Submersible digital in-line holographic microscope

Jericho, S. K.; Garcı́a-Sucerquia, Jorge; Xu, Wenbo; Jericho, M. H.; Kreuzer, H. J.

doi:10.1063/1.2193827

Cited by 120 publications

(80 citation statements)

References 14 publications

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“…The principles of digital inline holography and image reconstruction algorithms were published previously (Gabore 1948;Kreuzer et al 1992;Xu et al 2001;Xu et al 2003;Jericho et al 2006). Briefly, light from a laser is focused onto a pinhole, or in this case, one end of an optical fiber.…”

Section: Bochdansky Et Almentioning

confidence: 99%

“…The application of holography for imaging plankton organisms has a long history from initially those based on individual photographic plates to most recently those based on CCD and CMOS sensors (Knox 1966;Beers et al 1970;Solokov et al 1971, Malkiel et al 1999Watson et al 2003;Watson 2005;Sun et al 2007;Jericho et al 2006Jericho et al , 2010Lewis et al 2006;Xu et al 2001). Holography has been used in different embodiments either in its simplest form as Fraunhofer inline holography or off-axis holography (Vikram 1992).…”

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confidence: 99%

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Development and deployment of a point‐source digital inline holographic microscope for the study of plankton and particles to a depth of 6000 m

Bochdansky

Jericho

Herndl

2013

Limnology & Ocean Methods

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A point-source digital inline holographic microscope (DIHM) was designed for the imaging of particles from 50 µm to several millimeters in size. The DIHM operates autonomously without connection to external recording devices or power sources and delivers 4.2 megapixel images at a rate of approximately 7 images s -1 , each image representing a snapshot of 1.8 mL seawater. Reliance on largely off-the-shelf components, and simplification in its construction makes this camera system adaptable to various particle size ranges and environments, and easy-to-operate for nonexpert users. The DIHM produced sharp images of protists with skeletal structures (e.g., acantharians, tintinnids, dinoflagellates), mesoplankton (e.g., copepods, appendicularians, medusae), Trichodesmium colonies and marine snow particles while descending in the water column at 1 m s -1 , a typical velocity for deployments of tethered instruments and samplers from oceanographic vessels. To validate the usefulness of the new instrument in an oceanographic context, data are presented of the surface distribution of Trichodesmium spp., and of the vertical frequency distribution of fecal pellets and other particles in the deep sea. The point-source DIHM has the potential to become a standard instrument on the CTD rosette (i.e., on the basic oceanographic instrument and sampling frame) in the future providing a permanent archival record of the water column that can be mined for specific target particles in the future. Limnol. Oceanogr.: Methods 11, 2013Methods 11, , 28-40 © 2013, by the American Society of Limnology and Oceanography, Inc. LIMNOLOGY and OCEANOGRAPHY: METHODSof hard drives, and miniaturization of embedded computers with conventional software that can be programmed by nonexpert users. We describe our design innovations and software integration and illustrate our experience during the first oceanographic deployment in the tropical and subtropical Atlantic to a maximum depth of 6000 m, by far the deepest deployment of any holographic camera to date.

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Section: Bochdansky Et Almentioning

confidence: 99%

mentioning

confidence: 99%

Development and deployment of a point‐source digital inline holographic microscope for the study of plankton and particles to a depth of 6000 m

Bochdansky

Jericho

Herndl

2013

Limnology & Ocean Methods

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“…Factors that limit the achievable resolution in DIHM have been treated extensively with developed criteria for achieving lateral as well as depth resolution [GXJKJK06a,GXJKJK06b,JGXJK06]. The FOV in DIHM is defined as the area in the object plane magnified by the incident spherical reference field and captured in the reconstructed hologram.…”

