86 publications

2021

• Ronen, R., Attias, Y., Schechner, Y. Y., Jaffe, J. S., & Orenstein, E. (2021). Plankton reconstruction through robust statistical optical tomography. Journal of the Optical Society of America a-Optics Image Science and Vision, 38(9), 1320-1331. doi: 10.1364/josaa.423037
• Pagniello, C., Butler, J., Rosen, A., Sherwood, A., Roberts, P., Parnell, E., ... Sirovic, A. (2021). An Optical Imaging System for Capturing Images in Low-Light Aquatic Habitats Using Only Ambient Light. Oceanography, 34(3), 71-77. doi: 10.5670/oceanog.2021.305
• Lertvilai, P., Roberts, P. L. D., & Jaffe, J. S. (2021). In situ underwater average flow velocity estimation using a low-cost video velocimeter. Journal of Atmospheric and Oceanic Technology, 38(6), 1143-1156. doi: 10.1175/jtech-d-20-0115.1
• Butler, J., Pagniello, C., Jaffe, J. S., Parnell, P. E., & Sirovic, A. (2021). Diel and seasonal variability in kelp forest soundscapes off the Southern California coast. Frontiers in Marine Science, 8(629643). doi: 10.3389/fmars.2021.629643

2020

• Orenstein, E. C., Ratelle, D., Briseno-Avena, C., Carter, M. L., Franks, P. J. S., Jaffe, J. S., & Roberts, P. L. D. (2020). The Scripps Plankton Camera system: A framework and platform for in situ microscopy. Limnology and Oceanography-Methods. doi: 10.1002/lom3.10394
• Orenstein, E. C., Kenitz, K. M., Roberts, P. L. D., Franks, P. J. S., Jaffe, J. S., & Barton, A. D. (2020). Semi- and fully supervised quantification techniques to improve population estimates from machine classifiers. Limnology and Oceanography-Methods. doi: 10.1002/lom3.10399
• Garwood, J. C., Lucas, A. J., Naughton, P., Roberts, P. L. D., Jaffe, J. S., DeGelleke, L., & Franks, P. J. S. (2020). Larval cross-shore transport estimated from internal waves with a background flow: The effects of larval vertical position and depth regulation. Limnology and Oceanography. doi: 10.1002/lno.11632
• Briseno-Avena, C., Prairie, J. C., Franks, P. J. S., & Jaffe, J. S. (2020). Comparing Vertical Distributions of Chl-a Fluorescence, Marine Snow, and Taxon-Specific Zooplankton in Relation to Density Using High-Resolution Optical Measurements. Frontiers in Marine Science, 7(602). doi: 10.3389/fmars.2020.00602
• Kenitz, K. M., Orenstein, E. C., Roberts, P. L. D., Franks, P. J. S., Jaffe, J. S., Carter, M. L., & Barton, A. D. (2020). Environmental drivers of population variability in colony-forming marine diatoms. Limnology and Oceanography. doi: 10.1002/lno.11468

2019

• Garwood, J. C., Lucas, A. J., Naughton, P., Alford, M. H., Roberts, P. L. D., Jaffe, J. S., ... Franks, P. J. S. (2019). A novel cross-shore transport mechanism revealed by subsurface, robotic larval mimics: Internal wave deformation of the background velocity field. Limnology and Oceanography. doi: 10.1002/lno.11400
• Lombard, F., Boss, E., Waite, A. M., Vogt, M., Uitz, J., Stemmann, L., ... Appeltans, W. (2019). Globally consistent quantitative observations of planktonic ecosystems. Frontiers in Marine Science, 6(196). doi: 10.3119/fmars.2019.00196

