Automated segmentation and enhancement of optical coherence tomography-acquired images of rodent brain

Utku Baran, Wenbin Zhu, Woo June Choi, Michael Omori, Wenri Zhang, Nabil J. Alkayed, Ruikang K. Wang

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


Background Optical coherence tomography (OCT) is a non-invasive optical imaging method that has proven useful in various fields such as ophthalmology, dermatology and neuroscience. In ophthalmology, significant progress has been made in retinal layer segmentation and enhancement of OCT images. There are also segmentation algorithms to separate epidermal and dermal layers in OCT-acquired images of human skin. New method We describe simple image processing methods that allow automatic segmentation and enhancement of OCT images of rodent brain. Results We demonstrate the effectiveness of the proposed methods for OCT-based microangiography (OMAG) and tissue injury mapping (TIM) of mouse cerebral cortex. The results show significant improvement in image contrast, delineation of tissue injury, allowing visualization of different layers of capillary beds. Comparison with existing methods Previously reported methods for other applications are yet to be used in neuroscience due to the complexity of tissue anatomy, unique physiology and technical challenges. Conclusions OCT is a promising tool that provides high resolution in vivo microvascular and structural images of rodent brain. By automatically segmenting and enhancing OCT images, structural and microvascular changes in mouse cerebral cortex after stroke can be monitored in vivo with high contrast.

Original languageEnglish (US)
Pages (from-to)132-137
Number of pages6
JournalJournal of Neuroscience Methods
StatePublished - Sep 1 2016


  • Image reconstruction techniques
  • Optical coherence tomography
  • Optical microangiography
  • Stroke

ASJC Scopus subject areas

  • Neuroscience(all)


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