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What is Autoscoper?

Autoscoper enables the 3D tracking of structures within images collected via single, bi-, and multi-plane videoradiography. (Most commonly bi-plane videoradiography or BVR). It has been used for tracking the shoulder, spine, wrist, hip, knee, and ankle joints.

Autoscoper is distributed through SlicerAutoscoperM (SAM), a free, open source and multi-platform 3D Slicer extension. To learn more about the relationship between Autoscoper and SAM, see https://autoscoperm.slicer.org/.

In addition to Autoscoper, SAM includes a Pre-Processing module for Autoscoper videoradiography inputs, a Tracking Evaluation module for BVR sample data outputs, and the 3D Hierarchical Registration module for registration of structures collected via 4DCT and sequential 3D CT.

License

The SAM software is distributed under a BSD-style open source license that is broadly compatible with the Open Source Definition by The Open Source Initiative and contains no restrictions on legal uses of the software. For more information, see the Autoscoper License File

Historical Notes about the License

The Autoscoper license is an adaptation of the BSD-3 license with customized additions to the Disclaimer of Warranty and Limitation of Liability that were drafted by Brown University lawyers in 2011. These additional clauses go beyond the standard BSD-3 disclaimer by explicitly stating that Brown University provides no warranties or representations of any kind, including those for design, merchantability, and fitness for purpose, and disclaims any errors or infringement on third-party proprietary rights. The Autoscoper license also limits Brown University’s liability for damages arising out of the use of the software, including direct and indirect damages, as well as any loss of data or profits.

History of Autoscoper

In November 2020, the development was transitioned from bitbucket to GitHub. See https://github.com/BrownBiomechanics/Autoscoper/

From 2018 to 2020, Dr.Bardiya Akhbari from Brown University maintained the software on bitbucket, worked on addressing the reported issues, further optimized the CUDA kernels, and implemented support for the Particle Swarm Optimization (PSO) algorithm to improve the accuracy and speed of registration.

From 2014 to 2018, Autoscoper v2 was developed at Brown University by Dr. Benjamin Knorlein. Multi-bone tracking and batch processing features were added, a socket-based protocol was designed for interaction with third-party software (mainly Matlab), the build system was transitioned to CMake and the UI was transitioned from Qt4 and GTK to Qt5. Version 2 combined the sources of both the CUDA and OpenCL versions and allows usage of either one. The source code was organized at https://bitbucket.org/xromm/autoscoper-v2.

From 2012 to 2013, Autoscoper v1 was developed at Brown University by Andy Loomis and Mark Howison. Andy developed the original CUDA version and Mark developed the OpenCL reimplementation. Source code was organized at https://bitbucket.org/mhowison/xromm-autoscoper.

How to cite

When citing SlicerAutoscoperM in your scientific research, please mention the following work to support increased visibility and dissemination of our software:

Morton AM, Holtgrewe JD, Beveridge JE, Yoon D, Rainbow MJ, Lopez C, Zhao KD, Paniagua B, Fillion-Robin JC, Lombardi AJ, Moore DC, Crisco JJ. An accuracy assessment of SlicerAutoscoperM − software for tracking skeletal structures in multi-plane videoradiography datasets. Journal of Biomechanics. 2025 Aug;189:112810.

See https://www.sciencedirect.com/science/article/pii/S0021929025003227

For your convenience, you may use the following BibTex entry:

@article{MORTON2025112810,
title    = {An accuracy assessment of SlicerAutoscoperM − software for tracking skeletal structures in multi-plane videoradiography datasets},
journal  = {Journal of Biomechanics},
volume   = {189},
pages    = {112810},
year     = {2025},
issn     = {0021-9290},
doi      = {https://doi.org/10.1016/j.jbiomech.2025.112810},
url      = {https://www.sciencedirect.com/science/article/pii/S0021929025003227},
author   = {Amy M. Morton and John D. Holtgrewe and Jillian E. Beveridge and Dajung Yoon and Michael J. Rainbow and Cesar Lopez and Kristin D. Zhao and Beatriz Paniagua and Jean-Christophe Fillion-Robin and Anthony J. Lombardi and Douglas C. Moore and Joseph J. Crisco},
keywords = {Autoscoper, Kinematics, 3DSlicer, Videoradiography, Skeletal Tracking},
}

Related work

You may also consider referencing the following earlier publication, which demonstrates Autoscoper’s accuracy in the context of wrist kinematics using biplane videoradiography:

Akhbari, B., Morton, A. M., Moore, D. C., Weiss, A-P. C., Wolfe, W. S., Crisco, J. J., 2019. Accuracy of Biplane Videoradiography for Quantifying Dynamic Wrist Kinematics, Journal of Biomechanics.

See https://www.sciencedirect.com/science/article/abs/pii/S0021929019303847

For your convenience, here is the corresponding BibTeX entry:

@article{AKHBARI2019120,
  title    = {Accuracy of biplane videoradiography for quantifying dynamic wrist kinematics},
  journal  = {Journal of Biomechanics},
  volume   = {92},
  pages    = {120-125},
  year     = {2019},
  issn     = {0021-9290},
  doi      = {https://doi.org/10.1016/j.jbiomech.2019.05.040},
  url      = {https://www.sciencedirect.com/science/article/pii/S0021929019303847},
  author   = {Bardiya Akhbari and Amy M. Morton and Douglas C. Moore and Arnold-Peter C. Weiss and Scott W. Wolfe and Joseph J. Crisco},
  keywords = {Biplane videoradiography, Wrist kinematics, Accuracy study, Markerless tracking},
}

Contact Us

We want to hear from you! If you have any questions, bug reports, or enhancement requests regarding SlicerAutoscoperM or Autoscoper, there are several communication channels available for you:

SlicerAutoscoperM Forum

Visit the SlicerAutoscoperM category on the Slicer Discourse forum for community-driven support, to share your experiences, exchange ideas and best practices, and to discuss challenges.

Issue Tracker

Use our public issue tracker to report any bugs or request enhancements. This tracker is a ticket-based system that allows you to keep track of your issues and follow up on their progress.

If you already know to witch component your request pertains, you may explicitly use the SlicerAutoscoperM or Autoscoper issue tracker.