2018

• Briseno-Avena, C., Franks, P. J. S., Roberts, P. L. D., & Jaffe, J. S. (2018). A diverse group of echogenic particles observed with a broadband, high frequency echosounder. Ices Journal of Marine Science, 75(2), 471-482. doi: 10.1093/icesjms/fsx171
• Naughton, P., Roux, P., Schurgers, C., Kastner, R., Jaffe, J. S., & Roberts, P. L. D. (2018). Self-localization of a deforming swarm of underwater vehicles using impulsive sound sources of opportunity. Ieee Access, 6, 1635-1646. doi: 10.1109/access.2017.2779835

2017

• Jaffe, J. S., Franks, P. J. S., Roberts, P. L. D., Mirza, D., Schurgers, C., Kastner, R., & Boch, A. (2017). A swarm of autonomous miniature underwater robot drifters for exploring submesoscale ocean dynamics. Nature Communications, 8, 14189. doi: 10.1038/ncomms14189

2016

• Naughton, P., Roux, P., Yeakle, R., Schurgers, C., Kastner, R., Jaffe, J. S., & Roberts, P. L. D. (2016). Ambient noise correlations on a mobile, deformable array. Journal of the Acoustical Society of America, 140(6), 4260-4270. doi: 10.1121/1.4971172
• Liao, R., Roberts, P. L. D., & Jaffe, J. S. (2016). Sizing submicron particles from optical scattering data collected with oblique incidence illumination. Applied Optics, 55(33), 9440-9449. doi: 10.1364/ao.55.009440
• Mullen, A. D., Treibitz, T., Roberts, P. L. D., Kelly, E. L. A., Horwitz, R., Smith, J. E., & Jaffe, J. S. (2016). Underwater microscopy for in situ studies of benthic ecosystems. Nature Communications, 7. doi: 10.1038/ncomms12093

2015

• Yi, J. W., Mirza, D., Kastner, R., Schurgers, C., Roberts, P., & Jaffe, J. (2015). ToA-TS: Time of arrival based joint time synchronization and tracking for mobile underwater systems. Ad Hoc Networks, 34, 211-223. doi: 10.1016/j.adhoc.2014.10.010
• Taniguchi, D. A. A., Gagnon, Y., Wheeler, B. R., Johnsen, S., & Jaffe, J. S. (2015). Cuttlefish Sepia officinalis preferentially respond to bottom rather than side stimuli when not allowed adjacent to tank walls. Plos One, 10(10). doi: 10.1371/journal.pone.0138690
• Pepper, R. E., Jaffe, J. S., Variano, E., & Koehl, M. A. R. (2015). Zooplankton in flowing water near benthic communities encounter rapidly fluctuating velocity gradients and accelerations. Marine Biology, 162(10), 1939-1954. doi: 10.1007/s00227-015-2713-x
• Jaffe, J. S. (2015). Underwater optical imaging: The past, the present, and the prospects. Ieee Journal of Oceanic Engineering, 40(3), 683-700. doi: 10.1109/joe.2014.2350751
• Briseño-Avena, C., Roberts, P. L. D., Franks, P. J. S., & Jaffe, J. S. (2015). ZOOPS-O2: A broadband echosounder with coordinated stereo optical imaging for observing plankton in situ. Methods in Oceanography, 12(Supplement C), 36-54. doi: 10.1016/j.mio.2015.07.001

2014

• Haag, J. M., Roberts, P. L. D., Papen, G. C., Jaffe, J. S., Li, L., & Stramski, D. (2014). Deep-sea low-light radiometer system. Optics Express, 22(24), 30074-30091. doi: 10.1364/OE.22.030074
• Berdalet, E., McManus, M. A., Ross, O. N., Burchard, H., Chavez, F. P., Jaffe, J. S., ... Yamazaki, H. (2014). Understanding harmful algae in stratified systems: Review of progress and future directions. Deep-Sea Research Part Ii-Topical Studies in Oceanography, 101, 4-20. doi: 10.1016/j.dsr2.2013.09.042

