DiversityScanner 4K: A High Resolution Extended Focus Camera Setup as Extension for the DiversityScanner

Manual examination of invertebrate species diversity and abundance in Malaise trap samples is a time-consuming and costly task that requires expert knowledge. Automated solutions based on robotics and artificial intelligence can assist experts in evaluating the large number of samples collected, especially when the phenotype of individual species in a sample needs to be assessed and classified. Therefore, we have developed the DiversityScanner, a robotic solution that provides the ability to automatically image, measure, classify, and sort invertebrates (< 3 mm) into 96-well microplates for barcoding. Because it is necessary to document even the smallest details, such as tiny bristles, on a specimen, we have significantly improved the image quality of the detailed images in the DiversityScanner 4k. This is achieved by using an extended focus system and a 12-megapixel camera. By using an electrically focus tunable lens from Optotune, extended focus images can be created from multiple z-stack images with different focus planes. An algorithm then automatically aligns the images, detecting sharp areas in each image, and produces high-resolution extended-focus images. Finally, the object can be classified by a convolutional neural network and the biomass of the insect can be estimated from the image