Vortex: An open-source library for building real-time optical coherence tomography engines

University Of Michigan At Ann Arbor, Ann Arbor MI

Investigators

Abstract

PROJECT SUMMARY This proposal seeks to support the Vortex open-source project which meets a progress-limiting need for software in optical coherence tomography (OCT) research. OCT is a laser-based imaging technique for real-time in vivo volumetric microscopy that has transformed the diagnosis and management of eye disease. Modern OCT instruments are complex mechatronic systems that match carefully designed hardware with application-specific software to achieve real-time display of high-quality images. Lack of appropriate software hampers scientific efforts as novel OCT hardware requires similarly novel software, although the latter is infrequently the research focus or subject of publication. We launched the Vortex open-source project to provide a collection of well-designed and interoperable C++ components which the user can assemble into application-specific OCT software in Python or C++. Since development began in 2020, Vortex-powered software has produced multiple peer-reviewed publications in academic research and accelerated the technology development process in multiple startup companies. This proposal now seeks to continue Vortex’s maturation as an open-source library through the following specific aims. (1) Restructure Vortex’s memory management scheme to improve flexibility and functionality. By implementing standards-compliant buffer manipulation routines following a test-driven development strategy, we will simplify hardware support and lift data type restrictions for Python bindings. (2) Update Vortex’s Python and logging interfaces to improve interoperability. In migrating Python bindings from pybind11 to the newer nanobind, we will standardize memory sharing, eliminate dependencies, streamline integration of logging, and increase performance. (3) Complete Vortex’s documentation and automated testing suite to improve usability. Through full documentation of Vortex’s Python bindings and high code coverage for testing, we will provide an accessible library that is robust and reliable. Work on each aim will occur in Vortex’s Gitlab public repository, where we will use issues, pull requests, and milestones to manage the software development process, in accordance with software industry best practices. We will disseminate these updates to Vortex through public releases on Gitlab, publication of manuscripts, and presentations/workshops at conferences. Completing these aims will yield substantial improvements in Vortex from a software engineering standpoint and produce a library that is both verifiably correct and well-documented. We believe these improvements will position Vortex as a turnkey tool on which OCT researchers and developers can rely as they advance the state-of-the-art.