2013

• Haag, J. M., Jaffe, J. S., & Sweeney, A. M. (2013). Measurement system for marine animal reflectance functions. Opt. Express, 21(3), 3603-3616. doi: 10.1364/OE.21.003603

2011

• Roberts, P. L. D., Steinbuck, J. V., Jaffe, J. S., Horner-Devine, A. R., Franks, P. J. S., & Simonet, F. (2011). Estimation of in situ 3-D particle distributions from a stereo laser imaging profiler. IEEE Journal of Oceanic Engineering, 36(4), 586-601. doi: 10.1109/joe.2011.2165923
• Jaffe, J. S., & Roberts, P. L. D. (2011). Acoustic reflections on marine populations. Physics Today, 64(9), 76-77. doi: 10.1063/PT.3.1260
• Prairie, J. C., Franks, P. J. S., Jaffe, J. S., Doubell, M. J., & Yamazaki, H. (2011). Physical and biological controls of vertical gradients in phytoplankton. Limnology & Oceanography: Fluids & Environments, 1, 75-90. doi: 10.1215/21573698-1267403
• Jaffe, J. S., & Roberts, P. L. D. (2011). Estimating fish orientation from broadband, limited-angle, multiview, acoustic reflections. Journal of the Acoustical Society of America, 129(2), 670-680. doi: 10.1121/1.3523430
• Roberts, P. L. D., Jaffe, J. S., & Trivedi, M. M. (2011). Multiview, broadband acoustic classification of marine fish: a machine learning framework and comparative analysis. IEEE Journal of Oceanic Engineering, 36(1), 90-104. doi: 10.1109/joe.2010.2101235

2010

• Prairie, J. C., Franks, P. J. S., & Jaffe, J. S. (2010). Cryptic peaks: Invisible vertical structure in fluorescent particles revealed using a planar laser imaging fluorometer. Limnology and Oceanography, 55(5), 1943-1958. doi: 10.4319/lo.2010.55.5.1943
• Steinbuck, J. V., Roberts, P. L. D., Troy, C. D., Horner-Devine, A. R., Simonet, F., Uhlman, A. H., ... Franks, P. J. S. (2010). An autonomous open-ocean stereoscopic PIV profiler. Journal of Atmospheric and Oceanic Technology, 27(8), 1362-1380. doi: 10.1175/2010jtecho694.1
• Jaffe, J. S. (2010). Enhanced extended range underwater imaging via structured illumination. Optics Express, 18(12), 12328-12340.
• Li, W., & Jaffe, J. S. (2010). Sizing homogeneous spherical particles from intensity-only angular scatter. Journal of the Optical Society of America a-Optics Image Science and Vision, 27(2), 151-158.

2009

• Karakoylu, E. M., Franks, P. J. S., Tanaka, Y., Roberts, P. L. D., & Jaffe, J. S. (2009). Copepod feeding quantified by planar laser imaging of gut fluorescence. Limnology and Oceanography-Methods, 7, 33-41. doi: 10.4319/lom.2009.7.33

2008

• Roberts, P. L. D., & Jaffe, J. S. (2008). Classification of live, untethered zooplankton from observations of multiple-angle acoustic scatter. Journal of the Acoustical Society of America, 124(2), 796-802. doi: 10.1121/1.2945114
• Franks, P. J. S., & Jaffe, J. S. (2008). Microscale variability in the distributions of large fluorescent particles observed in situ with a planar laser imaging fluorometer. Journal of Marine Systems, 69(3-4), 254-270. doi: 10.1016/j.jmarsys.2006.03.027
• Jaffe, J. S. (2008). Sensing plankton: acoustics and optical imaging. Real-time coastal observing systems for marine ecosystem dynamics and harmful algal blooms : theory, instrumentation and modelling (pp. 385-412). Paris: UNESCO.

