2005 |
Ai, Yuhui; Jaffe, Jules S Design and preliminary tests of a family of adaptive waveforms to measure blood vessel diameter and wall thickness Journal Article IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control: Special Issue on Coded Waveforms, 52 (2), pp. 250-260, 2005, ISSN: 0885-3010. @article{Ai2005, title = {Design and preliminary tests of a family of adaptive waveforms to measure blood vessel diameter and wall thickness}, author = { Yuhui Ai and Jules S. Jaffe}, issn = {0885-3010}, year = {2005}, date = {2005-01-01}, journal = {IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control: Special Issue on Coded Waveforms}, volume = {52}, number = {2}, pages = {250-260}, publisher = {IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC}, address = {445 HOES LANE, PISCATAWAY, NJ 08855 USA}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jaffe, Jules S Performance bounds on synchronous laser line scan systems Journal Article Optics Express, 13 (3), pp. 738-748, 2005, ISSN: 1094-4087. @article{Jaffe2005, title = {Performance bounds on synchronous laser line scan systems}, author = { Jules S. Jaffe}, issn = {1094-4087}, year = {2005}, date = {2005-01-01}, journal = {Optics Express}, volume = {13}, number = {3}, pages = {738-748}, publisher = {OPTICAL SOC AMER}, address = {2010 MASSACHUSETTS AVE NW, WASHINGTON, DC 20036 USA}, abstract = {In this article a performance bound is derived for feasible image resolution among a class of imaging systems that can be referred to as synchronous laser line scan systems. Most often, these systems use a narrow beam projected source ( typically a laser) in conjunction with a very small field of view receiver that is synchronously scanned. Here, a bound on the maximum system resolution is derived when both source and receiver are textquotelefttextquoteleftdelta function liketextquoterighttextquoteright. The bound demonstrates that the best achievable overall system point spread function is the square of the one way point spread function for the medium. (C) 2005 Optical Society of America.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this article a performance bound is derived for feasible image resolution among a class of imaging systems that can be referred to as synchronous laser line scan systems. Most often, these systems use a narrow beam projected source ( typically a laser) in conjunction with a very small field of view receiver that is synchronously scanned. Here, a bound on the maximum system resolution is derived when both source and receiver are textquotelefttextquoteleftdelta function liketextquoterighttextquoteright. The bound demonstrates that the best achievable overall system point spread function is the square of the one way point spread function for the medium. (C) 2005 Optical Society of America. |
Yahel, R; Yahel, G; Berman, T; Jaffe, Jules S; Genin, A Diel pattern with abrupt crepuscular changes of zooplankton over a coral reef Journal Article Limnology And Oceanography, 50 (3), pp. 930–944, 2005. @article{Yahel2005, title = {Diel pattern with abrupt crepuscular changes of zooplankton over a coral reef}, author = { R. Yahel and G. Yahel and T. Berman and Jules S. Jaffe and A. Genin}, year = {2005}, date = {2005-01-01}, journal = {Limnology And Oceanography}, volume = {50}, number = {3}, pages = {930–944}, publisher = {Amer Soc Limnology Oceanography}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jaffe, Jules S Sensing Plankton: Acoustics and Optical Imaging Book Chapter European Workshop on Harmful Algal Blooms, 2005. @inbook{Jaffe2005b, title = {Sensing Plankton: Acoustics and Optical Imaging}, author = { Jules S. Jaffe}, year = {2005}, date = {2005-01-01}, booktitle = {European Workshop on Harmful Algal Blooms}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } |
Genin, Amatzia; Jaffe, Jules S; Reef, Ruth ; Richter, Claudio ; Franks, Peter J S Swimming Against the Flow: A Mechanism of Zooplankton Aggregation Journal Article Science, 308 (5723), pp. 860-862, 2005. @article{Genin2005, title = {Swimming Against the Flow: A Mechanism of Zooplankton Aggregation}, author = { Amatzia Genin and Jules S. Jaffe and Ruth Reef and Claudio Richter and Peter J.S. Franks}, url = {http://www.sciencemag.org/cgi/content/abstract/308/5723/860}, year = {2005}, date = {2005-01-01}, journal = {Science}, volume = {308}, number = {5723}, pages = {860-862}, abstract = {Zooplankton reside in a constantly flowing environment. However, information about their response to ambient flow has remained elusive, because of the difficulties of following the individual motions of these minute, nearly transparent animals in the ocean. Using a three-dimensional acoustic imaging system, we tracked >375,000 zooplankters at two coastal sites in the Red Sea. Resolution of their motion from that of the water showed that the animals effectively maintained their depth by swimming against upwelling and downwelling currents moving at rates of up to tens of body lengths per second, causing their accumulation at frontal zones. This mechanism explains how oceanic fronts become major feeding grounds for predators and targets for fishermen.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Zooplankton reside in a constantly flowing environment. However, information about their response to ambient flow has remained elusive, because of the difficulties of following the individual motions of these minute, nearly transparent animals in the ocean. Using a three-dimensional acoustic imaging system, we tracked >375,000 zooplankters at two coastal sites in the Red Sea. Resolution of their motion from that of the water showed that the animals effectively maintained their depth by swimming against upwelling and downwelling currents moving at rates of up to tens of body lengths per second, causing their accumulation at frontal zones. This mechanism explains how oceanic fronts become major feeding grounds for predators and targets for fishermen. |
Jaffe, Jules S Three-dimensional probability density functions via tomographic inversion Journal Article Siam Journal On Applied Mathematics, 65 (5), pp. 1506–1525, 2005. @article{Jaffe2005b, title = {Three-dimensional probability density functions via tomographic inversion}, author = { Jules S. Jaffe}, year = {2005}, date = {2005-01-01}, journal = {Siam Journal On Applied Mathematics}, volume = {65}, number = {5}, pages = {1506–1525}, publisher = {Siam Publications}, abstract = {In many experimental observation systems where the goal is to record a three-dimensional observation of an object, or a set of objects, a lower-dimensional projection of the intended subject is obtained. In some situations only the statistical properties of such objects are desired: the three-dimensional probability density function. This article demonstrates that under special symmetries this function can be obtained from either a one- or two-dimensional probability density function which has been obtained from the observed, projected data. Standard tomographic theorems can be used to guarantee the uniqueness of this function, and a natural basis set can be used in computing the three-dimensional function from the one- or two-dimensional projection. The theory of this inversion is explored using theoretical and computational methods with examples of data taken from scientific experiments.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In many experimental observation systems where the goal is to record a three-dimensional observation of an object, or a set of objects, a lower-dimensional projection of the intended subject is obtained. In some situations only the statistical properties of such objects are desired: the three-dimensional probability density function. This article demonstrates that under special symmetries this function can be obtained from either a one- or two-dimensional probability density function which has been obtained from the observed, projected data. Standard tomographic theorems can be used to guarantee the uniqueness of this function, and a natural basis set can be used in computing the three-dimensional function from the one- or two-dimensional projection. The theory of this inversion is explored using theoretical and computational methods with examples of data taken from scientific experiments. |
2004 |
Roberts, Paul L D; Jaffe, Jules S Identifying stable frequencies for performing animal abundance estimation with a multifrequency system Conference Acoustical Society of America, San Diego, CA, 2004. @conference{2004, title = {Identifying stable frequencies for performing animal abundance estimation with a multifrequency system}, author = { Paul L. D. Roberts and Jules S. Jaffe}, year = {2004}, date = {2004-01-01}, booktitle = {Acoustical Society of America}, address = {San Diego, CA}, keywords = {}, pubstate = {published}, tppubtype = {conference} } |
