CT-Based Automatic Spine Segmentation Using Patch-Based Deep Learning

Syed Furqan Qadri, Hongxiang Lin, Linlin Shen, Mubashir Ahmad, Salman Qadri, Salabat Khan, Maqbool Khan, Syeda Shamaila Zareen, Muhammad Azeem Akbar, Md Belal Bin Heyat, Saqib Qamar

Research output: Journal PublicationArticlepeer-review

44 Citations (Scopus)


CT vertebral segmentation plays an essential role in various clinical applications, such as computer-assisted surgical interventions, assessment of spinal abnormalities, and vertebral compression fractures. Automatic CT vertebral segmentation is challenging due to the overlapping shadows of thoracoabdominal structures such as the lungs, bony structures such as the ribs, and other issues such as ambiguous object borders, complicated spine architecture, patient variability, and fluctuations in image contrast. Deep learning is an emerging technique for disease diagnosis in the medical field. This study proposes a patch-based deep learning approach to extract the discriminative features from unlabeled data using a stacked sparse autoencoder (SSAE). 2D slices from a CT volume are divided into overlapping patches fed into the model for training. A random under sampling (RUS)-module is applied to balance the training data by selecting a subset of the majority class. SSAE uses pixel intensities alone to learn high-level features to recognize distinctive features from image patches. Each image is subjected to a sliding window operation to express image patches using autoencoder high-level features, which are then fed into a sigmoid layer to classify whether each patch is a vertebra or not. We validate our approach on three diverse publicly available datasets: VerSe, CSI-Seg, and the Lumbar CT dataset. Our proposed method outperformed other models after configuration optimization by achieving 89.9% in precision, 90.2% in recall, 98.9% in accuracy, 90.4% in F-score, 82.6% in intersection over union (IoU), and 90.2% in Dice coefficient (DC). The results of this study demonstrate that our model's performance consistency using a variety of validation strategies is flexible, fast, and generalizable, making it suited for clinical application.

Original languageEnglish
Article number2345835
JournalInternational Journal of Intelligent Systems
Publication statusPublished - 2023
Externally publishedYes

ASJC Scopus subject areas

  • Software
  • Theoretical Computer Science
  • Human-Computer Interaction
  • Artificial Intelligence


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