2007

• Jaffe, J. S. (2007). A tomographic approach to inverse Mie particle characterization from scattered light. Optics Express, 15(19), 12217-12229. doi: 10.1364/oe.15.012217
• Roberts, P. L. D., & Jaffe, J. S. (2007). Multiple angle acoustic classification of zooplankton. Journal of the Acoustical Society of America, 121(4), 2060-2070. doi: 10.1121/1.2697471
• Jaffe, J. S., Simonet, F., Roberts, P. L. D., & Bowles, A. E. (2007). Measurement of the acoustic reflectivity of sirenia (Florida manatees) at 171 kHz. Journal of the Acoustical Society of America, 121(1), 158-165. doi: 10.1121/1.2384845

2006

• Shao, B., Jaffe, J. S., Chachisvilis, M., & Esener, S. C. (2006). Angular resolved light scattering for discriminating among marine picoplankton: modeling and experimental measurements. Optics Express, 14(25), 12473-12484. doi: 10.1364/oe.14.012473
• Jaffe, J. S. (2006). Using multi-angle scattered sound to size fish swimbladders. Ices Journal of Marine Science, 63(8), 1397-1404. doi: 10.1016/j.icejms.2006.04.024

2005

• Genin, A., Jaffe, J. S., Reef, R., Richter, C., & Franks, P. J. S. (2005). Swimming against the flow: A mechanism of zooplankton aggregation. Science, 308(5723), 860-862. doi: 10.1126/science.1107834
• Yahel, R., Yahel, G., Berman, T., Jaffe, J. S., & Genin, A. (2005). Diel pattern with abrupt crepuscular changes of zooplankton over a coral reef. Limnology and Oceanography, 50(3), 930-944.
• Ai, Y. H., & Jaffe, J. S. (2005). Design and preliminary tests of a family of adaptive waveforms to measure blood vessel diameter and wall thickness. IEEE Transactions on Ultrasonics Ferroelectrics and Frequency Control, 52(2), 250-260. doi: 10.1109/tuffc.2005.1406551
• Jaffe, J. S. (2005). Performance bounds on synchronous laser line scan systems. Optics Express, 13(3), 738-748. doi: 10.1364/opex.13.000738
• Jaffe, J. S. (2005). Three-dimensional probability density functions via tomographic inversion. SIAM Journal on Applied Mathematics, 65(5), 1506-1525. doi: 10.1137/s003613990342390x

2004

• Schell, C., & Jaffe, J. S. (2004). Experimental verification of an interpolation algorithm for improved estimates of animal position. Journal of the Acoustical Society of America, 116(1), 254-261. doi: 10.1121/1.1756894

2003

• De Robertis, A., Schell, C., & Jaffe, J. S. (2003). Acoustic observations of the swimming behavior of the euphausiid Euphausia pacifica Hansen. Ices Journal of Marine Science, 60(4), 885-898. doi: 10.1016/s1054-3139(03)00070-5
• Zawada, D. G., & Jaffe, J. S. (2003). Changes in the fluorescence of the Caribbean coral Montastraea faveolata during heat-induced bleaching. Limnology and Oceanography, 48(1), 412-425.

2002

• Fuchs, E., Zimmerman, R. C., & Jaffe, J. S. (2002). The effect of elevated levels of phaeophytin in natural water on variable fluorescence measured from phytoplankton. Journal of Plankton Research, 24(11), 1221-1229. doi: 10.1093/plankt/24.11.1221
• Moore, K. D., & Jaffe, J. S. (2002). Time-evolution of high-resolution topographic measurements of the sea floor using a 3-D laser line scan mapping system. IEEE Journal of Oceanic Engineering, 27(3), 525-545. doi: 10.1109/joe.2002.1040936
• Fuchs, E., Jaffe, J. S., Long, R. A., & Azam, F. (2002). Thin laser light sheet microscope for microbial oceanography. Optics Express, 10(2), 145-154. doi: 10.1364/OE.10.000145