Schell, C; Jaffe, Jules S Experimental verification of an interpolation algorithm for improved estimates of animal position Journal Article Journal of the Acoustical Socieity of America, 116 (1), pp. 254-261, 2004, ISSN: 0001-4966. @article{Schell2004, title = {Experimental verification of an interpolation algorithm for improved estimates of animal position}, author = { C Schell and Jules S. Jaffe}, issn = {0001-4966}, year = {2004}, date = {2004-01-01}, journal = {Journal of the Acoustical Socieity of America}, volume = {116}, number = {1}, pages = {254-261}, publisher = {ACOUSTICAL SOC AMER AMER INST PHYSICS}, address = {STE 1 NO 1, 2 HUNTINGTON QUADRANGLE, MELVILLE, NY 11747-4502 USA}, abstract = {This article presents experimental verification of an interpolation algorithm that was previously proposed in Jaffe [J. Acoust. Soc. Am. 105, 3168-3175 (1999)]. The goal of the algorithm is to improve estimates of both target position and target strength by minimizing a least-squares residual between noise-corrupted target measurement data and the output of a model of the sonartextquoterights amplitude response to a target at a set of known locations. Although this positional estimator was shown to be a maximum likelihood estimator, in principle, experimental verification was desired because of interest in understanding, its true performance. Here, the accuracy of the algorithm is investigated by analyzing the correspondence between a targettextquoterights true position and the algorithmtextquoterights estimate. True target position was measured by precise translation of a small test target (bead) or from the analysis of images of fish from a coregistered optical imaging system. Results with the stationary spherical test bead in a high signal-to-noise environment indicate that a large increase in resolution is possible, while results with commercial aquarium fish indicate a smaller increase is obtainable. However, in both experiments the algorithm provides improved estimates of target position over those obtained by simply accepting the angular positions of the sonar beam with maximum output as target position. In addition, increased accuracy in target strength estimation is possible by considering the effects of the sonar beam patterns relative to the interpolated position. A benefit of the algorithm is that it can be applied textquotelefttextquoteleftex post factotextquoterighttextquoteright to existing data sets from commercial multibeam sonar systems when only the beam intensities have been stored after suitable calibration. (C) 2004 Acoustical Society of America.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This article presents experimental verification of an interpolation algorithm that was previously proposed in Jaffe [J. Acoust. Soc. Am. 105, 3168-3175 (1999)]. The goal of the algorithm is to improve estimates of both target position and target strength by minimizing a least-squares residual between noise-corrupted target measurement data and the output of a model of the sonartextquoterights amplitude response to a target at a set of known locations. Although this positional estimator was shown to be a maximum likelihood estimator, in principle, experimental verification was desired because of interest in understanding, its true performance. Here, the accuracy of the algorithm is investigated by analyzing the correspondence between a targettextquoterights true position and the algorithmtextquoterights estimate. True target position was measured by precise translation of a small test target (bead) or from the analysis of images of fish from a coregistered optical imaging system. Results with the stationary spherical test bead in a high signal-to-noise environment indicate that a large increase in resolution is possible, while results with commercial aquarium fish indicate a smaller increase is obtainable. However, in both experiments the algorithm provides improved estimates of target position over those obtained by simply accepting the angular positions of the sonar beam with maximum output as target position. In addition, increased accuracy in target strength estimation is possible by considering the effects of the sonar beam patterns relative to the interpolated position. A benefit of the algorithm is that it can be applied textquotelefttextquoteleftex post factotextquoterighttextquoteright to existing data sets from commercial multibeam sonar systems when only the beam intensities have been stored after suitable calibration. (C) 2004 Acoustical Society of America. |
2003 |
Zawada, DG; Jaffe, Jules S Changes in the fluorescence of the Caribbean coral Montastraea faveolata during heat-induced bleaching Journal Article Limnology and Oceanography, 48 (1, Part 2), pp. 412-425, 2003, ISSN: 0024-3590. @article{Zawada2003, title = {Changes in the fluorescence of the Caribbean coral Montastraea faveolata during heat-induced bleaching}, author = { DG Zawada and Jules S. Jaffe}, issn = {0024-3590}, year = {2003}, date = {2003-01-01}, journal = {Limnology and Oceanography}, volume = {48}, number = {1, Part 2}, pages = {412-425}, publisher = {AMER SOC LIMNOLOGY OCEANOGRAPHY}, address = {5400 BOSQUE BLVD, STE 680, WACO, TX 76710-4446 USA}, abstract = {In order to evaluate the response of commonly occurring green and orange fluorescent host-based pigments, a thermal stress experiment was performed on specimens of the Caribbean coral Montastraea faveolata. Seven paired samples were collected from a small oceanic reef near Lee Stocking Island in the Bahamas. Seven of the fourteen corals were subjected to elevated temperatures for 28 d, followed by a recovery period lasting 53 d. Throughout the experiment, high-resolution (similar to400 mum pixel(-1)) multispectral images of induced fluorescence were recorded at wavelengths corresponding to the green and orange host pigments, plus chlorophyll. These images revealed that the fluorescence of both host pigments was concentrated at polyp centers and declined by 70-90% in regions between polyps. Chlorophyll fluorescence, however, was distributed almost uniformly across the entire coral surface, but with decreases of 10-30% around polyp centers. A normalized difference ratio between the green and orange pigments (GO ratio) was developed to facilitate comparison with chlorophyll fluorescence as a bleaching indicator. Analysis showed a high correspondence between a sustained GO ratio of less than zero and the death of corals. Finally, this ratio was resistant to contamination from other sources of chlorophyll fluorescence, such as filamentous algae.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In order to evaluate the response of commonly occurring green and orange fluorescent host-based pigments, a thermal stress experiment was performed on specimens of the Caribbean coral Montastraea faveolata. Seven paired samples were collected from a small oceanic reef near Lee Stocking Island in the Bahamas. Seven of the fourteen corals were subjected to elevated temperatures for 28 d, followed by a recovery period lasting 53 d. Throughout the experiment, high-resolution (similar to400 mum pixel(-1)) multispectral images of induced fluorescence were recorded at wavelengths corresponding to the green and orange host pigments, plus chlorophyll. These images revealed that the fluorescence of both host pigments was concentrated at polyp centers and declined by 70-90% in regions between polyps. Chlorophyll fluorescence, however, was distributed almost uniformly across the entire coral surface, but with decreases of 10-30% around polyp centers. A normalized difference ratio between the green and orange pigments (GO ratio) was developed to facilitate comparison with chlorophyll fluorescence as a bleaching indicator. Analysis showed a high correspondence between a sustained GO ratio of less than zero and the death of corals. Finally, this ratio was resistant to contamination from other sources of chlorophyll fluorescence, such as filamentous algae. |
Robertis, De A; Schell, C; Jaffe, Jules S Acoustic observations of the swimming behavior of the euphausiid Euphausia pacifica Hansen Journal Article ICES Journal of Marine Science, 60 (4), pp. 885-898, 2003, ISSN: 1054-3139. @article{DeRobertis2003, title = {Acoustic observations of the swimming behavior of the euphausiid Euphausia pacifica Hansen}, author = { A De Robertis and C Schell and Jules S. Jaffe}, issn = {1054-3139}, year = {2003}, date = {2003-01-01}, journal = {ICES Journal of Marine Science}, volume = {60}, number = {4}, pages = {885-898}, publisher = {ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD}, address = {24-28 OVAL RD, LONDON NW1 7DX, ENGLAND}, abstract = {A high-resolution, 445 kHz, multi-beam sonar and new data-processing techniques were used to characterize the swimming behavior of the euphausiid Euphausia pacifica Hansen, in Saanich Inlet, British Columbia. The instrument was deployed when the euphausiids were at depth during the day and during dusk periods of population ascent. Three-dimensional swimming paths of individual euphausiids were reconstructed by linking successive, acoustically-determined positions. Median swimming speeds were 1.8 cm s(-1) during the day and 2.2-3.5 cm s(-1) during dusk periods of vertical ascent. The presence of a fish at distances of 20-300 cm did not affect the swimming speed or turning of the euphausiids, suggesting that they did not respond to the presence of a potential predator at these distances. Euphausiids moved primarily obliquely in the vertical plane, with few individuals moving directly up or down, even during periods of vertical migration at dusk. We hypothesize that oblique swimming trajectories of euphausiids may reduce vulnerability to visual predators by allowing them to maintain bioluminescent counter-illumination during vertical migration. (C) 2003 International Council for the Exploration of the Sea. Published by Elsevier Ltd. