References

3 color maximum operator

Cochrane, N.A., Sameoto, D., Herman, A.W. and Neilson, J. (1991) Multiple-frequency acoustic backscattering and zooplankton aggregations in the inner Scotian Shelf basins. Can. J. Fish. Aquat. Sci. 48: 340-355.

Kloser, R. J., Ryan, T., Sakov, P., and Koslow, J. A. (2002) Species identification in deep water using multiple frequencies. Canadian Journal of Fisheries and Aquatic Sciences, 59: 1065-1077.

Absorption coefficient

Francois R.E. and Garrison G.R. (1982) Sound absorption based on measurements. Part II: Boric acid contribution and equation for total absorption. J. Acoust. Soc. Am., 72, 1879-90.

Background noise removal

Boswell, K.M., Wilson, M.P., and Wilson, C.A. (2007) Hydroacoustics as a tool for assessing fish biomass and size distribution associated with discrete shallow water estuarine habitats in Louisiana. Estuaries and Coasts, 30, 607-617.

De Robertis, A., and Higginbottom, I. (2007) A post-processing technique for estimation of signal-to-noise ratio and removal of echosounder background noise. ICES Journal of Marine Science, 64, 1282-1291.

Higginbottom I., and Pauly T. (1997) Echo integration in low signal to noise regimes: methods of noise estimation and removal. CCAMLR Working Group on Ecosystem Monitoring and Management paper WG-EMM-97/74.

Kieser, R., Reynisson, P., and Mulligan, T. J. (2005) Definition of signal-to-noise ratio and its critical role in split-beam measurements. ICES Journal of Marine Science 62: 123-130.

Korneliussen R. J., (2000) Measurement and removal of echo integration noise. ICES Journal of Marine Science 57: 1204-1217.

Kovesi P. (1999) Phase Preserving Denoising of Image. The Australian Pattern Recognition Society Conference: DICTA'99. December 1999. Perth WA. pp 212-217

Nunnallee E. P. (1990) An alternative to thresholding during echo-integration data collection. Rapports et Proces-verbaux des Réunions. Conseil International pour l'Éxploration de la Mer 189: 92-94.

Noise removal

Ryan T. E., Downie R. A., Kloser R. J., Keith G. (2015) Reducing bias due to noise and attenuation in open-ocean echo integration. ICES Journal of Marine Science 72, 2482-2493

Biomass

MacLennan David. N. and Simmonds E. John (1992) Fisheries Acoustics. Chapter 8: Data analysis. Chapman and Hall, London (ISBN 0 412 3306 1 0 or 0 422 31472 8 in USA).

Sawada, K., Furusawa, M., and Williamson, N.J. (1993) Conditions for the precise measurement of fish TS in situ. J. Mar. Acoust. Soc. Japan 20: 73–79.

Gauthier S. and Rose G. A. (2001) Diagnostic tools for unbiased in situ target strength estimation. Canadian Journal of Fisheries and Aquatic Sciences, 58(11): 2149-2155.

Blur and sharpen convolution kernels

Reid D.G. and Simmonds E.J. (1993) Image analysis techniques for the study of fish school structure from acoustic survey data, Can. J. Fish. Aquat. Sci. Vol 50.

Bottom classification

Anderson J. T. (Editor) (2007) Acoustic seabed classification of marine physical and biological landscapes. ICES Cooperative research report No. 286.

Calinski, T., and Harabasz, J. (1974). A dendrite method for cluster analysis. Commun. Stat. 3: 1–27.

Ellingsen K. E., Gray J. S., Bjørnbom E. (2002) Acoustic classification of seabed habitats using the QTC VIEW system. ICES Journal of Marine Science, 59: 825-835.

Hamilton L. J. (2001) Acoustic seabed classification systems. DSTO-TN-0401.

Kloser R.J., Bax N.J., Ryan T., Williams A., Barker B.A. (2001) Remote sensing of seabed types in the Australian South East Fishery; Development and application of normal incident acoustic techniques and associated ‘ground truthing'. Marine and Freshwater Research, 52: 475-89.

Legendre P. (2002) Acoustic seabed classification methodology: a user's statistical comparison. Départment de sciences biologiques, Université de Montréal. C. P. 6128, succursale Centre-ville Montréal, Quebec H3C 3J7, Canada.

