Publications


Le, K. T., Yuan, Z., Syed, A., Ratelle, D., Orenstein, E. C., Carter, M. L., Strang, S., Kenitz, K. M., Morgado, P., Franks, P. J. S., Vasconcelos, N., & Jaffe, J. S. (2022). Benchmarking and Automating the Image Recognition Capability of an In Situ Plankton Imaging System. Frontiers in Marine Science, 9, 869088. https://doi.org/10.3389/fmars.2022.869088
Lertvilai, P., & Jaffe, J. S. (2022). In situ size and motility measurement of aquatic invertebrates with an underwater stereoscopic camera system using tilted lenses. Methods in Ecology and Evolution, 9. https://doi.org/10.1111/2041-210x.13855
Sauer, J. S., Mayer, K. J., Lee, C., Alves, M. R., Amiri, S., Bahaveolos, C. J., Franklin, E. B., Crocker, D. R., Dang, D. Y., Dinasquet, J., Garofalo, L. A., Kaluarachchi, C. P., Kilgour, D. B., Mael, L. E., Mitts, B. A., Moon, D. R., Moore, A. N., Morris, C. K., Mullenmeister, C. A., … Prather, K. A. (2022). The Sea Spray Chemistry and Particle Evolution study (SeaSCAPE): overview and experimental methods. Environmental Science-Processes & Impacts, 26. https://doi.org/10.1039/d1em00260k
Merz, E., Kozakiewicz, T., Reyes, M., Ebi, C., Isles, P., Baity-Jesi, M., Roberts, P., Jaffe, J. S., Dennis, S. R., Hardeman, T., Stevens, N., Lorimer, T., & Pomati, F. (2021). Underwater dual-magnification imaging for automated lake plankton monitoring. Water Research, 203, 12. https://doi.org/10.1016/j.watres.2021.117524
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. https://doi.org/10.1364/josaa.423037
Pagniello, C., Butler, J., Rosen, A., Sherwood, A., Roberts, P., Parnell, E., Jaffe, J., & Sirovic, A. (2021). An optical imaging system for capturing images in low-light aquatic habitats using only ambient light. Oceanography, 34(3), 71–77. https://doi.org/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. https://doi.org/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. https://doi.org/10.3389/fmars.2021.629643
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. https://doi.org/10.1002/lom3.10399
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. https://doi.org/10.1002/lom3.10394
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. https://doi.org/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. https://doi.org/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. https://doi.org/10.1002/lno.11468
Garwood, J. C., Lucas, A. J., Naughton, P., Alford, M. H., Roberts, P. L. D., Jaffe, J. S., DeGelleke, L., & 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. https://doi.org/10.1002/lno.11400
Lombard, F., Boss, E., Waite, A. M., Vogt, M., Uitz, J., Stemmann, L., Sosik, H. M., Schulz, J., Romagnan, J. B., Picheral, M., Pearlman, J., Ohman, M. D., Niehoff, B., Moller, K. M., Miloslavich, P., Lara-Lpez, A., Kudela, R., Lopes, R. M., Kiko, R., … Appeltans, W. (2019). Globally consistent quantitative observations of planktonic ecosystems. Frontiers in Marine Science, 6. https://doi.org/10.3119/fmars.2019.00196
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. https://doi.org/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. https://doi.org/10.1109/access.2017.2779835
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. https://doi.org/10.1038/ncomms14189
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. https://doi.org/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. https://doi.org/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. https://doi.org/10.1038/ncomms12093
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. https://doi.org/10.1016/j.adhoc.2014.10.010
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. https://doi.org/10.1007/s00227-015-2713-x
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). https://doi.org/10.1371/journal.pone.0138690
Jaffe, J. S. (2015). Underwater optical imaging: The past, the present, and the prospects. Ieee Journal of Oceanic Engineering, 40(3), 683–700. https://doi.org/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. https://doi.org/10.1016/j.mio.2015.07.001
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. https://doi.org/10.1364/OE.22.030074
Berdalet, E., McManus, M. A., Ross, O. N., Burchard, H., Chavez, F. P., Jaffe, J. S., Jenkinson, I. R., Kudela, R., Lips, I., Lips, U., Lucas, A., Rivas, D., Ruiz-de la Torre, M. C., Ryan, J., Sullivan, J. M., & 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. https://doi.org/10.1016/j.dsr2.2013.09.042
Haag, J. M., Jaffe, J. S., & Sweeney, A. M. (2013). Measurement system for marine animal reflectance functions. Opt. Express, 21(3), 3603–3616. https://doi.org/10.1364/OE.21.003603
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. https://doi.org/10.1109/joe.2011.2165923
Jaffe, J. S., & Roberts, P. L. D. (2011). Acoustic reflections on marine populations. Physics Today, 64(9), 76–77. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/10.1109/joe.2010.2101235
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. https://doi.org/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., Jaffe, J. S., Monismith, S. G., & Franks, P. J. S. (2010). An autonomous open-ocean stereoscopic PIV profiler. Journal of Atmospheric and Oceanic Technology, 27(8), 1362–1380. https://doi.org/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.
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. https://doi.org/10.4319/lom.2009.7.33
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. https://doi.org/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. https://doi.org/10.1016/j.jmarsys.2006.03.027
Jaffe, J. S. (2008). Sensing plankton: acoustics and optical imaging. In M. Babin, C. S. Roesler, & J. J. Cullen (Eds.), Real-time coastal observing systems for marine ecosystem dynamics and harmful algal blooms : theory, instrumentation and modelling (pp. 385–412). UNESCO.
Jaffe, J. S. (2007). A tomographic approach to inverse Mie particle characterization from scattered light. Optics Express, 15(19), 12217–12229. https://doi.org/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. https://doi.org/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. https://doi.org/10.1121/1.2384845
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. https://doi.org/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. https://doi.org/10.1016/j.icejms.2006.04.024
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. https://doi.org/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.
Jaffe, J. S. (2005). Performance bounds on synchronous laser line scan systems. Optics Express, 13(3), 738–748. https://doi.org/10.1364/opex.13.000738