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A high-resolution, 445 kHz, multi-beam sonar and new data-processing techniques were used to characterize the swimming behavior of the euphausiid Euphausia pacifica Hansen, in Saanich Inlet, British Columbia. The instrument was deployed when the euphausiids were at depth during the day and during dusk periods of population ascent. Three-dimensional swimming paths of individual euphausiids were reconstructed by linking successive, acoustically-determined positions. Median swimming speeds were 1.8 cm s(-1) during the day and 2.2-3.5 cm s(-1) during dusk periods of vertical ascent. The presence of a fish at distances of 20-300 cm did not affect the swimming speed or turning of the euphausiids, suggesting that they did not respond to the presence of a potential predator at these distances. Euphausiids moved primarily obliquely in the vertical plane, with few individuals moving directly up or down, even during periods of vertical migration at dusk. We hypothesize that oblique swimming trajectories of euphausiids may reduce vulnerability to visual predators by allowing them to maintain bioluminescent counter-illumination during vertical migration. (C) 2003 International Council for the Exploration of the Sea. Published by Elsevier Ltd. All rights reserved. |
2002 |
Moore, K D; Jaffe, Jules S Time-evolution of high-resolution topographic measurements of the sea floor using a 3-D laser line scan mapping system Journal Article IEEE Journal of Oceanic Engineering, 27 (3), pp. 525-545, 2002, ISSN: 0364-9059. @article{Moore2002, title = {Time-evolution of high-resolution topographic measurements of the sea floor using a 3-D laser line scan mapping system}, author = { K.D. Moore and Jules S. Jaffe}, issn = {0364-9059}, year = {2002}, date = {2002-01-01}, journal = {IEEE Journal of Oceanic Engineering}, volume = {27}, number = {3}, pages = {525-545}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Fuchs, E; Jaffe, Jules S; Long, RA ; Azam, F Thin laser light sheet microscope for microbial oceanography Journal Article Optics Express, 10 (2), pp. 145-154, 2002, ISSN: 1094-4087. @article{Fuchs2002a, title = {Thin laser light sheet microscope for microbial oceanography}, author = { E Fuchs and Jules S. Jaffe and RA Long and F Azam}, issn = {1094-4087}, year = {2002}, date = {2002-01-01}, journal = {Optics Express}, volume = {10}, number = {2}, pages = {145-154}, publisher = {OPTICAL SOC AMER}, address = {2010 MASSACHUSETTS AVE NW, WASHINGTON, DC 20036 USA}, abstract = {Despite a growing need, oceanographers are limited by existing technological constrains and are unable to observe aquatic microbes in their natural setting. In order to provide a simple and easy to implement solution for such studies, a new Thin Light Sheet Microscope (TLSM) has been developed. The TLSM utilizes a well-defined sheet of laser light, which has a narrow (23 micron) axial dimension over a 1 mm x 1 mm field of view. This light sheet is positioned precisely within the depth of field of the microscopetextquoterights objective lens. The technique thus utilizes conventional microscope optics but replaces the illumination system. The advantages of the TLSM are two-fold: First, it concentrates light only where excitation is needed, thus maximizing the efficiency of the illumination source. Secondly, the TLSM maximizes image sharpness while at the same time minimizing the level of background noise. Particles that are not located within the objectivetextquoterights depth of field are not illuminated and therefore do not contribute to an out-of-focus image. Images from a prototype system that used SYBR Green I fluorescence stain in order to localize single bacteria are reported. The bacteria were in a relatively large and undisturbed volume of 4ml, which contained natural seawater. The TLSM can be used for fresh water studies of bacteria with no modification. The microscope permits the observation of interactions at the microscale and has potential to yield insights into how microbes structure pelagic ecosystems. (C) 2002 Optical Society of America.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Despite a growing need, oceanographers are limited by existing technological constrains and are unable to observe aquatic microbes in their natural setting. In order to provide a simple and easy to implement solution for such studies, a new Thin Light Sheet Microscope (TLSM) has been developed. The TLSM utilizes a well-defined sheet of laser light, which has a narrow (23 micron) axial dimension over a 1 mm x 1 mm field of view. This light sheet is positioned precisely within the depth of field of the microscopetextquoterights objective lens. The technique thus utilizes conventional microscope optics but replaces the illumination system. The advantages of the TLSM are two-fold: First, it concentrates light only where excitation is needed, thus maximizing the efficiency of the illumination source. Secondly, the TLSM maximizes image sharpness while at the same time minimizing the level of background noise. Particles that are not located within the objectivetextquoterights depth of field are not illuminated and therefore do not contribute to an out-of-focus image. Images from a prototype system that used SYBR Green I fluorescence stain in order to localize single bacteria are reported. The bacteria were in a relatively large and undisturbed volume of 4ml, which contained natural seawater. The TLSM can be used for fresh water studies of bacteria with no modification. The microscope permits the observation of interactions at the microscale and has potential to yield insights into how microbes structure pelagic ecosystems. (C) 2002 Optical Society of America. |
Fuchs, E; Zimmerman, Richard C; Jaffe, Jules S The effect of elevated levels of phaeophytin in natural water on variable fluorescence measured from phytoplankton Journal Article Journal of Plankton Research, 24 (11), pp. 1221-1229, 2002. @article{Fuchs2002, title = {The effect of elevated levels of phaeophytin in natural water on variable fluorescence measured from phytoplankton}, author = { E Fuchs and Richard C. Zimmerman and Jules S. Jaffe}, url = {http://plankt.oxfordjournals.org/cgi/content/abstract/24/11/1221}, year = {2002}, date = {2002-01-01}, journal = {Journal of Plankton Research}, volume = {24}, number = {11}, pages = {1221-1229}, abstract = {Variable fluorescence methods are becoming popular in studies related to aquatic photosynthesis. In natural ocean water, phytoplankton co-exist with their zooplankton and flagellate predators, viral parasites and the waste products of digested phytoplankton cells that contain phaeophytin (a chromo-phore produced by digestion of chlorophyll a). Fast repetition rate fluorometry, a technique mainly applied in phytoplankton studies, was used to evaluate and quantify the effect of phaeophytin abundance in sea water on variable fluorescence parameters: the photochemical quantum yield, PhiF (also known as Fv/Fm), and the functional cross-section of photosystem 2 (PS2), sigmaPS2. If the value of PhiF determined is lower than what it actually is, phytoplankton may be labeled as less healthy (or productive) than their true condition. Results were compared with data collected using another widely used variable fluorescence technique: pulse amplitude modulation (PAM). Our study concludes that for significantly elevated levels of phaeophytin in the water, the measured values of PhiF should be corrected to avoid misinterpretation. This conclusion is independent of the measuring instrument. In waters with phaeophytin levels that constitute less than [~]30% of the total measured pigment, no correction is required (<5% change in PhiF is expected). However, as phaeophytin levels rise, the effect on PhiF increases and becomes more significant (e.g. PhiF appears 25% lower when the phaeophytin to total pigment ratio is [~]70%). High concentrations of phaeophytin are not often reported in the open ocean. However, in highly productive coastal waters, high levels of phaeophytin can be encountered. The functional cross-section (sigmaPS2) measurements are not affected by the presence of phaeophytin in the water.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Variable fluorescence methods are becoming popular in studies related to aquatic photosynthesis. In natural ocean water, phytoplankton co-exist with their zooplankton and flagellate predators, viral parasites and the waste products of digested phytoplankton cells that contain phaeophytin (a chromo-phore produced by digestion of chlorophyll a). Fast repetition rate fluorometry, a technique mainly applied in phytoplankton studies, was used to evaluate and quantify the effect of phaeophytin abundance in sea water on variable fluorescence parameters: the photochemical quantum yield, PhiF (also known as Fv/Fm), and the functional cross-section of photosystem 2 (PS2), sigmaPS2. If the value of PhiF determined is lower than what it actually is, phytoplankton may be labeled as less healthy (or productive) than their true condition. Results were compared with data collected using another widely used variable fluorescence technique: pulse amplitude modulation (PAM). Our study concludes that for significantly elevated levels of phaeophytin in the water, the measured values of PhiF should be corrected to avoid misinterpretation. This conclusion is independent of the measuring instrument. In waters with phaeophytin levels that constitute less than [~]30% of the total measured pigment, no correction is required (<5% change in PhiF is expected). However, as phaeophytin levels rise, the effect on PhiF increases and becomes more significant (e.g. PhiF appears 25% lower when the phaeophytin to total pigment ratio is [~]70%). High concentrations of phaeophytin are not often reported in the open ocean. However, in highly productive coastal waters, high levels of phaeophytin can be encountered. The functional cross-section (sigmaPS2) measurements are not affected by the presence of phaeophytin in the water. |