2001

• Richardson, M. D., Briggs, K. B., Bibee, L. D., Jumars, P. A., Sawyer, W. B., Albert, D. B., ... Wheatcroft, R. A. (2001). Overview of SAX99: Environmental considerations. IEEE Journal of Oceanic Engineering, 26(1), 26-53. doi: 10.1109/48.917921
• Franks, P. J. S., & Jaffe, J. S. (2001). Microscale distributions of phytoplankton: initial results from a two-dimensional imaging fluorometer, OSST. Marine Ecology-Progress Series, 220, 59-72. doi: 10.3354/meps220059

2000

• De Robertis, A., Jaffe, J. S., & Ohman, M. D. (2000). Size-dependent visual predation risk and the timing of vertical migration in zooplankton. Limnology and Oceanography, 45(8), 1838-1844.
• Moore, K. D., Jaffe, J. S., & Ochoa, B. L. (2000). Development of a new underwater bathymetric laser imaging system: L-bath. Journal of Atmospheric and Oceanic Technology, 17(8), 1106-1117. doi: 10.1175/1520-0426(2000)017<1106:doanub>2.0.co;2

1999

• Jaffe, J. S., Ohman, M. D., & De Robertis, A. (1999). Sonar estimates of daytime activity levels of Euphausia pacifica in Saanich Inlet. Canadian Journal of Fisheries and Aquatic Sciences, 56(11), 2000-2010. doi: 10.1139/cjfas-56-11-2000
• Jaffe, J. S. (1999). Target localization for a three-dimensional multibeam sonar imaging system. Journal of the Acoustical Society of America, 105(6), 3168-3175. doi: 10.1121/1.424647

1998

• Rafii, K., & Jaffe, J. S. (1998). Adaptive ultrasonic measurement of blood vessel diameter and wall thickness: Theory and experimental results. IEEE Transactions on Ultrasonics Ferroelectrics and Frequency Control, 45(3), 593-603. doi: 10.1109/58.677604
• Jaffe, J. S., Ohman, M. D., & De Robertis, A. (1998). OASIS in the sea: measurement of the acoustic reflectivity of zooplankton with concurrent optical imaging. Deep-Sea Research Part Ii-Topical Studies in Oceanography, 45(7), 1239-1253. doi: 10.1016/s0967-0645(98)00030-7

1997

• Jaffe, J. S. (1997). Methods for three-dimensional sensing of animals. Animal groups in three dimensions (pp. 17-35). Cambridge; New York: Cambridge University Press.

1996

• Chandran, G., & Jaffe, J. S. (1996). Signal set design with constrained amplitude spectrum and specified time-bandwidth product. IEEE Transactions on Communications, 44(6), 725-732. doi: 10.1109/26.506389
• McGehee, D., & Jaffe, J. S. (1996). Three-dimensional swimming behavior of individual zooplankters: Observations using the acoustical imaging system FishTV. ICES Journal of Marine Science, 53(2), 363-369. doi: 10.1006/jmsc.1996.0050
• Jaffe, J. S. (1996). Temporal sampling of backscattered sonar signals. ICES Journal of Marine Science, 53(2), 359-361. doi: 10.1006/jmsc.1996.0049

1995

• Jaffe, J. S. (1995). Monte Carlo modeling of underwater image formation: validity of the linear and small angle approximations. Applied Optics, 34(24), 5413-5421.
• Jaffe, J. S., Reuss, E., McGehee, D., & Chandran, G. (1995). FTV: a sonar for tracking macrozooplankton in three dimensions. Deep-Sea Research Part I-Oceanographic Research Papers, 42(8), 1495-1512. doi: 10.1016/0967-0637(95)00030-a
• Palowitch, A. W., & Jaffe, J. S. (1995). Optical serial sectioned chlorophyll a microstructure. Journal of Geophysical Research-Oceans, 100(C7), 13267-13278. doi: 10.1029/95jc00462
• Maffione, R. A., & Jaffe, J. S. (1995). The average cosine due to an isotropic light source in the ocean. Journal of Geophysical Research-Oceans, 100(C7), 13179-13192. doi: 10.1029/95jc00461
• McGehee, D., & Jaffe, J. S. (1995). Segmented transducer design using an optimum mean square quantizer approach. Journal of the Acoustical Society of America, 97(4), 2316-2325. doi: 10.1121/1.411956

