From gigapixel time-lapse and UAVs to food security and adaptive conservation: software and hardware requirements for enabling NextGen ecology and phenomics

NextGen ecology and genomics will require much greater collaboration between biologists computer scientists and hardware engineers. Many solved problems in computer science and image analysis are still viewed as great challenges in plant sciences and ecology. Likewise, many emerging hardware technologies show great promise for improving ecology but are still technically complex to implement and so remain of limited use to biologists. I will discuss the hardware and software challenges for developing both high throughput plant imaging systems and NextGen landscape monitoring systems for field applications. In the lab we are developing a high throughput software/hardware pipeline for quantifying growth in up 2000 plants in climate chambers with multi-spectral LED lighting and dynamic environmental conditions. Any aspect of plant growth that can be quantified from time-lapse imagery can be tested for genetic association in our custom Genome Wide Association (GWAS) bioinformatics pipeline. In our field work we are seeking to extend standard environmental monitoring by orders of magnitude through gigapixel imaging systems, microclimate mesh sensor networks, UAVs and other emerging technologies. Enabling these efforts requires combining complex hardware and custom software into user-friendly turn-key systems.