2001 |
Richardson, M D; Briggs, K B; Bibee, L D; Jumars, P A; Sawyer, W B; Albert, D B; Bennett, R H; Berger, T K; Buckingham, M J; Chotiros, N P; Dahl, P H; Dewitt, N T; Fleischer, P; Flood, R; Greenlaw, C F; Holliday, D V; Hulbert, M H; Hutnak, M P; Jackson, P D; Jaffe, Jules S; Johnson, H P; Lavoie, D L; Lyons, A P; Martens, C S; McGehee, D E; Moore, K D; Orsi, T H; Piper, J N; a, Ray R I Overview of SAX99: environmental considerations Journal Article IEEE Journal of Oceanic Engineering, 26 (1), pp. 26-53, 2001, ISSN: 0364-9059. @article{Richardson2001, title = {Overview of SAX99: environmental considerations}, author = { M.D. Richardson and K.B. Briggs and L.D. Bibee and P.A. Jumars and W.B. Sawyer and D.B. Albert and R.H. Bennett and T.K. Berger and M.J. Buckingham and N.P. Chotiros and P.H. Dahl and N.T. Dewitt and P. Fleischer and R. Flood and C.F. Greenlaw and D.V. Holliday and M.H. Hulbert and M.P. Hutnak and P.D. Jackson and Jules S. Jaffe and H.P. Johnson and D.L. Lavoie and A.P. Lyons and C.S. Martens and D.E. McGehee and K.D. Moore and T.H. Orsi and J.N. Piper and R.I. Ray a}, issn = {0364-9059}, year = {2001}, date = {2001-01-01}, journal = {IEEE Journal of Oceanic Engineering}, volume = {26}, number = {1}, pages = {26-53}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Franks, Peter J S; Jaffe, Jules S Microscale distributions of phytoplankton: initial results from a two-dimensional imaging fluorometer, OSST Journal Article Marine Ecology Progress Series, 220 , pp. 59–72, 2001. @article{Franks2001, title = {Microscale distributions of phytoplankton: initial results from a two-dimensional imaging fluorometer, OSST}, author = { Peter J.S. Franks and Jules S. Jaffe}, url = {http://www.int-res.com/abstracts/meps/v220/p59-72/}, year = {2001}, date = {2001-01-01}, journal = {Marine Ecology Progress Series}, volume = {220}, pages = {59–72}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jaffe, Jules S; Moore, K D; McLean, J; Strand, M P Underwater optical imaging: Status and prospects Journal Article Oceanography, 14 , 2001. @article{Jaffe2001, title = {Underwater optical imaging: Status and prospects}, author = { Jules S. Jaffe and K.D. Moore and J. McLean and M.P. Strand}, year = {2001}, date = {2001-01-01}, journal = {Oceanography}, volume = {14}, chapter = {66}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2000 |
Moore, K D; Jaffe, Jules S; Ochoa, BL Development of a New Underwater Bathymetric Laser Imaging System: L-Bath Journal Article Journal of Atmospheric and Oceanic Technology, 17 (8), pp. 1106–1117, 2000. @article{Moore2000, title = {Development of a New Underwater Bathymetric Laser Imaging System: L-Bath}, author = { K.D. Moore and Jules S. Jaffe and BL Ochoa}, url = {http://dx.doi.org/10.1175%2F1520-0426%282000%29017%3C1106%3ADOANUB%3E2.0.CO%3B2}, year = {2000}, date = {2000-01-01}, journal = {Journal of Atmospheric and Oceanic Technology}, volume = {17}, number = {8}, pages = {1106–1117}, abstract = {The design, construction, and performance of a new high-resolution underwater bathymetric prototype system (L-Bath) with extended imaging capability is presented. The design offers simultaneous reflectance and depth information on a pixel-by-pixel basis so that high-resolution reflectance and bathymetric maps of underwater targets can be provided with exact registration. The design supports operation in shallow coastal waters under daylight conditions where high turbidity and the influence of ambient backscatter are particularly limiting for underwater imaging systems. Its configuration is similar to existing laser line scanning systems but uses a pulsed laser for the source and a fixed field-of-view high-resolution linear charge-coupled device (CCD) as receiver. The pulsed laser allows short camera integration times, thereby reducing the influence of the ambient daylight signal, and the fixed field of view of the detector provides a precision nonmoving multielement receiver with imaging capability. As the laser sweeps across the field of view of the CCD, the position and signal strength of each laser target spot is imaged, permitting a measure of bathymetry and reflectance. Using the CCD, a high-resolution slice through the reflected target spot radiance distribution is imaged so that system resolution can exceed the target spot size. The image of the target spot radiance distribution, modified by in-water scattering and target reflectance, provides new opportunities for image manipulation compared to typical underwater laser line scanning based systems. The simultaneous acquisition of reflectance and bathymetric maps permits discrimination capability between real objects of relief from scene reflectance variations.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The design, construction, and performance of a new high-resolution underwater bathymetric prototype system (L-Bath) with extended imaging capability is presented. The design offers simultaneous reflectance and depth information on a pixel-by-pixel basis so that high-resolution reflectance and bathymetric maps of underwater targets can be provided with exact registration. The design supports operation in shallow coastal waters under daylight conditions where high turbidity and the influence of ambient backscatter are particularly limiting for underwater imaging systems. Its configuration is similar to existing laser line scanning systems but uses a pulsed laser for the source and a fixed field-of-view high-resolution linear charge-coupled device (CCD) as receiver. The pulsed laser allows short camera integration times, thereby reducing the influence of the ambient daylight signal, and the fixed field of view of the detector provides a precision nonmoving multielement receiver with imaging capability. As the laser sweeps across the field of view of the CCD, the position and signal strength of each laser target spot is imaged, permitting a measure of bathymetry and reflectance. Using the CCD, a high-resolution slice through the reflected target spot radiance distribution is imaged so that system resolution can exceed the target spot size. The image of the target spot radiance distribution, modified by in-water scattering and target reflectance, provides new opportunities for image manipulation compared to typical underwater laser line scanning based systems. The simultaneous acquisition of reflectance and bathymetric maps permits discrimination capability between real objects of relief from scene reflectance variations. |
Robertis, Alex De; Jaffe, Jules S; Ohman, Mark D Size-Dependent Visual Predation Risk and the Timing of Vertical Migration in Zooplankton Journal Article Limnology and Oceanography, 45 (8), pp. 1838–1844, 2000, ISSN: 00243590. @article{DeRobertis2000, title = {Size-Dependent Visual Predation Risk and the Timing of Vertical Migration in Zooplankton}, author = { Alex De Robertis and Jules S. Jaffe and Mark D. Ohman}, url = {http://www.jstor.org/stable/2670643}, issn = {00243590}, year = {2000}, date = {2000-01-01}, journal = {Limnology and Oceanography}, volume = {45}, number = {8}, pages = {1838–1844}, publisher = {American Society of Limnology and Oceanography}, abstract = {Zooplankton commonly exhibit diel vertical migration (DVM), descending from food-rich surface waters during the day. If DVM is a tradeoff between avoiding size-selective visually hunting predators and maximizing energy gain, smaller bodied prey should enter surface waters earlier and leave later than larger, more visually conspicuous organisms. Conventional sampling technologies lack the temporal resolution to test this prediction. Here, we report on the first test of this prediction using a new submersible optical-acoustic imaging system capable of resolving the timing of migration of the euphausiid crustacean Euphausia pacifica Hansen. Smaller bodied animals consistently ascended as much as 30 min earlier and descended up to 45 min later than adults. The timing of vertical migration reflects how the size-dependent risk of attack by visual predators alters the tradeoff between feeding and predator avoidance, supporting the predator-avoidance hypothesis for DVM.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Zooplankton commonly exhibit diel vertical migration (DVM), descending from food-rich surface waters during the day. If DVM is a tradeoff between avoiding size-selective visually hunting predators and maximizing energy gain, smaller bodied prey should enter surface waters earlier and leave later than larger, more visually conspicuous organisms. Conventional sampling technologies lack the temporal resolution to test this prediction. Here, we report on the first test of this prediction using a new submersible optical-acoustic imaging system capable of resolving the timing of migration of the euphausiid crustacean Euphausia pacifica Hansen. Smaller bodied animals consistently ascended as much as 30 min earlier and descended up to 45 min later than adults. The timing of vertical migration reflects how the size-dependent risk of attack by visual predators alters the tradeoff between feeding and predator avoidance, supporting the predator-avoidance hypothesis for DVM. |
