CoFFee

Matlab toolbox for multibeam sonar data processing.

Description

CoFFee is a free and open-source MATLAB toolbox (i.e., a libary of functions) for reading multibeam sonar raw data files, visualizing their contents, and applying various processsing algorithms. It serves as the engine for several apps/GUIs designed for specific applications.

Disclaimer

CoFFee is the (messy) repository of functions written and edited over the authors' career, which started before they used git. As a result, many functions are obsolete, or don't work with newer functions, or even work at all. This is why this toolbox is noted as in pre-release and will remain so until the authors can clean it all up. Expect headaches if you try to use the less commonly-used functions!

Getting Started

Dependencies

• MATLAB. We are currently using R2020b, but it may work on other versions.
• Some MATLAB toolboxes (not all functions require them):
  • Mapping Toolbox
  • Parallel Computing Toolbox
  • Signal Processing Toolbox
  • Statistics and Machine Learning Toolbox

Installing and using

• Clone or download the repository.
• Add the toolbox's folder and subfolders to the Matlab's path by adding the following lines at the top of your scripts:

coffeeFolder = 'C:\my\path\to\CoFFee';
addpath(genpath(coffeeFolder));

Help

Head over to the wiki for documentation (in progress).

If you have any issues, please first check the project's issues section to search for a fix. Otherwise, let the authors know by creating a new issue.

For more information, contact the authors.

Past versions and updates

See the releases page for past released versions.

If you want to receive notifications of future releases (recommended), you may create a github account, and on this repository click on 'Watch', then 'Custom', and choose 'Releases'. Verify in your GitHub settings that you are set to receive 'Watching' notifications.

About

Authors and contributors

• Alexandre Schimel (alex.schimel@proton.me)
• Yoann Ladroit (Kongsberg Discovery)
• Amy Nau (CSIRO)
• Shyam Chand (The Geological Survey of Norway)

Copyright

2007-2025

• Alexandre Schimel

License

CoFFee is distributed under the MIT License. See LICENSE file for details.

CoFFee uses several pieces of third-party code, each being distributed under its own license. Each piece of code is contained in a separate sub-folder of the 'toolboxes' folder and includes the corresponding license file.

Support This Project 💖

If you use CoFFee in your research, teaching, or professional work, please consider supporting its development. Your support helps cover development time, MATLAB license costs, and ensures continued availability of free, open-source tools for multibeam sonar data analysis.

For monthly support, consider sponsoring on GitHub. For one-time donations, you can use PayPal.

See Also

Apps based on CoFFee

• Espresso: Multibeam water-column data visualization and processing
• Iskaffe: Multibeam backscatter quality control
• Grounds: Elevation Change Analysis

References

Articles using or about CoFFee, or apps based on CoFFee:

• Zainal, M. Z., Che Hasan, R., Abu Husain, M. K., Schimel, A. C. G., Mohd Zaki, N. A., & Zakariya, R. (2026). Improving the mapping of coral reefs with multibeam echosounder water column data. Estuarine, Coastal and Shelf Science, 332, 109744. https://doi.org/10.1016/j.ecss.2026.109744
• Berry, J., & Nanlal, C. (2025). Assessment of the application of each multibeam echosounder data product for monitoring of Laminaria digitata in the UK. Frontiers in Remote Sensing, 6. https://doi.org/10.3389/frsen.2025.1521958
• Nau, A. W., Lucieer, V., Schimel, A. C. G., Kunnath, H., Ladroit, Y., & Martin, T. (2025). Advanced Detection and Classification of Kelp Habitats Using Multibeam Echosounder Water Column Point Cloud Data. Remote Sensing, 17(3), 449. https://doi.org/10.3390/rs17030449
• Bäcklin, V. (2025). Identification of gas seeps associated with fracture zones in the southwestern Baltic Sea using open-source software. Bachelor Thesis, Stockholm University.
• Bai, Q., Amiri-Simkooei, A., Mestdagh, S., Simons, D. G., & Snellen, M. (2024). Mussel culture monitoring with semi-supervised machine learning on multibeam echosounder data using label spreading. Journal of Environmental Management, 369, 122250. https://doi.org/10.1016/j.jenvman.2024.122250
• Schimel, A., Ladroit, Y., & Watson, S. (2024b). Espresso: An Open-Source Software Tool for Visualizing and Analysing Multibeam Water-Column Data. EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-11043. https://doi.org/10.5194/egusphere-egu24-11043. Download the poster
• Schimel, A. C. G., Ladroit, Y., & Watson, S. (2024). Espresso: Open source software for the visualization of multibeam water column data. HYDRO International, 28(3), 22–25. Link to online version of article
• Lucieer, V., Flukes, E., Keane, J. P., Ling, S. D., Nau, A. W., & Shelamoff, V. (2023). Mapping warming reefs — An application of multibeam acoustic water column analysis to define threatened abalone habitat. Frontiers in Remote Sensing, 4(April), 1–15. https://doi.org/10.3389/frsen.2023.1149900
• Turco, F., Ladroit, Y., Watson, S. J., Seabrook, S., Law, C. S., Crutchley, G. J., Mountjoy, J., Pecher, I. A., Hillman, J. I. T., Woelz, S., & Gorman, A. R. (2022). Estimates of Methane Release From Gas Seeps at the Southern Hikurangi Margin, New Zealand. Frontiers in Earth Science, 10(March), 1–20. https://doi.org/10.3389/feart.2022.834047
• Porskamp, P., Schimel, A. C. G., Young, M., Rattray, A., Ladroit, Y., & Ierodiaconou, D. (2022). Integrating multibeam echosounder water‐column data into benthic habitat mapping. Limnology and Oceanography, 67(8), 1701–1713. https://doi.org/10.1002/lno.12160
• Nau, A. W., Scoulding, B., Kloser, R. J., Ladroit, Y., & Lucieer, V. (2022). Extended Detection of Shallow Water Gas Seeps From Multibeam Echosounder Water Column Data. Frontiers in Remote Sensing, 3(July), 1–18. https://doi.org/10.3389/frsen.2022.839417
• Schimel, A. C. G., Brown, C. J., & Ierodiaconou, D. (2020). Automated Filtering of Multibeam Water-Column Data to Detect Relative Abundance of Giant Kelp (Macrocystis pyrifera). Remote Sensing, 12(9), 1371. https://doi.org/10.3390/rs12091371
• Mountjoy, J. J., Howarth, J. D., Orpin, A. R., Barnes, P. M., Bowden, D. A., Rowden, A. A., Schimel, A. C. G., Holden, C., Horgan, H. J., Nodder, S. D., Patton, J. R., Lamarche, G., Gerstenberger, M., Micallef, A., Pallentin, A., & Kane, T. (2018). Earthquakes drive large-scale submarine canyon development and sediment supply to deep-ocean basins. Science Advances, 4(3). https://doi.org/10.1126/sciadv.aar3748
• Nau, A. W., Lucieer, V. L., & Alexandre Schimel, C. G. (2018). Modeling the along-track sidelobe interference artifact in multibeam sonar water-column data. OCEANS 2018 MTS/IEEE Charleston, 1–5. https://doi.org/10.1109/OCEANS.2018.8604866
• Schimel, A. C. G., Ierodiaconou, D., Hulands, L., & Kennedy, D. M. (2015). Accounting for uncertainty in volumes of seabed change measured with repeat multibeam sonar surveys. Continental Shelf Research, 111, 52–68. https://doi.org/10.1016/j.csr.2015.10.019
• Schimel, A. C. G., Healy, T. R., McComb, P., & Immenga, D. (2010). Comparison of a self-processed EM3000 multibeam echosounder dataset with a QTC view habitat mapping and a sidescan sonar imagery, Tamaki Strait, New Zealand. Journal of Coastal Research, 26(4). https://doi.org/10.2112/08-1132.1

For developers

Please maintain the CoFFee coding philosophy, which is that any core functionality (raw file reading, conversion, data processing, etc.) is coded as CoFFee functions, so that only user-interaction functionalities (display, user interface, callbacks, etc.) are coded in apps. This allows reusing core functionalities across apps. Therefore, the development of an app requires the joint development of CoFFee, and since there are multiple apps built on CoFFee, careful version-controlling and dependency-management is necessary to avoid breaking compatibility.

We use Semantic Versioning to attribute version numbers:

• The version of CoFFee is hard-coded in function CFF_coffee_version.m.
• The version of an app is (usually) a static property of the app (Version), alongside the CoFFee version it was built on (CoffeeVersion).

A careful sequence to develop an app is t