Automated three-dimensional identification and tracking of micro/nanobiological organisms by computational holographic microscopy

Inkyu Moon, Mehdi Daneshpanah, Bahram Javidi, Adrian Stern

Research output: Contribution to journalArticlepeer-review

99 Scopus citations


The ability to sense, track, identify, and monitor biological micro/nanoorganisms in a real-time, automated, and integrated system is of great importance from both scientific and technological standpoints. Such a system and its possible variants would have numerous applications in a wide spectrum of fields, including defense against biological warfare, disease control, environmental health and safety, and medical treatments. In this paper, we review a comprehensive mixture of optical and computational tools developed in our group aiming at real-time sensing and recognition of biological microorganisms. Digital in-line holographic microscopy is used with both coherent and partially coherent illumination to probe the specimen interferometerically. The interference pattern is then recorded on an optoelectronic image sensor and transferred to a computer where special statistical algorithms are performed to segment, recognize, and track the microorganisms within the field of view of the microscope. The advantages of proposed holographic sensing are described compared to conventional two-dimensional imaging systems. In addition, the theoretical aspects and fundamental limitations of digital in-line holographic microscopy are discussed, which determine the relationship between system parameters and achievable performance. The proposed optical-digital integrated system for automated, real-time sensing and recognition of biological microorganisms has been deemed promising with the potential of widespread application. We demonstrate how the proposed techniques function together in a series of experiments.

Original languageEnglish
Article number4939403
Pages (from-to)990-1010
Number of pages21
JournalProceedings of the IEEE
Issue number6
StatePublished - 1 Jan 2009


  • Biophotonics
  • Gabor feature extraction
  • Holographic microscopy
  • Noninvasive biosensing
  • Three-dimensional image recognition
  • Three-dimensional image segmentation and tracking
  • Three-dimensional optical imaging

ASJC Scopus subject areas

  • Computer Science (all)
  • Electrical and Electronic Engineering


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