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Open-source software tracks wrist bone motion in 3D and 4D CT scans
In a development that could reshape how scientists study the mechanics of human movement, a team of biomedical engineers and computer scientists has unveiled an open-source software tool capable of tracking the tiny, intricate bones of the wrist as they glide and rotate during motion. The new tool, called Hierarchical 3D Registration, or 3DH, is a module within the SlicerAutoscoperM extension of the widely used 3DSlicer computing environment. Described in a study published in BioMedical Engineering OnLine, the software was validated against previously established methods using both sequential three-dimensional computed tomography, or 3DCT, scans of living participants performing thumb tasks and dynamic four-dimensional CT, or 4DCT, images of cadaveric wrists moving through flexion and extension. The results demonstrate that the open-source approach can match the accuracy of independent, previously published methodologies while offering researchers everywhere a free and reproducible path to quantifying skeletal kinematics.
The wrist has long been one of the most challenging joints for biomechanists to study. It contains eight small carpal bones, including the scaphoid and lunate, along with the radius of the forearm and the metacarpal bones of the hand, all articulating in a tightly packed arrangement that allows the remarkable range of motion humans rely on every day. Understanding how these bones move relative to one another, a field of study known as arthrokinematics, is essential for unraveling the causes of wrist instability, osteoarthritis, ligament injuries and the long-term outcomes of surgical repairs. Yet measuring those movements in living, moving joints has historically required either invasive techniques, labor-intensive manual analysis or proprietary software that few laboratories can access or verify.
Quantitative tracking of skeletal structures in vivo, with both efficiency and high temporal resolution, matters to a wide range of questions in biomechanical research, and the authors of the new study argue that the field has been held back by a shortage of accessible, semi-automated registration tools. Image registration, the computational process of aligning one three-dimensional image volume to another, lies at the heart of motion tracking from CT data. When a bone moves between two scans, its position and orientation change, and a registration algorithm must find the transformation that best overlays the bone’s image from one time point onto the next. Done well, this yields precise measurements of rotation and translation. Done poorly or inconsistently, it introduces errors that can swamp the small movements of carpal bones, which may shift by only a few millimeters and a few degrees during normal function.
The new 3DH module addresses this problem with a hierarchical strategy for registering bones across sequences of image volumes. The researchers presented and evaluated the software using two distinct classes of data drawn from previous studies. The first consisted of sequential 3DCT datasets of human participants performing various thumb tasks, in which the radius, the first metacarpal and the trapezium were the target bones. The second consisted of dynamic 4DCT datasets capturing simulated flexion-extension motion in cadaveric wrists, providing time-resolved, three-dimensional image volumes of the scaphoid and lunate in motion. By testing the tool on both static sequential scans and true dynamic imaging, the team was able to demonstrate that 3DH is not limited to a single imaging paradigm but can serve as a unified tracking solution across modalities.
To determine whether the new open-source tool could be trusted, the investigators compared the arthrokinematics computed with 3DH against values that had been previously calculated using independent approaches for the same 3DCT and 4DCT datasets. The statistical framework for this comparison was the Bland-Altman analysis, a standard method for assessing agreement between two measurement techniques. Rather than simply correlating the two sets of results, Bland-Altman analysis quantifies the mean bias, the systematic difference between methods, and the 95 percent limits of agreement, the range within which most individual differences between the methods are expected to fall. This approach is particularly well suited to method-comparison studies because it reveals whether a new technique introduces systematic error and how widely individual measurements might deviate from those of the established gold standard.
The performance figures reported in the study are striking. For the 3DCT data, in which the radius, first metacarpal and trapezium were tracked, the mean bias for the helical angle, a single-axis description of three-dimensional rotation, was just minus 0.06 degrees, with 95 percent limits of agreement ranging between minus 1.87 degrees and 1.74 degrees. Translation measurements fared nearly as well: the mean bias was 0.12 millimeters, with limits of agreement spanning from minus 2.23 millimeters to 2.00 millimeters. In practical terms, the open-source tool reproduced the rotational and translational measurements of the earlier methods to within roughly two degrees and two millimeters at the extremes, differences small enough to preserve the biological signal in most wrist kinematics experiments.
The dynamic 4DCT results told a similar story for the carpal bones. Tracking the scaphoid and lunate through simulated flexion-extension, 3DH produced mean biases of the Euler angle rotations, which decompose three-dimensional rotation into three orthogonal components, of less than 0.77 degrees about any direction. The widest 95 percent limits of agreement ranged between minus 7.11 degrees and 8.65 degrees. For translations, mean biases were less than 0.5 millimeters in any direction, with the widest limits of agreement ranging between minus 2.36 millimeters and 1.43 millimeters. The wider limits of agreement for rotations in the dynamic data likely reflect the added challenges of time-resolved imaging, including motion blur and the smaller, more complexly shaped carpal bones, but the near-zero mean biases indicate that the tool does not systematically drift away from established values.