Legendre P., Ellingsen K. E., Bjørnbom E., Casgrain P. (2002) Acoustic seabed classification: improved statistical method. Can. J. Fish. Aquat. Sci 59: 1085-1089.

Milligan, G.W., and Cooper, M.C. (1985). An examination of procedures for determining the number of clusters in a data set. Psychometrika, 50: 159–179.

Siwabessy J. W., Tseng Y., Gavrilov A. N. (2004) Seabed habitat mapping in coastal waters using a normal incident acoustic technique. Proceedings of ACOUSTICS 2004. 3-5 November 2004, Gold Coast, Australia. 187-192.

Siwabessy P. J. W., Penrose J. D., Fox D. R., Kloser R. J. (2000) Bottom Classification in the Continental Shelf: A Case Study for the North-west and South-east Shelf of Australia. Acoustics 2000 Australian Acoustical Society conference Joondalup, Australia. 15-17 November 2000. 1- 6.

Siwabessy J., Penrose J., Kloser R., Fox D., (1999) Seabed habitat classification. Shallow Survey '99 - International Conference on High Resolution Surveys in Shallow Water. Sydney, Australia. Oct 1999.

Calibration

Foote K.G, Knudsen H.P., Vestnes G., MacLennan D.N., and Simmonds E.J. (1987) Calibration of acoustic instruments for fish density estimation: a practical guide ICES Cooperative Research Report No 144 69 pp.

Foote C. J., Chu D., Hammar T. R., Baldwin K. C., Mayer L. A., Hufnagle L. C., Jech J. M. (2005) Protocols for calibrating multibeam sonar. Journal of the Acoustical Society of America, Vol 117, Issue 4, 2013-2027.

Honkalehto T. and Ryan T.E. (2003) Analysis of industry acoustic observations of orange roughy (Hoplostethus atlanticus) spawning aggregations on the Cascade Plateau off southeastern Tasmania in June and July 2003. Report to the Deepwater Assessment Group. Copy available from CSIRO Marine and Atmospheric Research Library, Hobart, Tasmania, Australia.

Demer, D.A., Berger, L., Bernasconi, M., Bethke, E., Boswell, K., Chu, D., Domokos, R., et al. (2015) Calibration of acoustic instruments. ICES Cooperative Research Report No. 326.

Calibration sphere modeling

MacLennan, D.N. (1981) The theory of solid spheres as sonar calibration targets. Scottish Fisheries Research. Report Number 22.

Cross filter

Balk, H., Lindem, T., Kubečka J., (2009) New Cubic Cross filter detector for multi beam data recorded with DIDSON acoustic camera. In : Papadakis, J.S., Bjorno, L., (eds.), Underwater acoustic measurements, Technologies & Results. Foundation for Research & Technology, Heraklion, Greece, ISBN 978-960-98883-3-2: 1461-1468.

Deadzone

Kloser R.J., Ryan T.E., Williams A., Lewis M. (2001) Final Report FRDC Project 99/111 Development and application of a combined industry/scientific acoustic survey of orange roughy in the eastern zone.

Kloser R.J.(1996) Improved precision of acoustic surveys of benthopelagic fish by means of a deep-towed transducer. ICES Journal of Marine Science 53: 407-413.

Kloser R.J., Koslow J.A., and Williams A. (1996) Acoustic Assessment of the Biomass of a Spawning Aggregation of Orange Roughy (Hoplostethus atlanticus, Collet) off South-eastern Australia, 1990-93. Marine and Freshwater Research 47: 1015-24.

Ona E. and Mitson R.B. (1996) Acoustic sampling and signal processing near the seabed: the deadzone revisited. ICES Journal of Marine Science 53: 677-690.

Density index

Parker-Stetter, S.L., Rudstam, L.G., Sullivan, P.J., and Warner, D.M. (2009) Standard operating procedures for fisheries acoustic surveys in the Great Lakes. Great Lakes Fisheries Commission Special Publication. 09-01.

Sawada, K., Furusawa, M., and Williamson, N.J. (1993) Conditions for the precise measurement of fish TS in situ. J. Mar. Acoust. Soc. Japan. 20: 73-79.

Equivalent two way beam angle

MacLennan David N. and Simmonds E. John (1992) Fisheries Acoustics. Chapman and Hall, London (ISBN 0 412 3306 1 0 or 0 422 31472 8 in USA).

