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R&D partnership to count salmon lice for breeding purposes

Wednesday, May 18, 2022

The Danish Technological Institute (DTI) and Benchmark Genetics Norway AS have entered an R&D collaboration that involves using artificial intelligence (AI) to count sea lice to improve the accuracy of selecting resistant fish for breeding purposes.

To assess the degree of resistance of Atlantic salmon to sea lice, the breeding companies count the number of parasites on each fish following a period of infection. This is a laborious and time-consuming process involving many people needed to count the lice manually. However, this process can now change, thanks to an R&D collaboration between the Danish Technological Institute (DTI) and Benchmark Genetics Norway. By taking photos of each fish and using artificial intelligence (AI) to analyze images in real-time, the work obtained an accurate number of lice infections per animal.

The imaging technology uses a combination of a half-circular light-dome (CSS dome light HPD2-400FC) and a 5-megapixel monochrome camera to take an image of each salmon. The high-power light dome has three individual triggered color diodes: red (622 nm), green (525 nm) and blue (470 nm). The mono-camera takes one picture at each wavelength, and then images are post-processed using the developed AI. It was found that this imaging system provides the user with the best visibility and contrast between the lice and the fish. The algorithm uses a deep learning segmentation model based on a multiple convolutional network architecture U-net image model, initially developed for biomedical image segmentation.

The AI model is trained to segment the sea lice and salmon. After the image segmentation, the sea lice are filtered and counted. By repeating this process many times and automatically augmenting the image appearance in various ways, the model learns the shape and becomes robust against varying fish and lice sizes, image angles, illumination variations, etc. The training dataset is created by manually marking pixels with lice in the image. The model can then compare its results against the training dataset and gets trained. The bigger the training dataset, the more accurate the algorithm can detect lice. The model’s performance improvement is verified by keeping a subset of the annotated data for model validation.

With the new technology implemented, Benchmark expects to gain a higher quality of the phenotypic datasets and improve the precision in selecting the best breeding candidates for resistance to sea lice.

 

Photo caption: Hooman Moghadam, Senior Research Scientist, Benchmark Genetics Norway AS.

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