Deep focus-extended darkfield imaging for in situ observation of marine plankton

Darkfield imaging can achieve in situ observation of marine plankton with unique advantages of high-resolution, high-contrast and colorful imaging for plankton species identification, size measurement and abundance estimation. However, existing underwater darkfield imagers have very shallow depth-of-field, leading to inefficient seawater sampling for plankton observation. We develop a data-driven method that can algorithmically refocus planktonic objects in their defocused darkfield images, equivalently achieving focus-extension for their acquisition imagers. We devise a set of dual-channel imaging apparatus to quickly capture paired images of live plankton with different defocus degrees in seawater samples, simulating the settings as in in situ darkfield plankton imaging. Through a series of registration and preprocessing operations on the raw image pairs, a dataset consisting of 55 000 pairs of defocused-focused plankter images have been constructed with an accurate defocus distance label for each defocused image. We use the dataset to train an end-to-end deep convolution neural network named IsPlanktonFE, and testify its focus-extension performance through extensive experiments. The experimental results show that IsPlanktonFE has extended the depth-of-field of a 0.5× darkfield imaging system to ~7 times of its original value. Moreover, the model has exhibited good content and instrument generalizability, and considerable accuracy improvement for a pre-trained ResNet-18 network to classify defocused plankton images. This focus-extension technology is expected to greatly enhance the sampling throughput and efficiency for the future in situ marine plankton observation systems, and promote the wide applications of darkfield plankton imaging instruments in marine ecology research and aquatic environment monitoring programs.