1994

• Palowitch, A. W., & Jaffe, J. S. (1994). Three-dimensional ocean chlorophyll distributions from underwater serial sectioned fluorescence images. Applied Optics, 33(14), 3023-3033.
• McGehee, D., & Jaffe, J. S. (1994). Beamforming with dense random arrays: The development of a spatially shaded polyvinylidene fluoride acoustic transducer. Journal of the Acoustical Society of America, 95(1), 318-323. doi: 10.1121/1.408364

1993

• Jaffe, J. S. (1993). A simplified derivation of the performance of edge-connected crossed-electrode arrays for two-dimensional projection and beamforming. IEEE Transactions on Signal Processing, 41(1), 446-449. doi: 10.1109/tsp.1993.193175

1992

• Sutton, D. W., & Jaffe, J. S. (1992). Acoustic bedload velocity estimates using a broadband pulse–pulse time correlation technique. Journal of the Acoustical Society of America, 92(3), 1692-1698. doi: 10.1121/1.403908
• Cobra, D. T., Oppenheim, A. V., & Jaffe, J. S. (1992). Geometric distortions in side-scan sonar images: a procedure for their estimation and correction. IEEE Journal of Oceanic Engineering, 17(3), 252-268. doi: 10.1109/48.153442
• Pretorius, D. H., Nelson, T. R., & Jaffe, J. S. (1992). 3-dimensional sonographic analysis based on color flow Doppler and gray scale image data: a preliminary report. Journal of Ultrasound in Medicine, 11(5), 225-232.

1990

• Olson, T., & Jaffe, J. S. (1990). An explanation of the effects of Squashing in limited angle tomography. IEEE Transactions on Medical Imaging, 9(3), 242-246. doi: 10.1109/42.57761
• Jaffe, J. S. (1990). Limited angle reconstruction using stabilized algorithms. IEEE Transactions on Medical Imaging, 9(3), 338-344. doi: 10.1109/42.57772
• Jaffe, J. S., Cassereau, P. M., & Glassbrenner, D. J. (1990). Code design and performance characterization for code multiplexed imaging. IEEE Transactions on Acoustics Speech and Signal Processing, 38(8), 1321-1329. doi: 10.1109/29.57567
• Jaffe, J. S. (1990). Computer modeling and the design of optimal underwater imaging systems. IEEE Journal of Oceanic Engineering, 15(2), 101-111. doi: 10.1109/48.50695

1988

• Jaffe, J. S., & Cassereau, P. M. (1988). Multibeam imaging using spatially variant insonification. Journal of the Acoustical Society of America, 83(4), 1458-1464. doi: 10.1121/1.395953
• Jaffe, J. S. (1988). Underwater optical imaging: the design of optimal systems. Oceanography Society Journal, 1(2), 40-41.

1987

• Jaffe, J. S., & Glaeser, R. M. (1987). Difference Fourier analysis of “surface features” of bacteriorhodopsin using glucose-embedded and frozen-hydrated purple membrane. Ultramicroscopy, 23(1), 17-28. doi: 10.1016/0304-3991(87)90223-3
• Jaffe, J. S., & Fricke, R. (1987). Constrained reconstruction of complex waveforms. J. Opt. Soc. Am. A, 4(1), 216-220.

1984

• Jaffe, J. S., & Glaeser, R. M. (1984). Preparation of frozen-hydrated specimens for high resolution electron microscopy. Ultramicroscopy, 13(4), 373-377. doi: 10.1016/0304-3991(84)90003-2