Advanced imaging system for accelerating and automating arthropod bio-surveillance

点击翻译按钮获取中文摘要

One of the most pressing challenges in today's biodiversity science is the need to gather quantitative data on organismal diversity and abundance over space and time. This information is essential to understand how species community assemble and change as well as to support monitoring programs that assess how biodiversity responds to natural and anthropogenic disturbance. Two methodological and technological advances over the past decade have made it possible to satisfy this urgent need for comprehensive biomonitoring. Firstly, identification systems based on the analysis of sequence variation in short, standardized gene regions (i.e. DNA barcodes) are very effective in species discrimination. Secondly, high-throughput sequencers permit the inexpensive acquisition of millions of DNA sequence records. These developments are enabling biodiversity surveys at speeds and scales that were previously inconceivable. This application seeks support to acquire a digital microscopy system for integration into current workflows to advance the production of DNA barcode records. Recent technological developments have increased automation of most steps in the barcode workflow from initial data entry to contextualization of results. The greatest remaining bottleneck to further increases in production derive from the current need for skilled technicians to enter each specimen record and associated collateral data including digital image information. The new system will make it possible to gather high resolution, in-focus digital images of every specimen and it will generate files that are ideally suited for the development of machine learning approaches that will employ pattern recognition algorithms to automate a high-level taxonomic assignment (order, family) for each specimen.Such an automated pipeline that will transform specimen-loaded plates into specimen records complete with their associated image and taxonomic assignment. The impact on research programs and on biodiversity science will be dramatic.