VORTEX#

vortex is a high-performance C++ library with Python bindings for building real-time OCT engines. It provides:

  • modular components out of which an OCT engine is built

  • a flexible OCT engine that accommodates most use cases

  • extensive Python bindings that interoperate with NumPy and CuPy

vortex is designed from the ground up to:

  • promote reproducibility in data acquisition and processing

  • guarantee synchronization between data streams

  • support on-the-fly changes for interactive use cases

  • integrate cleanly with user interfaces

  • facilitate rapid prototyping with high-level abstractions and sane defaults

  • minimize restrictions and assumptions

vortex is developed and maintained by Mark Draelos in the Izatt Lab at Duke University.

Note

vortex is an acronym for Variable OCT for Real-Time Execution. Its logo is a warning sign that depicts a cyclone, emblematic of the goal to provide maximum throughput.

Notable Features#

vortex has several multiple features that make it particularly suitable for the OCT research and development community.

  • Motion Planner for Scan Generation

    Generate dynamically feasible scan patterns for your hardware. vortex will transparently insert the minimum number of inactive samples to avoid scan distortion and automatically crop out flyback.

  • Scan Markers for Flexible Patterns

    The scan pattern is encoded by markers that annotate the scan waveforms rather than a rigid structure. vortex reconstructs the scan after the acquisition by decoding the markers. This decouples scan pattern generation from the core OCT engine.

  • High-performance Processing Pipeline

    vortex implements a reconfigurable engine that performs your acquisition and processing once given a description of your system. The engine pre-allocates resources for quick startup after initialization.

  • Multiple GPU Support

    vortex’s engine can easily distribute large workloads over multiple GPUs. The engine will infer the necessary transfers between GPUs or rely on peer-to-peer access, if supported.

  • Extensive Python Bindings

    vortex is fully usable from Python and C++. The detailed Python bindings provide nearly a one-to-one correspondence with low-level C++ capabilities without needing to recompile between application changes.

  • Full OCT Application Feature Set

    vortex supports UI inactivity, real-time data storage to disk is popular file formats, synchronized I/O, and other usability features necessary to build a complete OCT application.

  • Permissive BSD-3 License

    vortex is released under the permissive BSD-3 license that supports commercial and research use.

Quickstart#

  1. Follow the Getting Started guide for Python or C++.

  2. Configure and run some Demos.

  3. Check out the Build Guide to customize vortex.