Kenitz, K. M., Orenstein, E. C., Anderson, C. R., Barth, A. J., Briseño‐Avena, C., Caron, D. A., Carter, M. L., Eggleston, E., Franks, P. J. S., Fumo, J. T., Jaffe, J. S., McBeain, K. A., Odell, A., Seech, K., Shipe, R., Smith, J., Taniguchi, D. A. A., Venrick, E. L., & Barton, A. D. (2023). Convening Expert Taxonomists to Build Image Libraries for Training Automated Classifiers. Limnology and Oceanography Bulletin. https://doi.org/10.1002/lob.10584

Stock, B. C., Mullen, A. D., Jaffe, J. S., Candelmo, A., Heppell, S. A., Pattengill-Semmens, C. V., McCoy, C. M., Johnson, B. C., & Semmens, B. X. (2023). Protected fish spawning aggregations as self-replenishing reservoirs for regional recovery. Proceedings of the Royal Society B: Biological Sciences, 290(1998), 20230551. https://doi.org/10.1098/rspb.2023.0551

Kenitz, K. M., Anderson, C. R., Carter, M. L., Eggleston, E., Seech, K., Shipe, R., Smith, J., Orenstein, E. C., Franks, P. J. S., Jaffe, J. S., & Barton, A. D. (2023). Environmental and ecological drivers of harmful algal blooms revealed by automated underwater microscopy. Limnology and Oceanography. https://doi.org/https://doi.org/10.1002/lno.12297

Jaffe, J. S., Schull, S., Kühl, M., & Wangpraseurt, D. (2022). Non-invasive estimation of coral polyp volume and surface area using optical coherence tomography. Frontiers in Marine Science, 9, 1049440. https://doi.org/10.3389/fmars.2022.1049440

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

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

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

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

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

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

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

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