3D vertebrae labeling in spine CT: An accurate, memory-efficient (Ortho2D) framework

Y. Huang, A. Uneri, C. K. Jones, X. Zhang, M. D. Ketcha, N. Aygun, P. A. Helm, J. H. Siewerdsen

Research output: Contribution to journalArticlepeer-review


Purpose. Accurate localization and labeling of vertebrae in computed tomography (CT) is an important step toward more quantitative, automated diagnostic analysis and surgical planning. In this paper, we present a framework (called Ortho2D) for vertebral labeling in CT in a manner that is accurate and memory-efficient. Methods. Ortho2D uses two independent faster R-convolutional neural network networks to detect and classify vertebrae in orthogonal (sagittal and coronal) CT slices. The 2D detections are clustered in 3D to localize vertebrae centroids in the volumetric CT and classify the region (cervical, thoracic, lumbar, or sacral) and vertebral level. A post-process sorting method incorporates the confidence in network output to refine classifications and reduce outliers. Ortho2D was evaluated on a publicly available dataset containing 302 normal and pathological spine CT images with and without surgical instrumentation. Labeling accuracy and memory requirements were assessed in comparison to other recently reported methods. The memory efficiency of Ortho2D permitted extension to high-resolution CT to investigate the potential for further boosts to labeling performance. Results. Ortho2D achieved overall vertebrae detection accuracy of 97.1%, region identification accuracy of 94.3%, and individual vertebral level identification accuracy of 91.0%. The framework achieved 95.8% and 83.6% level identification accuracy in images without and with surgical instrumentation, respectively. Ortho2D met or exceeded the performance of previously reported 2D and 3D labeling methods and reduced memory consumption by a factor of ∼50 (at 1 mm voxel size) compared to a 3D U-Net, allowing extension to higher resolution datasets than normally afforded. The accuracy of level identification increased from 80.1% (for standard/low resolution CT) to 95.1% (for high-resolution CT). Conclusions. The Ortho2D method achieved vertebrae labeling performance that is comparable to other recently reported methods with significant reduction in memory consumption, permitting further performance boosts via application to high-resolution CT.

Original languageEnglish (US)
Article number125020
JournalPhysics in medicine and biology
Issue number12
StatePublished - Jun 21 2021


  • deep learning
  • object detection
  • spine surgery
  • surgical data science
  • vertebrae labeling

ASJC Scopus subject areas

  • Radiological and Ultrasound Technology
  • Radiology Nuclear Medicine and imaging


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