Automatic mouse embryo brain ventricle segmentation from 3D 40-MHz ultrasound data

Jen Wei Kuo, Yao Wang, Orlando Aristizabal, Jeffrey A. Ketterling, Jonathan Mamou

Research output: Chapter in Book/Report/Conference proceedingConference contribution


Volumetric analysis of brain ventricles is important to the study of normal and abnormal development of the central nervous system of mouse embryos. High-frequency ultrasound (HFU) is frequently used to image embryos because HFU is real-time, non-invasive, and provides fine-resolution images. However, manual segmentation of ventricles from 3D HFU volumes remains challenging and time consuming. In this study, in utero and in vivo volumetric ultrasound data were acquired from pregnant mice using a 5-element, 40-MHz annular array. An automatic segmentation algorithm based on active shape model (ASM) was developed to segment the brain ventricles of the embryos; ASM allows us to efficiently 'learn' from training data (i.e., manually segmented data). The algorithm was further enhanced by using detail-preserving reference shapes (also learned from training data) and region growing constrained by the reference shape. The hybrid algorithm was applied to three 12.5-day-old embryos. Results were qualitatively analyzed and compared with manual segmentation results in regions typically difficult to segment (e.g., thin brain ventricle connections). In addition, quantitative analysis using the Dice similarity coefficient (DSC) was used to compare the automatic segmentation results with manual segmentation. We obtained average DSC values of 0.848±0.015 for the brain ventricles and our method produced morphologically accurate results. Therefore, our method could streamline current HFU longitudinal studies of brain development that require manual segmentation.

Original languageEnglish (US)
Title of host publication2013 IEEE International Ultrasonics Symposium, IUS 2013
Number of pages4
StatePublished - 2013
Event2013 IEEE International Ultrasonics Symposium, IUS 2013 - Prague, Czech Republic
Duration: Jul 21 2013Jul 25 2013

Publication series

NameIEEE International Ultrasonics Symposium, IUS
ISSN (Print)1948-5719
ISSN (Electronic)1948-5727


Other2013 IEEE International Ultrasonics Symposium, IUS 2013
Country/TerritoryCzech Republic


  • Brain
  • High-frequency ultrasound
  • Mouse embryo
  • Segmentation

ASJC Scopus subject areas

  • Acoustics and Ultrasonics


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