False bottom echoes

Renfree, J.S., and Demer, D.A. (2016) Optimizing transmit interval and logging range while avoiding aliased seabed echoes. ICES Journal of Marine Science 73(8), 1955–1964.

Fish length equation

See references cited for the Target length algorithm.

Fish track detection

Blackman S.S. (1999) Design and analysis of modern tracking systems, Artech House, Massachusetts.

Blackman Samuel S. (1986) Multiple Target Tracking with Radar Applications, Artech House, Massachusetts.

Balk H. and Lindem T. (2000) Improved fish detection in data from split-beam sonar. Aquat. Living Resour. 13: 297-303.

Dawson J. and Mulligan T. (2000) Echo selection and trace formation: techniques, interactions, and advancements. Proceedings of the Fifth European Conference on Underwater Acoustics, ECUA 2000: 1455-1460.

Dawson J., Wiggins D., Degan D., Geiger H., Hart D. and Adams B. (2000) Point-source violations: split-beam tracking of fish at close range. Aquat. Living Resour. 13: 291-295.

Eggers D.M., Skvorc P.A. II, and Burwen D. (1995) Abundance estimates of Chinook Salmon in the Kenai River using dual-beam sonar. Alaska Fishery Research Bulletin 2(1): 1-22.

Johnson L.J. and Moursund (2000) Evaluation of juvenile salmon behaviour at Bonneville Dam, Columbia River, using a multibeam technique. Aquat. Living Resour. 13: 313-318.

Mulligan T. Personal communication.

Xie Y. (2000) A Range-dependent echo-association algorithm and its application in split-beam sonar tracking of migratory salmon in the Fraser River watershed. IEEE Journal of Oceanic Engineering. 25(3): 387-398.

Xie Y., Cronkite, G. and Mulligan, T.J. (1997) A split beam echosounder perspective on migratory salmon in the Fraser River: A progress report on the split-beam experiment at Mission, B.C., in 1995. Pacific Salmon Commission, Technical Report No. 8.

Fisheries acoustics texts

Parker-Stetter, S.L., Rudstam, L.G., Sullivan, P.J., and Warner, D.M. 2009. Standard operating procedures for fisheries acoustic surveys in the Great Lakes. Great Lakes Fisheries Commission Special Publication. 09-01.

Simmonds J. and MacLennan D. (2005) Fisheries Acoustics: Theory and Practice. Second edition, Blackwell Science. Fish and Aquatic Resources Series 10. (ISBN-10: 0-632-05994-X, ISBN-13: 978-0-632-05994-2).

Data Analysis - 9.5.2 Contour and distribution maps (Bayesian method)

Brierley, A. S, Gull, S. F. and Wafey, M. H. (2003) A Bayesian maximum entropy reconstruction of stock distribution and inference of stock density from line-transect acoustic-survey data. ICES. Journal of Marine Science. 60, 446-52.

Data Analysis - 9.6.2 Stratified random transects (Block averaging)

Jolly, G. M. and Hampton, I. (1990) A stratified random transect design for acoustic surveys of fish stocks. Canadian Journal of Fisheries and Aquatic Science, 47, 1282-91.

Data Analysis - 9.6.2 Stratified random transects (Geostatistics)

Simmonds, E. J. and Fryer, R. J. (1996) Which are better, random or systematic acoustic surveys? A simulation using North Sea herring as an example. ICES, Journal of Marine Science. 53, 39-50.

Frequency response graph

Korneliussen R. and Ona E (2003) Synthetic echograms generated from relative frequency response. ICES Journal of Marine Science, 60:636-640.

Andersen L. N., Chu D., Handegard N. O., Heimvoll H., Korneliussen R., Macaulay G. J., Ona E., Patel R., Pedersen G. (2023) Quantitative processing of broadband data as implemented in a scientific splitbeam echosounder, Methods in Ecology and Evolution, 15(2): 317-328.

Fundamental properties of sea water

Fofonoff, N.P., Millard, R.C. (1983) Algorithms for computation of fundamental properties of seawater. UNESCO technical papers in marine science. p25-27 (4. Pressure to Depth conversion)

HAC standard data format

Simard Y., McQuinn I.,Montminy M., Lang C., Miller D., Stevens C., Wiggins D. and Marchalot C. (1997) Description of the HAC standard format for raw and edited acoustic data, version 1.0, Canadian Technical Report of Fisheries and Aquatic Sciences 2174.