Crucially, all target bones were successfully tracked in both the 3DCT and 4DCT datasets, meaning the hierarchical registration algorithm converged on correct solutions in every case tested. This robustness matters because registration algorithms can occasionally fail, locking onto incorrect alignments or diverging entirely, and such failures typically demand time-consuming manual intervention. A semi-automated tool that reliably succeeds across diverse bones, motion tasks and imaging protocols removes a significant bottleneck. Manual bone tracking in CT volume sequences can take hours per bone per trial, and the labor multiplies rapidly in studies involving multiple participants, multiple bones and dozens of motion cycles. By automating this process within a validated framework, 3DH promises to accelerate the pace at which wrist biomechanics data can be collected and analyzed.
The choice to build the module inside 3DSlicer, and specifically within the SlicerAutoscoperM extension, is a deliberate strategic decision with implications well beyond the wrist. 3DSlicer is a free, open-source platform for medical image computing and visualization with a large international user base spanning research, clinical and educational communities. By embedding 3DH in this ecosystem, the developers have made the tool immediately available to any laboratory already working with 3DSlicer, complete with the platform’s established infrastructure for loading DICOM data, segmenting anatomical structures and visualizing results. The authors note that the ability to track bones from both 3DCT and 4DCT data sources, with agreement to prior methodologies, demonstrates that the 3DH approach is a capable tool that could promote collaboration and consistency of results through open-source software.
Consistency is a quietly urgent issue in biomechanics. When different laboratories use different proprietary tools with undisclosed algorithms, it becomes difficult to distinguish true biological differences between study populations from mere methodological discrepancies. Open-source registration changes that calculus: the code can be inspected, verified, extended and reused, and results from different institutions become directly comparable because they are produced by identical algorithms. This transparency also lowers the barrier to entry for research groups in settings that cannot afford commercial licenses, potentially broadening the global community capable of conducting rigorous skeletal kinematics research.
The study itself emerged from a collaboration spanning several institutions. The team included Joseph J. Crisco, Amy M. Morton and John D. Holtgrewe of the Department of Orthopedics at The Warren Alpert Medical School of Brown University and Rhode Island Hospital; Cesar Lopez, Andrew Thoreson and Kristin D. Zhao of the Assistive and Restorative Technology Laboratory and the Department of Physical Medicine and Rehabilitation at the Mayo Clinic in Rochester, Minnesota; and Jean-Christophe Fillion-Robin and Beatriz Paniagua of Kitware Inc. in Clifton Park, New York. The involvement of Kitware, a company known for its leadership in open-source scientific computing, underscores the blend of academic rigor and software engineering expertise required to produce a research tool robust enough for widespread distribution. Funding was provided by the National Institute of Arthritis and Musculoskeletal and Skin Diseases of the National Institutes of Health under award numbers AR059185, AR078924 and AR071338.
The implications of this work extend naturally to the future of musculoskeletal imaging. As newer CT technologies, including photon-counting detector systems, deliver ever-finer spatial resolution and as dynamic 4DCT becomes more widely available, the volume of image data available for kinematic analysis will grow dramatically. Tools like 3DH, which are fast, semi-automated and validated across modalities, will be essential for converting that imaging bounty into quantitative biomechanical knowledge. For patients with wrist disorders, the downstream promise is equally tangible: better measurements of how carpal bones actually move in living joints can inform more accurate diagnoses, improved surgical planning, more realistic computational models of joint loading and ultimately better-designed treatments for conditions ranging from scapholunate instability to thumb-base arthritis. With the tool now openly available in the 3DSlicer environment, researchers around the world can begin putting it to work.
Article Title: Kinematic tracking of the small bones of the wrist in sequential 3DCT and dynamic 4DCT volume images using open-source Hierarchical 3D Registration, a module within SlicerAutoscoperM
Article References: Crisco, J. J., Morton, A. M., Lopez, C., Thoreson, A., Zhao, K. D., Holtgrewe, J. D., Fillion-Robin, J.-C., & Paniagua, B. (2026). Kinematic tracking of the small bones of the wrist in sequential 3DCT and dynamic 4DCT volume images using open-source Hierarchical 3D Registration, a module within SlicerAutoscoperM. BioMedical Engineering OnLine. https://doi.org/10.1186/s12938-026-01601-x
Image Credits: AI Generated
DOI: 10.1186/s12938-026-01601-x
Keywords: Computed tomography, 3DCT, 4DCT, Bone tracking, 3DH, 3DSlicer, Image registration, Wrist kinematics, Arthrokinematics, Open-source software, SlicerAutoscoperM, Bland-Altman analysis