1999 |
Jaffe, Jules S; Ohman, Mark D; Robertis, De A Sonar estimates of daytime activity levels of Euphausia pacifica in Saanich Inlet Journal Article Canadian Journal of Fisheries and Aquatic Sciences, 56 (11), pp. 2000-2010, 1999, ISSN: 0706-652X. @article{Jaffe1999, title = {Sonar estimates of daytime activity levels of Euphausia pacifica in Saanich Inlet}, author = { Jules S. Jaffe and Mark D. Ohman and A De Robertis}, issn = {0706-652X}, year = {1999}, date = {1999-01-01}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, volume = {56}, number = {11}, pages = {2000-2010}, publisher = {NATL RESEARCH COUNCIL CANADA}, address = {RESEARCH JOURNALS, MONTREAL RD, OTTAWA, ONTARIO K1A 0R6, CANADA}, abstract = {A three-dimensional multibeam tracking sonar system (FishTV) was deployed in the stratified waters of Saanich Inlet in July-August of 1996 and 1997 to assess the swimming behavior of euphausiids in situ. Here, a new algorithm is used to estimate swimming velocities of animals from the uncorrelated displacements of acoustic targets in pairs of sonar frames with increasing time delays between frames. Assuming isotropic motions of euphausiids, the superior spatial resolution of the sonar in one dimension (range) is used to infer the three-dimensional motions. We applied the algorithm to sonar tracks of groups of 10 000 - 25 000 euphausiids recorded in the daytime at depths just above the oxycline on six different occasions. The animal movements were described with a probability density function for velocity which suggests that about 60-70% of the animals were moving less than or equal to 0.3-1.2 cm.s(-1). These distributions imply remarkably low swimming speeds and quiescent behavior. Limited motility in the daytime would confer two major advantages on the euphausiids: reduction of encounter rates with ambush predators and decreased metabolic costs.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A three-dimensional multibeam tracking sonar system (FishTV) was deployed in the stratified waters of Saanich Inlet in July-August of 1996 and 1997 to assess the swimming behavior of euphausiids in situ. Here, a new algorithm is used to estimate swimming velocities of animals from the uncorrelated displacements of acoustic targets in pairs of sonar frames with increasing time delays between frames. Assuming isotropic motions of euphausiids, the superior spatial resolution of the sonar in one dimension (range) is used to infer the three-dimensional motions. We applied the algorithm to sonar tracks of groups of 10 000 - 25 000 euphausiids recorded in the daytime at depths just above the oxycline on six different occasions. The animal movements were described with a probability density function for velocity which suggests that about 60-70% of the animals were moving less than or equal to 0.3-1.2 cm.s(-1). These distributions imply remarkably low swimming speeds and quiescent behavior. Limited motility in the daytime would confer two major advantages on the euphausiids: reduction of encounter rates with ambush predators and decreased metabolic costs. |
Jaffe, Jules S Target localization for a three-dimensional multibeam sonar imaging system Journal Article Journal of the Acoustical Society of America, 105 (6), pp. 3168-3175, 1999. @article{Jaffe1999b, title = {Target localization for a three-dimensional multibeam sonar imaging system}, author = { Jules S. Jaffe}, url = {http://link.aip.org/link/?JAS/105/3168/1}, year = {1999}, date = {1999-01-01}, journal = {Journal of the Acoustical Society of America}, volume = {105}, number = {6}, pages = {3168-3175}, publisher = {ASA}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
1998 |
Jaffe, Jules S; Moore, K D; Zawada, DG ; Ochoa, BL ; Zege, E Underwater optical imaging: New hardware & software Journal Article Sea Technology, 39 (7), pp. 70-74, 1998, ISSN: 0093-3651. @article{Jaffe1998, title = {Underwater optical imaging: New hardware & software}, author = { Jules S. Jaffe and K.D. Moore and DG Zawada and BL Ochoa and E Zege}, issn = {0093-3651}, year = {1998}, date = {1998-01-01}, journal = {Sea Technology}, volume = {39}, number = {7}, pages = {70-74}, publisher = {COMPASS PUBL INC}, address = {SUITE 1000 1117 N 19 ST, ARLINGTON, VA 22209 USA}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Rafii, K; Jaffe, Jules S Adaptive ultrasonic measurement of blood vessel diameter and wall thickness: theory and experimental results Journal Article IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, 45 (3), pp. 593-603, 1998, ISSN: 0885-3010. @article{Rafii1998, title = {Adaptive ultrasonic measurement of blood vessel diameter and wall thickness: theory and experimental results}, author = { K. Rafii and Jules S. Jaffe}, issn = {0885-3010}, year = {1998}, date = {1998-01-01}, journal = {IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control}, volume = {45}, number = {3}, pages = {593-603}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jaffe, Jules S; Ohman, Mark D; Robertis, De A OASIS in the sea: measurement of the acoustic reflectivity of zooplankton with concurrent optical imaging Journal Article Deep Sea Research Part II: Topical Studies in Oceanography, 45 , pp. 1239-1253, 1998. @article{Jaffe1998b, title = {OASIS in the sea: measurement of the acoustic reflectivity of zooplankton with concurrent optical imaging}, author = { Jules S. Jaffe and Mark D. Ohman and A De Robertis}, year = {1998}, date = {1998-01-01}, journal = {Deep Sea Research Part II: Topical Studies in Oceanography}, volume = {45}, pages = {1239-1253}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jaffe, Jules S; Franks, Peter J S; Leising, Andrew W Simultaneous imaging of phytoplankton and zooplankton distributions Journal Article Oceanography, 11 , pp. 24-29, 1998. @article{Jaffe1998b, title = {Simultaneous imaging of phytoplankton and zooplankton distributions}, author = { Jules S. Jaffe and Peter J.S. Franks and Andrew W. Leising}, year = {1998}, date = {1998-01-01}, journal = {Oceanography}, volume = {11}, pages = {24-29}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
1996 |
Chandran, G; Jaffe, Jules S Signal set design with constrained amplitude spectrum and specified time-bandwidth product Journal Article IEEE Transactions on Communications, 44 (6), pp. 725-732, 1996, ISSN: 0090-6778. @article{Jaffe1996, title = {Signal set design with constrained amplitude spectrum and specified time-bandwidth product}, author = { G. Chandran and Jules S. Jaffe}, issn = {0090-6778}, year = {1996}, date = {1996-01-01}, journal = {IEEE Transactions on Communications}, volume = {44}, number = {6}, pages = {725-732}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jaffe, Jules S Temporal sampling of backscattered sonar signals Journal Article ICES Journal of Marine Science, 53 , pp. 359-361(3), 1996. @article{Jaffe1996a, title = {Temporal sampling of backscattered sonar signals}, author = { Jules S. Jaffe}, url = {http://www.ingentaconnect.com/content/ap/jm/1996/00000053/00000002/art00049}, year = {1996}, date = {1996-01-01}, journal = {ICES Journal of Marine Science}, volume = {53}, pages = {359-361(3)}, abstract = { This article considers the subject of the temporal sampling of backscattered sound from an active sonar system. Here, it is demonstrated how the beam patterns of the sonar, when considered along with the velocity of the animal, prescribe a minimal sampling rate such that an unaliased version of the backscattered signal can be constructed. Thus, an equation is derived which relates a minimum sampling interval to the maximal angular velocity of targets which are moving through the beams. Observation of this minimal temporal sampling criteria is necessary in order to obtain unaliased data. },keywords = {}, pubstate = {published}, tppubtype = {article} } <P> This article considers the subject of the temporal sampling of backscattered sound from an active sonar system. Here, it is demonstrated how the beam patterns of the sonar, when considered along with the velocity of the animal, prescribe a minimal sampling rate such that an unaliased version of the backscattered signal can be constructed. Thus, an equation is derived which relates a minimum sampling interval to the maximal angular velocity of targets which are moving through the beams. Observation of this minimal temporal sampling criteria is necessary in order to obtain unaliased data.</P> |
