multiple customer projects, including
- Large-scale web data analytics
- Tactical airborne cyber defense
- Forensic Intelligence using AI/ML
- Automated IoT and Industrial Control System security
- Geospatial applications of Transfer Learning.
- Modern email security
Developed engineering processes and facilitated firm-wide adoption
Planned, scheduled, designed, and implemented special projects, both internal and customer-facing

Jan 2016 - Mar 2020
Owings Mills, MD

Developed a large-scale (600 TB) web data collection and analysis platform
- Designed and implemented in Scala a framework for storing and analyzing billions of web resources
- Designed and built a distributed, high-performance web crawler using Apache Spark
Developed components of an airborne cyber defense solution for tactical IP networks
Developed Great DANE, a collection of DANE SMIMEA tools enabling email privacy and security using S/MIME
Orchestrated software demos for Army, Air Force, SOCOM, and industry stakeholders

Sep 2011 – Dec 2015
Bethesda, MD

Developed the ISMRM Raw Data format:
- Designed and implemented unit tests for the core C/C++ library
- Developed Python, Java, and Golang implementations/bindings of the ISMRMRD specification
- Deployed a continuous integration solution using Travis-CI and Github
Contributed to the Gadgetron Medical Image Reconstruction Framework
- Added DICOM image generation support
- Developed continuous integration system, tests, and scripts for retrieving test data
- Developed methods of interoperability with Python using Boost
Designed and implemented an image archiving application indexing 1.2 billion MRI DICOM images
Refactored QA analysis and visualization software for five MRI scanners using Python
Constructed a C library for creating vendor-neutral ISMRMRD files from proprietary MRI data files
Deployed secure, collaborative project environments using NFSv4, Kerberos and POSIX ACLs on Linux VMs

M.S. in Computer Science: Georgia Institute of Technology, Fall 2018
B.S. in Computer Engineering: University of Maryland, College Park, Summer 2011

Inati, S. J., Naegele, J. D., Zwart, N. R., Roopchansingh, V., Lizak, M. J., Hansen, D. C., Liu, C.-Y., Atkinson, D., Kellman, P., Kozerke, S., Xue, H., Campbell-Washburn, A. E., Sørensen, T. S. and Hansen, M. S. (2017). ISMRM Raw data format: A proposed standard for MRI raw datasets.. Magnetic Resonance in Medicine Vol. 77(1), 411-421. doi: 10.1002/mrm.26089

2016 Orloff Innovations Award

National Heart, Lung, and Blood Institute (NHLBI)

For developing image reconstruction software that enables deployment of high-performance MRI techniques in a clinical setting.

2015 Distinguished Achievement Award

Kelly Government Solutions

For computing environment improvements and contributions to ISMRMRD and Gadgetron.

2013 Distinguished Achievement Award

Kelly Government Solutions

For technical skill, enthusiasm, capacity for learning, and completion of several complex projects.

I have served as a maintainer of the following projects:

Pingvin: A new, stream-oriented medical image reconstruction framework.
MRD2: The next generation Magnetic Resonance Data format.
Yardl: A schema language and command-line tool that generates domain types and serialization code.
Gadgetron: An open source framework for medical image reconstruction.
ISMRMRD: SDKs for the Magnetic Resonance Data (MRD) format, a vendor neutral standard for describing data from MR acquisitions and reconstructions.

Luci - a lightweight programming language

DuneOS - simple x86 Unix-like operating system

Go ACLs - Go bindings to POSIX Access Control Lists

Nolli - a prototype embeddable, statically-typed programming language

Thruput - a TCP/UDP network throughput measurement tool