Simard Y., McQuinn I., Diner N., Simmonds J. and Higginbottom I. (2000) Common data format: 2000 progress report, ICES Fisheries Acoustics Sciences and Technology WG. Haarlem, Netherlands, April 2000.

Simard Y., McQuinn I, Montminy M., Lang C., Stevens C., Goulet F., Lapierre J.-P., Beaulieu J.-L., Landry J., Samson Y., and Gagné M. (2000) CH2, Canadian hydroacoustic data analysis tool 2 user's manual (version 2.0). Canadian Technical Report of Fisheries and Aquatic Sciences 2332.

Horizontal beaming

Boswell, K.M., Miller, M.W. and Wilson, C.A. (2007) A lightweight transducer platform for use in shallow water horizontal-aspect acoustic surveys. Fisheries Research, 85, 291-294.

Boswell, K.M., Kaller, M.D., Cowan, J.H. and Wilson, C.A. (2008) Evaluation of target strength–fish length equation choices for estimating estuarine fish biomass. Hydrobiologia, 610, 113-123.

Boswell, K. M., and Wilson, C.A. (2008) Side-aspect target strength measurements of bay anchovy (Anchoa mitchilli) and Gulf menhaden (Brevoortia patronus) derived from ex situ experiments. ICES Journal of Marine Science, 65, 1012–1020.

Duncan A. and Kubecka, J. (1996) Patchiness of longitudinal fish distributions in a river as revealed by a continuous hydroacoustic survey. ICES Journal of Marine Science, 53(2), 161-165.

Guillard J. and Colon B. (1998) Hydroacoustic estimation of the number of fish passing through Beaucaire-Vallabregues lock (Rhone). Bulletin Francais de la Peche et de la Disciculture, 348, 79-90.

Knudsen F.R., Saegrov H. (2002) Benefits from horizontal beaming during acoustic survey: application to three Norwegian lakes. Fisheries Research, 56, 205-211.

Kubecka J. (1994) Simple model on the relationship between fish acoustical target strength and aspect for high-frequency sonar in shallow waters. J. Appl. Ichthyol., 10(2-3), 75-81.

Kubecka J. and Duncan A. (1998) Acoustic size vs. real size relationships for common species of riverine fish. Fisheries Research, 35, 115-125.

Kubecka J., Duncan, A., Duncan W.M., Sinclair D., Butterworth A.J. (1994) Brown trout populations of three Scottish lochs estimated by horizontal sonar and multimesh gillnets. Fisheries Research, 20, 29-48.

Kubecka J. and Wittingerova M. (1998) Horizontal beaming as a crucial component of acoustic fish stock assessment in freshwater reservoirs. Fisheries Research, 35, 99-106.

Lyons J. (1998) A hydroacoustic assessment of fish stocks in the River Trent, England. Fisheries Research, 35, 83-90.

Yule D.L. (2000) Comparison of Horizontal Acoustic and Purse-Seine Estimates of Salmonid Densities and Sizes in Eleven Wyoming Waters. N. Am. J. Fish. Manage., 20(3), 759-775.

ICES SONAR-netCDF4

Macaulay, G. and Peña, H. (Eds.). 2018. The SONAR-netCDF4 convention for sonar data, Version 1.0. ICES Cooperative Research Report No. 341. 33 pp.

New versions of the convention are developed and discussed at this site: https://github.com/ices-publications/SONAR-netCDF4

k-means

Elkans C. (2003) Using the Triangle Inequality to Accelerate k-Means. Proceedings of the Twentieth International Conference on Machine Learning (ICML-2003), Washington DC, 2003.

Monochrome operator

Haines E. and Akenine-Moller T. (2002) Real-time rendering, 2nd Edition, A.K. Peters, Natick, Massachusetts, 188-194.

Motion correction (Dunford method) operator

Adam J. Dunford (2005) Correcting echo-integration data for transducer motion (L), J Acoust. Soc. Am. 118 (4) 2121-2123.

Multiple frequency

Korneliussen, R. J., Diner, N., Ona, E., Berger, L., & Fernandes, P. G. (2008). Proposals for the collection of multifrequency acoustic data. ICES Journal of Marine Science: Journal du Conseil, 65(6), 982.

Multiple frequency analysis

dB difference references

Jech, J. M. & Michaels, W. L. (2006). A multifrequency method to classify and evaluate fisheries acoustics data. Canadian Journal of Fisheries and Aquatic Sciences 63, 2225–2235.