McGehee, D E; Jaffe, Jules S Three-dimensional swimming behavior of individual zooplankters: observations using the acoustical imaging system FishTV Journal Article ICES Journal of Marine Science, 53 , pp. 363-369(7), 1996. @article{Jaffe1996b, title = {Three-dimensional swimming behavior of individual zooplankters: observations using the acoustical imaging system FishTV}, author = { D.E. McGehee and Jules S. Jaffe}, url = {http://www.ingentaconnect.com/content/ap/jm/1996/00000053/00000002/art00050}, year = {1996}, date = {1996-01-01}, journal = {ICES Journal of Marine Science}, volume = {53}, pages = {363-369(7)}, abstract = { There is increasing recognition that three-dimensional tracks of individual zoo-plankters are needed for studies in biological oceanography, including, for example, the role of individual behavior in patch formation and maintenance. The three-dimensional acoustical imaging system FishTV provides a means of non-invasively examining zooplankton swimming behavior. The system forms a set of 64 acoustic beams in an 8 by 8 pattern, each beam 2$#$&176; by 2$#$&176;, for a total coverage of 16$#$&176; by 16$#$&176;. The 8 by 8 beams form two dimensions of the image; range provides the third dimension. The system has 20 kHz of bandwidth and operates at a center frequency of 445 kHz. Observations of zooplankton swimming at 37 m depth were made from the research platform RP "FLIP" at a site in the San Diego Trough, 28 km south-west of San Diego, California, USA. In a 1-min-long sequence of 60 images, acquired at 2101 h, 24 March 1993, 314 plankters were tracked for lengths of time ranging from 2 to 13 s. The animals ranged from -83.0 dB re 1 m to -57.7 dB target strength. Movement of each animal was divided into directed and random components. The directed component was attributed to currents, waves and (possibly) a slight vertical migration. The random component was attributed to random behavior. Analysis of random velocities and turning behavior showed an inverse relationship between swimming speed and path curvature. Turning rates were approximately 1.2 rad s regardless of the size or speed of the animals. Mean swimming speeds were positively correlated with distance from a pair of bright lights (part of a video system), while mean path curvatures were negatively correlated. These observations are consistent with a model for swimming behavior that leads to aggregation. },keywords = {}, pubstate = {published}, tppubtype = {article} } <P> There is increasing recognition that three-dimensional tracks of individual zoo-plankters are needed for studies in biological oceanography, including, for example, the role of individual behavior in patch formation and maintenance. The three-dimensional acoustical imaging system FishTV provides a means of non-invasively examining zooplankton swimming behavior. The system forms a set of 64 acoustic beams in an 8 by 8 pattern, each beam 2$#$&176; by 2$#$&176;, for a total coverage of 16$#$&176; by 16$#$&176;. The 8 by 8 beams form two dimensions of the image; range provides the third dimension. The system has 20 kHz of bandwidth and operates at a center frequency of 445 kHz. Observations of zooplankton swimming at 37 m depth were made from the research platform RP "FLIP" at a site in the San Diego Trough, 28 km south-west of San Diego, California, USA. In a 1-min-long sequence of 60 images, acquired at 2101 h, 24 March 1993, 314 plankters were tracked for lengths of time ranging from 2 to 13 s. The animals ranged from -83.0 dB re 1 m to -57.7 dB target strength. Movement of each animal was divided into directed and random components. The directed component was attributed to currents, waves and (possibly) a slight vertical migration. The random component was attributed to random behavior. Analysis of random velocities and turning behavior showed an inverse relationship between swimming speed and path curvature. Turning rates were approximately 1.2 rad s regardless of the size or speed of the animals. Mean swimming speeds were positively correlated with distance from a pair of bright lights (part of a video system), while mean path curvatures were negatively correlated. These observations are consistent with a model for swimming behavior that leads to aggregation.</P> |
1995 |
Palowitch, A W; Jaffe, Jules S Optical Serial Sectioned Chlorophyll-Alpha Microstructure Journal Article Journal of Geophysical Research-Oceans, 100 (C7), pp. 13267-13278, 1995, ISSN: 0148-0227. @article{Palowitch1995, title = {Optical Serial Sectioned Chlorophyll-Alpha Microstructure}, author = { A. W. Palowitch and Jules S. Jaffe}, issn = {0148-0227}, year = {1995}, date = {1995-01-01}, journal = {Journal of Geophysical Research-Oceans}, volume = {100}, number = {C7}, pages = {13267-13278}, publisher = {AMER GEOPHYSICAL UNION}, address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009}, abstract = {An underwater serial sectioning tomography technique is shown capable of determining three-dimensional Chlorophyll a (Chl a) microstructure in phytoplankton distributions. The technique involves scanning a 457-nm illumination plane through a range of distances parallel to the imaging plane of a digital CCD camera. Images of induced fluorescence at 685 nm in the sequentially illuminated planes are recorded. A theoretical model of the imaging process in the form of i = In c + Ac + x shows that the image i is a function of a spatially varying c (Chi a) dependent absorption component A and a spatially invariant attenuation component x. A numerical inverse method, incorporating an environmentally dependent calibration constant, is used to calculate Chi a values from the image intensities for three-dimensional presentation. A stable reconstruction, not affected by noise-induced error propagation, is demonstrated.}, keywords = {}, pubstate = {published}, tppubtype = {article} } An underwater serial sectioning tomography technique is shown capable of determining three-dimensional Chlorophyll a (Chl a) microstructure in phytoplankton distributions. The technique involves scanning a 457-nm illumination plane through a range of distances parallel to the imaging plane of a digital CCD camera. Images of induced fluorescence at 685 nm in the sequentially illuminated planes are recorded. A theoretical model of the imaging process in the form of i = In c + Ac + x shows that the image i is a function of a spatially varying c (Chi a) dependent absorption component A and a spatially invariant attenuation component x. A numerical inverse method, incorporating an environmentally dependent calibration constant, is used to calculate Chi a values from the image intensities for three-dimensional presentation. A stable reconstruction, not affected by noise-induced error propagation, is demonstrated. |
Maffione, R ~A; Jaffe, Jules S The average cosine due to an isotropic light source in the ocean Journal Article Journal of Geophysical Research, 100 , pp. 13179-13192, 1995. @article{Maffione1995, title = {The average cosine due to an isotropic light source in the ocean}, author = { R.~A. Maffione and Jules S. Jaffe}, year = {1995}, date = {1995-01-01}, journal = {Journal of Geophysical Research}, volume = {100}, pages = {13179-13192}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jaffe, Jules S; Reuss, Edward ; McGehee, D E; Chandran, G FTV: a sonar for tracking macrozooplankton in three dimensions Journal Article Deep Sea Research Part I: Oceanographic Research Papers, 42 (8), pp. 1495 - 1512, 1995, ISSN: 0967-0637. @article{Jaffe1995, title = {FTV: a sonar for tracking macrozooplankton in three dimensions}, author = { Jules S. Jaffe and Edward Reuss and D.E. McGehee and G. Chandran}, url = {http://www.sciencedirect.com/science/article/B6VGB-3YS8ND3-1M/2/dda34da7a1e67ed0adcabd840b6efedb}, issn = {0967-0637}, year = {1995}, date = {1995-01-01}, journal = {Deep Sea Research Part I: Oceanographic Research Papers}, volume = {42}, number = {8}, pages = {1495 - 1512}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jaffe, Jules S Monte Carlo modeling of underwater-image formation: validity of the linear and small-angle approximations Journal Article Applied Optics, 34 (24), pp. 5413–5421, 1995. @article{Jaffe1995a, title = {Monte Carlo modeling of underwater-image formation: validity of the linear and small-angle approximations}, author = { Jules S. Jaffe}, url = {http://ao.osa.org/abstract.cfm?URI=ao-34-24-5413}, year = {1995}, date = {1995-01-01}, journal = {Applied Optics}, volume = {34}, number = {24}, pages = {5413–5421}, publisher = {OSA}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
McGehee, D E; Jaffe, Jules S Segmented transducer design using an optimum mean square quantizer approach Journal Article Journal of the Acoustical Society of America, 97 , pp. 2316-2325, 1995. @article{McGehee1995, title = {Segmented transducer design using an optimum mean square quantizer approach}, author = { D.E. McGehee and Jules S. Jaffe}, year = {1995}, date = {1995-01-01}, journal = {Journal of the Acoustical Society of America}, volume = {97}, pages = {2316-2325}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
1994 |
