New case study: advancing early warning systems for harmful plankton in Scottish aquaculture
Harmful plankton events - such as harmful algal blooms (HABs), microjellyfish and hydrozoans - pose a growing threat to salmon farming in Scotland. These organisms can damage the fills of fish, and their frequency is increasing due to changing environmental conditions. Early, accurate detection is crucial for effective mitigation.
Led by Scottish Sea Farms with partners Scottish Association for Marine Science (SAMS), UHI Shetland, University of Aberdeen, Mowi, and Bakkafrost, this project set out to strengthen Scotland’s early warning capabilities through integrated monitoring and forecasting tools. Building on previous SAICfunded work, the project combined cuttingedge imaging technologies, realtime environmental monitoring, and enhanced modelling systems. The total value of the project was £716k.
At the heart of the project was the deployment of an Imaging FlowCytobot (IFCB) at a farm in Shetland - the world’s only longterm, 24/7 automated plankton monitoring system operating at a finfish site. Over the project, it captured more than 78 million images, supported by environmental data streamed in real time. Machinelearning models were refined to improve plankton identification and quantification, strengthening the system’s value to farm managers.
To monitor conditions throughout the water column, the team developed a bespoke automated profiling system, enabling repeated sampling at multiple depths. Although some manufacturerrelated faults affected continuous profiling, the system worked effectively when operational and can be fully refined for future deployments.
The project also advanced Scotland’s forecasting capability. Hydrodynamic models (WeStCOMS v3 and NORWESTCOMS) were upgraded to improve coastal current and temperature predictions, supporting bloomtransport forecasting. Statistical ensemble models - successful in shellfish aquaculture - were adapted for salmon farming datasets, showing promising results for some harmful species.
Finally, the team successfully developed and deployed a subsea holographic imaging system capable of detecting harmful microjellyfish, providing a breakthrough in automated monitoring of organisms beyond the IFCB’s size range.
Together, these innovations significantly enhance Scotland’s ability to anticipate harmful plankton events - supporting fish health, farm management, and environmental resilience across the sector.
The full name of this project is ‘Advanced early warning systems for harmful plankton in Scottish aquaculture’.
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