Aarhus University Seal

Automatic segmentation of the olfactory bulb

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review


  • Dmitriy Desser, Technische Universität Dresden
  • ,
  • Francisca Assunção, University of Minho
  • ,
  • Xiaoguang Yan, Technische Universität Dresden
  • ,
  • Victor Alves, University of Minho
  • ,
  • Henrique Fernandes
  • ,
  • Thomas Hummel, Technische Universität Dresden

The olfactory bulb (OB) has an essential role in the human olfactory pathway. A change in olfactory function is associated with a change of OB volume. It has been shown to predict the prognosis of olfactory loss and its volume is a biomarker for various neurodegenerative diseases, such as Alzheimer’s disease. Thus far, obtaining an OB volume for research purposes has been per-formed by manual segmentation alone; a very time-consuming and highly rater-biased process. As such, this process dramatically reduces the ability to produce fair and reliable comparisons between studies, as well as the processing of large datasets. Our study aims to solve this by proposing a novel methodological framework for the unbiased measurement of OB volume. In this paper, we present a fully automated tool that successfully performs such a task, accurately and quickly. In order to develop a stable and versatile algorithm and to train the neural network, we used four datasets consisting of whole-brain T1 and high-resolution T2 MRI scans, as well as the corresponding clinical information of the subject’s smelling ability. One dataset contained data of patients suffering from anosmia or hyposmia (N = 79), and the other three datasets contained data of healthy controls (N = 91). First, the manual segmentation labels of the OBs were created by two experienced raters, inde-pendently and blinded. The algorithm consisted of the following four different steps: (1) multi-modal data co-registration of whole-brain T1 images and T2 images, (2) template-based localization of OBs, (3) bounding box construction, and lastly, (4) segmentation of the OB using a 3D-U-Net. The results from the automated segmentation algorithm were tested on previously unseen data, achiev-ing a mean dice coefficient (DC) of 0.77 ± 0.05, which is remarkably convergent with the inter-rater DC of 0.79 ± 0.08 estimated for the same cohort. Additionally, the symmetric surface distance (ASSD) was 0.43 ± 0.10. Furthermore, the segmentations produced using our algorithm were man-ually rated by an independent blinded rater and have reached an equivalent rating score of 5.95 ± 0.87 compared to a rating score of 6.23 ± 0.87 for the first rater’s segmentation and 5.92 ± 0.81 for the second rater’s manual segmentation. Taken together, these results support the success of our tool in producing automatic fast (3–5 min per subject) and reliable segmentations of the OB, with virtu-ally matching accuracy with the current gold standard technique for OB segmentation. In conclu-sion, we present a newly developed ready-to-use tool that can perform the segmentation of OBs based on multimodal data consisting of T1 whole-brain images and T2 coronal high-resolution im-ages. The accuracy of the segmentations predicted by the algorithm matches the manual segmenta-tions made by two well-experienced raters. This method holds potential for immediate implemen-tation in clinical practice. Furthermore, its ability to perform quick and accurate processing of large datasets may provide a valuable contribution to advancing our knowledge of the olfactory system, in health and disease. Specifically, our framework may integrate the use of olfactory bulb volume (OBV) measurements for the diagnosis and treatment of olfactory loss and improve the prognosis and treatment options of olfactory dysfunctions.

Original languageEnglish
Article number1141
JournalBrain sciences
Number of pages12
Publication statusPublished - Sept 2021

Bibliographical note

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.

    Research areas

  • Deep learning, Olfactory bulb, Olfactory loss, Segmentation

See relations at Aarhus University Citationformats

ID: 222984504