Palowitch, A W; Jaffe, Jules S 3-Dimensional Ocean Chlopophyll Distributions from Underwater Serial-Sectioned Fluoresence Images Journal Article Applied Optics, 33 (14), pp. 3023-3033, 1994, ISSN: 0740-3224. @article{Palowitch1994, title = {3-Dimensional Ocean Chlopophyll Distributions from Underwater Serial-Sectioned Fluoresence Images}, author = { A. W. Palowitch and Jules S. Jaffe}, issn = {0740-3224}, year = {1994}, date = {1994-01-01}, journal = {Applied Optics}, volume = {33}, number = {14}, pages = {3023-3033}, publisher = {OPTICAL SOC AMER}, address = {2010 MASSACHUSETTS AVE NW, WASHINGTON, DC 20036}, abstract = {An underwater optical serial-sectioning technique is developed to measure in situ three-dimensional distributions of biological particles. The technique involves scanning of a thin plane of laser light through a range of distances parallel to the imaging plane of a digital CCD camera. Images of induced fluorescence in the sequentially illuminated planes are recorded. An inverse method is then used to reconstruct three-dimensional chlorophyll a distributions from the plane images. Computer simulations of the image formation and reconstruction process indicate that the underwater optical serial-sectioning technique is practical for in situ determination and analysis of chlorophyll a microstructures for concentrations as low as 0.1 mg of chlorophyll a per cubic meter in 1-m3 water volumes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } An underwater optical serial-sectioning technique is developed to measure in situ three-dimensional distributions of biological particles. The technique involves scanning of a thin plane of laser light through a range of distances parallel to the imaging plane of a digital CCD camera. Images of induced fluorescence in the sequentially illuminated planes are recorded. An inverse method is then used to reconstruct three-dimensional chlorophyll a distributions from the plane images. Computer simulations of the image formation and reconstruction process indicate that the underwater optical serial-sectioning technique is practical for in situ determination and analysis of chlorophyll a microstructures for concentrations as low as 0.1 mg of chlorophyll a per cubic meter in 1-m3 water volumes. |
McGehee, D E; Jaffe, Jules S Beamforming with dense random arrays: The development of a spatially shaded polyvinylidene fluoride acoustic transducer Journal Article Journal of the Acoustical Society of America, 95 (1), pp. 318-323, 1994. @article{McGehee1994, title = {Beamforming with dense random arrays: The development of a spatially shaded polyvinylidene fluoride acoustic transducer}, author = { D.E. McGehee and Jules S. Jaffe}, url = {http://link.aip.org/link/?JAS/95/318/1}, year = {1994}, date = {1994-01-01}, journal = {Journal of the Acoustical Society of America}, volume = {95}, number = {1}, pages = {318-323}, publisher = {ASA}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
1993 |
Jaffe, Jules S A Simplified Derivation of the Performance of Edge-Connected Crossed-Electrode Arrays for Two-Dimensional Projection and Beamforming Journal Article IEEE Transactions on Signal Processing, 41 (1), pp. 446-, 1993, ISSN: 1053-587X. @article{Jaffe1993, title = {A Simplified Derivation of the Performance of Edge-Connected Crossed-Electrode Arrays for Two-Dimensional Projection and Beamforming}, author = { Jules S. Jaffe}, issn = {1053-587X}, year = {1993}, date = {1993-01-01}, journal = {IEEE Transactions on Signal Processing}, volume = {41}, number = {1}, pages = {446-}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
1992 |
Cobra, D T; Oppenheim, A V; Jaffe, Jules S Geometric distortions in side-scan sonar images: a procedure for their estimation and correction Journal Article IEEE Journal of Oceanic Engineering, 17 (3), pp. 252-268, 1992, ISSN: 0364-9059. @article{Cobra1992, title = {Geometric distortions in side-scan sonar images: a procedure for their estimation and correction}, author = { D.T. Cobra and A.V. Oppenheim and Jules S. Jaffe}, issn = {0364-9059}, year = {1992}, date = {1992-01-01}, journal = {IEEE Journal of Oceanic Engineering}, volume = {17}, number = {3}, pages = {252-268}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pretorius, D H; Nelson, T R; Jaffe, Jules S 3-dimensional sonographic analysis based on color flow Doppler and gray scale image data: a preliminary report Journal Article Journal of Ultrasound in Medicine, 11 (5), pp. 225-232, 1992. @article{Pretorius1992, title = {3-dimensional sonographic analysis based on color flow Doppler and gray scale image data: a preliminary report}, author = { D. H. Pretorius and T. R. Nelson and Jules S. Jaffe}, url = {http://www.jultrasoundmed.org/cgi/content/abstract/11/5/225}, year = {1992}, date = {1992-01-01}, journal = {Journal of Ultrasound in Medicine}, volume = {11}, number = {5}, pages = {225-232}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sutton, D ~W; Jaffe, Jules S Acoustic bedload velocity estimates using a broadband pulse-pulse time correlation technique Journal Article Acoustical Society of America Journal, 92 , pp. 1692-1698, 1992. @article{Sutton1992, title = {Acoustic bedload velocity estimates using a broadband pulse-pulse time correlation technique}, author = { D.~W. Sutton and Jules S. Jaffe}, year = {1992}, date = {1992-01-01}, journal = {Acoustical Society of America Journal}, volume = {92}, pages = {1692-1698}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
1990 |
Jaffe, Jules S Limited angle reconstruction using stabilized algorithms Journal Article IEEE Transactions on Medical Imaging, 9 (3), pp. 338-344, 1990, ISSN: 0278-0062. @article{Jaffe1990b, title = {Limited angle reconstruction using stabilized algorithms}, author = { Jules S. Jaffe}, issn = {0278-0062}, year = {1990}, date = {1990-01-01}, journal = {IEEE Transactions on Medical Imaging}, volume = {9}, number = {3}, pages = {338-344}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jaffe, Jules S; Cassereau, PM ; Glassbrenner, D J Code design and performance characterization for code multiplexed imaging Journal Article IEEE Transactions on Acoustics, Speech and Signal Processing, 38 (8), pp. 1321-1329, 1990, ISSN: 0096-3518. @article{Jaffe1900a, title = {Code design and performance characterization for code multiplexed imaging}, author = { Jules S. Jaffe and PM Cassereau and D.J. Glassbrenner}, issn = {0096-3518}, year = {1990}, date = {1990-01-01}, journal = {IEEE Transactions on Acoustics, Speech and Signal Processing}, volume = {38}, number = {8}, pages = {1321-1329}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jaffe, Jules S Computer Modeling and the Design of Optimal Underwater Imaging-Systems Journal Article IEEE Journal of Oceanic Engineering, 15 (2), pp. 101-111, 1990, ISSN: 0364-9059. @article{Jaffe1990, title = {Computer Modeling and the Design of Optimal Underwater Imaging-Systems}, author = { Jules S. Jaffe}, issn = {0364-9059}, year = {1990}, date = {1990-01-01}, journal = {IEEE Journal of Oceanic Engineering}, volume = {15}, number = {2}, pages = {101-111}, publisher = {IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC}, address = {345 E 47TH ST, NEW YORK, NY 10017-2394}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Olson, T; Jaffe, Jules S An explanation of the effects of Squashing in limited angle tomography. Journal Article IEEE Transactions on Medical Imaging, 9 (3), pp. 242-6, 1990, ISSN: 0278-0062. @article{Olson1990, title = {An explanation of the effects of Squashing in limited angle tomography.}, author = { T. Olson and Jules S. Jaffe}, issn = {0278-0062}, year = {1990}, date = {1990-01-01}, journal = {IEEE Transactions on Medical Imaging}, volume = {9}, number = {3}, pages = {242-6}, abstract = {The effects of Squashing, an algorithm introduced by J.A. Reeds and L.A. Shepp (see ibid., vol.MI-6, no.2, p.89-97, June 1987), are described. It is proven that Squashing induces a weight function upon the projections. Intuitive and numerical evidence is presented showing that this weight function is not desirable at limited angles. A method to counteract the effects of the weight function and extend the usefulness of the algorithm to 120 degrees is proposed.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The effects of Squashing, an algorithm introduced by J.A. Reeds and L.A. Shepp (see ibid., vol.MI-6, no.2, p.89-97, June 1987), are described. It is proven that Squashing induces a weight function upon the projections. Intuitive and numerical evidence is presented showing that this weight function is not desirable at limited angles. A method to counteract the effects of the weight function and extend the usefulness of the algorithm to 120 degrees is proposed. |
1988 |
Jaffe, Jules S; Cassereau, PM Multibeam imaging using spatially variant insonification Journal Article Journal of the Acoustical Society of America, 83 (4), pp. 1458-1464, 1988, ISSN: 0001-4966. @article{JAFFE1988, title = {Multibeam imaging using spatially variant insonification}, author = { Jules S. Jaffe and PM Cassereau}, issn = {0001-4966}, year = {1988}, date = {1988-01-01}, journal = {Journal of the Acoustical Society of America}, volume = {83}, number = {4}, pages = {1458-1464}, publisher = {AMER INST PHYSICS}, address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
1987 |