Section: Field Of View and Reconstructed Object Magnificationmentioning

confidence: 99%

“…Consequently, this limits the obtainable resolution in the reconstructed image. Other resolution-limiting factors in DIHM include the size and position of the CCD, pixel density in the hologram, location of the object between the pinhole and CCD, and wavelength of the reference wave [GXJKJK06b,JGXJK06,RPP04,KJMX01]. Another limiting effect of the size of pinhole used is the restriction of the field of view (area captured) in the reconstructed image, especially when imaging an object that extends over an area of larger dimension compared to the numerical aperture of the system.…”

Section: Introductionmentioning

confidence: 99%

Programmable Point-source Digital In-line Holography Using Digital Micro-mirror Devices

Adeyemi¹,

Darcie²

2011

Holography, Research and Technologies

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“…A few instruments rely on bringing samples closer to the imaging system by suctioning or 75 otherwise restricting movement of plankton [266], [311], [59], [179], [137]. Avoidance in these devices is likely, or the strategies for capture (i.e., a narrow slit that the plankton enter naturally [179]) are not scalable to zooplankton which have strong escape responses to ‡uid perturbations, such as copepods [47], [426], [168].…”

Section: Development: Lab To Oceanmentioning

confidence: 99%

Computational imaging and automated identification for aqueous environments

Loomis¹

2011

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Sampling the vast volumes of the ocean requires tools capable of observing from a distance while retaining detail necessary for biology and ecology, ideal for optical methods. Algorithms that work with existing SeaBED AUV imagery are developed, including habitat classi…cation with bag-of-words models and multi-stage boosting for rock…sh detection. Methods for extracting images of …sh from videos of longline operations are demonstrated.A prototype digital holographic imaging device is designed and tested for quantitative in situ microscale imaging. Theory to support the device is developed, including particle noise and the e¤ects of motion. A Wigner-domain model provides optimal settings and optical limits for spherical and planar holographic references.Algorithms to extract the information from real-world digital holograms are created. Focus metrics are discussed, including a novel focus detector using local Zernike moments. Two methods for estimating lateral positions of objects in holograms without reconstruction are presented by extending a summation kernel to spherical references and using a local frequency signature from a Riesz transform. A new metric for quickly estimating object depths without reconstruction is proposed and tested. An example application, quantifying oil droplet size distributions in an underwater plume, demonstrates the e¢ cacy of the prototype and algorithms. Course work at MIT and WHOI was helpful throughout this thesis. In particular, course materials and projects from Dr. Antonio Torralba (computer vision, detection, and boosting), Dr. Frédo Durand (computational imaging, segmentation, and probability), Dr. Rosalind Picard (machine learning, pattern recognition, and probability), Dr. Alan 4 Edelman (parallel computing and algorithms), and Dr. Barbastathis (optical systems) are re ‡ected directly, in several cases extended after the course to become complete sections of this thesis.The MIT Museum has provided unique outreach opportunities for the ideas presented in this thesis. Seth Riskin originally involved our lab in holography activities at the MIT Museum, then Kurt Hasselbalch later proposed and guided the development of an interactive display on plankton holography. The computational approaches I learned for the museum display led to further scienti…c development and spurred the use of GPUs for processing; Section 3.3.5 is a direct consequence, as is the majority of the data processing performed throughout this thesis.In reference to data processing, Matlab/MEX and NVIDIA's CUDA have been daily cornerstones for which I am continually thankful. Finally, mad props go to Dr. José "Pepe" Domínguez-Caballero, the most in ‡uential 5 person in my scienti…c development while at MIT. Pepe taught me digital holography and worked one-on-one with me throughout the beginning of my grad student career. He continued to be involved as a fellow holographer, a mentor, and a friend, discussing ideas, encouraging active experimentation, maintaining a curiosity about optics, and o¤ering eno...

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Submersible digital in-line holographic microscope

Cited by 120 publications

References 14 publications

Development and deployment of a point‐source digital inline holographic microscope for the study of plankton and particles to a depth of 6000 m

Development and deployment of a point‐source digital inline holographic microscope for the study of plankton and particles to a depth of 6000 m

Programmable Point-source Digital In-line Holography Using Digital Micro-mirror Devices

Computational imaging and automated identification for aqueous environments

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