Region descriptors

Urmy S.S., Horne J.K., and Barbee D.H. (2012) Measuring the vertical distributional variability of pelagic fauna in Monterey Bay. ICES Journal of Marine Science, 69(2), 184–196.

Sampled water volume estimation, wedge volume

Kieser R. and Mulligan T. J. (1984) Analysis of Echo Counting data: A Model, Canadian Journal of Fisheries and Aquatic Science, 41, 451-458.

School detection module

School Detection module references.

Haralabous J. and Georgakarakos S. (1996) Artificial neural networks as a tool for species identification of fish schools. ICES Journal of Marine Science, 53: 173–180

Scanning sonar school volume

Tang Y., Iida K., Mukai T., Nishimori Y. (2006) Estimation of fish school volume using omnidirectional multi-beam sonar: Scanning modes and algorithms. Japanese Journal of Applied Physics Part 1-Regular Papers Brief Communications & Review Papers 45, 4868-4874.

Single target detection algorithms

Ona E. and Barange M. (1999) Single Target Recognition. ICES Cooperative Research Report, 235: 28-43.

Soule M., Barange M., Solli H. and Hampton I. (1997) Performance of a new phase algorithm for discriminating between single and overlapping echoes in a split-beam echosounder. ICES Journal of Marine Science, 54: 934-938.

Soule, M., Barange, M. and Hampton, I. (1996) Potential improvements to current methods of recognizing single targets with a split-beam echosounder. ICES Journal of Marine Science, 53;237-243.

Soule M., Barange M. and Hampton I. (1995) Evidence of bias in estimates of target strength obtained with a split-beam echosounder. ICES Journal of Marine Science, 52: 139-144.

Balk, Helge & Lindem, Torfinn (2003). A new method for single target detection.

Sound speed

Wong G.S.K. and Zhu S. (1995) Speed of sound in seawater as a function of salinity, temperature and pressure J. Acoust. Soc. Am. 97(3) 1732-1736

Mackenzie K.V. (1981) Nine-term equation for sound speed in the ocean. J. acoust. Soc. Am., 70, 807-12.

Chen C-T. and Millero F.J. (1977) Speed of sound in seawater at high pressures. J. Acoust. Soc. Am. 62(5) 1129-1135.

Medwin, H. (1975) Speed of Sound in Water for Realistic Parameters. J. Acoust. Soc. Am., 58, 1318.

Del Grosso, VA and Mader C.W. (1972) Speed of sound in pure water. J. acoust. Soc. Am., 52, 1442-6.

Leroy C.C. (1969) Development of simple equations for accurate and more realistic calculation of the speed of sound in sea water. J. acoust. Soc. Am., 46, 216-26.

Symbols and definitions

MacLennan, D. N., Fernandes, P. G., and Dalen, J. (2002) A consistent approach to definitions and symbols in fisheries acoustics. ICES Journal of Marine Science, 59: 365–369.

Virtual echograms

Boswell KM, Wilson, M.P. and Cowan J.H. (2008) A Semiautomated Approach to Estimating Fish Size, Abundance, and Behavior from Dual-Frequency Identification Sonar (DIDSON) Data. North American Journal of Fisheries Management. Vol. 28, No. 3, 799–807

Higginbottom I.R., Pauly T.J. and Heatley D.C. (2000) Virtual echograms for visualization and post-processing of multiple-frequency echosounder data. Proceedings of the Fifth European Conference on Underwater Acoustics, ECUA 2000 (Ed. M.E. Zakharia), 1497-1502.

Mitson R.B., Simard Y. and Goss C. (1996) Use of a two-frequency algorithm to determine size and abundance of plankton in three widely spaced locations. ICES Journal of Marine Science, 53: 209-215.

Wideband

Demer D. A., Andersen L. N., Basset C., Berger L., et al (2017) 2016 USA–Norway EK80 Workshop Report: Evaluation of a wideband echosounder for fisheries and marine ecosystem science. ICES Cooperative Research Report No. 336 page 11

Kloser, R.J. and Sutton, C.A. (2020) Orange roughy eastern zone spawning biomass 2019. Report to South East Trawl Industry Association. Copy held at CSIRO Marine and Atmospheric Research, Hobart. CSIRO Report No. EP204430.