Jaffe, Jules S; Fricke, Robert Constrained reconstruction of complex waveforms Journal Article J. Opt. Soc. Am. A, 4 (1), pp. 216–220, 1987. @article{Jaffe1987, title = {Constrained reconstruction of complex waveforms}, author = { Jules S. Jaffe and Robert Fricke}, url = {http://josaa.osa.org/abstract.cfm?URI=josaa-4-1-216}, year = {1987}, date = {1987-01-01}, journal = {J. Opt. Soc. Am. A}, volume = {4}, number = {1}, pages = {216–220}, publisher = {OSA}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jaffe, Jules S; Glaeser, R M Difference Fourier analysis of surface features of bacteriorhodopsin using glucose-embedded and frozen-hydrated purple membrane Journal Article Ultramicroscopy, 23 (1), pp. 17 - 28, 1987, ISSN: 0304-3991. @article{Jaffe1987a, title = {Difference Fourier analysis of surface features of bacteriorhodopsin using glucose-embedded and frozen-hydrated purple membrane}, author = { Jules S. Jaffe and R. M. Glaeser}, url = {http://www.sciencedirect.com/science/article/B6TW1-46V5HK0-4/2/3306dd10ff0f177bd5c1ddaf348051f9}, issn = {0304-3991}, year = {1987}, date = {1987-01-01}, journal = {Ultramicroscopy}, volume = {23}, number = {1}, pages = {17 - 28}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
1984 |
Jaffe, Jules S; Glaeser, R M Preparation Of Frozen-Hydrated Specimens For High-Resolution Electron-Microscopy Journal Article Ultramicroscopy, 13 , pp. 373-377, 1984. @article{45, title = {Preparation Of Frozen-Hydrated Specimens For High-Resolution Electron-Microscopy}, author = { Jules S. Jaffe and R. M. Glaeser}, year = {1984}, date = {1984-01-01}, journal = {Ultramicroscopy}, volume = {13}, pages = {373-377}, chapter = {373}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Publications
2005 |
Design and preliminary tests of a family of adaptive waveforms to measure blood vessel diameter and wall thickness Journal Article IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control: Special Issue on Coded Waveforms, 52 (2), pp. 250-260, 2005, ISSN: 0885-3010. |
Performance bounds on synchronous laser line scan systems Journal Article Optics Express, 13 (3), pp. 738-748, 2005, ISSN: 1094-4087. |
Diel pattern with abrupt crepuscular changes of zooplankton over a coral reef Journal Article Limnology And Oceanography, 50 (3), pp. 930–944, 2005. |
Sensing Plankton: Acoustics and Optical Imaging Book Chapter European Workshop on Harmful Algal Blooms, 2005. |
Swimming Against the Flow: A Mechanism of Zooplankton Aggregation Journal Article Science, 308 (5723), pp. 860-862, 2005. |
Three-dimensional probability density functions via tomographic inversion Journal Article Siam Journal On Applied Mathematics, 65 (5), pp. 1506–1525, 2005. |
2004 |
Identifying stable frequencies for performing animal abundance estimation with a multifrequency system Conference Acoustical Society of America, San Diego, CA, 2004. |
Experimental verification of an interpolation algorithm for improved estimates of animal position Journal Article Journal of the Acoustical Socieity of America, 116 (1), pp. 254-261, 2004, ISSN: 0001-4966. |
2003 |
Changes in the fluorescence of the Caribbean coral Montastraea faveolata during heat-induced bleaching Journal Article Limnology and Oceanography, 48 (1, Part 2), pp. 412-425, 2003, ISSN: 0024-3590. |
Acoustic observations of the swimming behavior of the euphausiid Euphausia pacifica Hansen Journal Article ICES Journal of Marine Science, 60 (4), pp. 885-898, 2003, ISSN: 1054-3139. |
2002 |
Time-evolution of high-resolution topographic measurements of the sea floor using a 3-D laser line scan mapping system Journal Article IEEE Journal of Oceanic Engineering, 27 (3), pp. 525-545, 2002, ISSN: 0364-9059. |
Thin laser light sheet microscope for microbial oceanography Journal Article Optics Express, 10 (2), pp. 145-154, 2002, ISSN: 1094-4087. |
The effect of elevated levels of phaeophytin in natural water on variable fluorescence measured from phytoplankton Journal Article Journal of Plankton Research, 24 (11), pp. 1221-1229, 2002. |
2001 |
Overview of SAX99: environmental considerations Journal Article IEEE Journal of Oceanic Engineering, 26 (1), pp. 26-53, 2001, ISSN: 0364-9059. |
Microscale distributions of phytoplankton: initial results from a two-dimensional imaging fluorometer, OSST Journal Article Marine Ecology Progress Series, 220 , pp. 59–72, 2001. |
Underwater optical imaging: Status and prospects Journal Article Oceanography, 14 , 2001. |
2000 |
Development of a New Underwater Bathymetric Laser Imaging System: L-Bath Journal Article Journal of Atmospheric and Oceanic Technology, 17 (8), pp. 1106–1117, 2000. |
Size-Dependent Visual Predation Risk and the Timing of Vertical Migration in Zooplankton Journal Article Limnology and Oceanography, 45 (8), pp. 1838–1844, 2000, ISSN: 00243590. |
1999 |
Sonar estimates of daytime activity levels of Euphausia pacifica in Saanich Inlet Journal Article Canadian Journal of Fisheries and Aquatic Sciences, 56 (11), pp. 2000-2010, 1999, ISSN: 0706-652X. |
Target localization for a three-dimensional multibeam sonar imaging system Journal Article Journal of the Acoustical Society of America, 105 (6), pp. 3168-3175, 1999. |
1998 |
Underwater optical imaging: New hardware & software Journal Article Sea Technology, 39 (7), pp. 70-74, 1998, ISSN: 0093-3651. |
Adaptive ultrasonic measurement of blood vessel diameter and wall thickness: theory and experimental results Journal Article IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, 45 (3), pp. 593-603, 1998, ISSN: 0885-3010. |
OASIS in the sea: measurement of the acoustic reflectivity of zooplankton with concurrent optical imaging Journal Article Deep Sea Research Part II: Topical Studies in Oceanography, 45 , pp. 1239-1253, 1998. |
Simultaneous imaging of phytoplankton and zooplankton distributions Journal Article Oceanography, 11 , pp. 24-29, 1998. |
1996 |
Signal set design with constrained amplitude spectrum and specified time-bandwidth product Journal Article IEEE Transactions on Communications, 44 (6), pp. 725-732, 1996, ISSN: 0090-6778. |
Temporal sampling of backscattered sonar signals Journal Article ICES Journal of Marine Science, 53 , pp. 359-361(3), 1996. |
Three-dimensional swimming behavior of individual zooplankters: observations using the acoustical imaging system FishTV Journal Article ICES Journal of Marine Science, 53 , pp. 363-369(7), 1996. |
1995 |
Optical Serial Sectioned Chlorophyll-Alpha Microstructure Journal Article Journal of Geophysical Research-Oceans, 100 (C7), pp. 13267-13278, 1995, ISSN: 0148-0227. |
The average cosine due to an isotropic light source in the ocean Journal Article Journal of Geophysical Research, 100 , pp. 13179-13192, 1995. |
FTV: a sonar for tracking macrozooplankton in three dimensions Journal Article Deep Sea Research Part I: Oceanographic Research Papers, 42 (8), pp. 1495 - 1512, 1995, ISSN: 0967-0637. |
Monte Carlo modeling of underwater-image formation: validity of the linear and small-angle approximations Journal Article Applied Optics, 34 (24), pp. 5413–5421, 1995. |
Segmented transducer design using an optimum mean square quantizer approach Journal Article Journal of the Acoustical Society of America, 97 , pp. 2316-2325, 1995. |
1994 |
3-Dimensional Ocean Chlopophyll Distributions from Underwater Serial-Sectioned Fluoresence Images Journal Article Applied Optics, 33 (14), pp. 3023-3033, 1994, ISSN: 0740-3224. |
Beamforming with dense random arrays: The development of a spatially shaded polyvinylidene fluoride acoustic transducer Journal Article Journal of the Acoustical Society of America, 95 (1), pp. 318-323, 1994. |
1993 |
A Simplified Derivation of the Performance of Edge-Connected Crossed-Electrode Arrays for Two-Dimensional Projection and Beamforming Journal Article IEEE Transactions on Signal Processing, 41 (1), pp. 446-, 1993, ISSN: 1053-587X. |
1992 |
Geometric distortions in side-scan sonar images: a procedure for their estimation and correction Journal Article IEEE Journal of Oceanic Engineering, 17 (3), pp. 252-268, 1992, ISSN: 0364-9059. |
3-dimensional sonographic analysis based on color flow Doppler and gray scale image data: a preliminary report Journal Article Journal of Ultrasound in Medicine, 11 (5), pp. 225-232, 1992. |
Acoustic bedload velocity estimates using a broadband pulse-pulse time correlation technique Journal Article Acoustical Society of America Journal, 92 , pp. 1692-1698, 1992. |
1990 |
Limited angle reconstruction using stabilized algorithms Journal Article IEEE Transactions on Medical Imaging, 9 (3), pp. 338-344, 1990, ISSN: 0278-0062. |
Code design and performance characterization for code multiplexed imaging Journal Article IEEE Transactions on Acoustics, Speech and Signal Processing, 38 (8), pp. 1321-1329, 1990, ISSN: 0096-3518. |
Computer Modeling and the Design of Optimal Underwater Imaging-Systems Journal Article IEEE Journal of Oceanic Engineering, 15 (2), pp. 101-111, 1990, ISSN: 0364-9059. |
An explanation of the effects of Squashing in limited angle tomography. Journal Article IEEE Transactions on Medical Imaging, 9 (3), pp. 242-6, 1990, ISSN: 0278-0062. |
1988 |
Multibeam imaging using spatially variant insonification Journal Article Journal of the Acoustical Society of America, 83 (4), pp. 1458-1464, 1988, ISSN: 0001-4966. |
1987 |
Constrained reconstruction of complex waveforms Journal Article J. Opt. Soc. Am. A, 4 (1), pp. 216–220, 1987. |
Difference Fourier analysis of surface features of bacteriorhodopsin using glucose-embedded and frozen-hydrated purple membrane Journal Article Ultramicroscopy, 23 (1), pp. 17 - 28, 1987, ISSN: 0304-3991. |
1984 |
Preparation Of Frozen-Hydrated Specimens For High-Resolution Electron-Microscopy Journal Article Ultramicroscopy, 13 , pp. 373-377, 1984. |