A high-throughput and open-source platform for embryo phenomics

Abstract

Phenomics has the potential to facilitate significant advances in biology but requires the development of high-throughput technologies capable of generating and analysing high-dimensional data. There are significant challenges associated with building such technologies, not least those required for investigating dynamic processes such as embryonic development, during which high rates of temporal, spatial, and functional change are inherently difficult to capture. Here, we present EmbryoPhenomics, an accessible high-throughput platform for phenomics in aquatic embryos comprising an Open-source Video Microscope (OpenVIM) that produces high-resolution videos of multiple embryos under tightly controlled environmental conditions. These videos are then analysed by the Python package Embryo Computer Vision (EmbryoCV), which extracts phenomic data for morphological, physiological, behavioural, and proxy traits during the process of embryonic development. We demonstrate the broad-scale applicability of EmbryoPhenomics in a series of experiments assessing chronic, acute, and multistressor responses to environmental change (temperature and salinity) in >30 million images of >600 embryos of two species with markedly different patterns of development—the pond snail Radix balthica and the marine amphipod Orchestia gammarellus. The challenge of phenomics is significant but so too are the rewards, and it is particularly relevant to the urgent task of assessing complex organismal responses to current rates of environmental change. EmbryoPhenomics can acquire and process data capturing functional, temporal, and spatial responses in the earliest, most dynamic life stages and is potentially game changing for those interested in studying development and phenomics more widely.

Spectral phenotyping of embryonic development reveals integrative thermodynamic responses

“…Technology-enabled high-dimensional-organismal-phenotyping (HDOP) provides efficient measurement of phenotypic traits traditionally used in biology, and can also extend the study of the phenotype via proxy traits—measures with no direct traditional equivalent [ 1 – 5 ]. A new approach to measuring the phenotype is the use of energy proxy traits (EPTs), the amount of energy within different temporal frequencies in the pixel value fluctuations from video of live biological material.…”

“…A new approach to measuring the phenotype is the use of energy proxy traits (EPTs), the amount of energy within different temporal frequencies in the pixel value fluctuations from video of live biological material. Analysis of fluctuations in video pixel values has previously been used to measure cardiac activity in humans [ 6 ], model species [ 7 , 8 ] and aquatic invertebrate embryos [ 5 ]. While EPTs also have pixel value fluctuations as their basis, they are a holistic approach to measuring complex biological responses not limited by preconceived notions of the phenotype and the traits used to quantify it.…”

“…Rather, they are temporal frequency spectra, capturing fluctuations in mean pixel values, a simple image summary statistic, arising from any biological source visible in video. EPTs have proven an effective approach to the study of aquatic embryos, including incorporation of the ontogeny of heart function, muscle movement, rotation and net movement of the embryo within EPT datasets [ 5 ]. The application of spectral frequency analysis has been demonstrated to be an effective method for interrogating complex biological responses in applications including movement ecology [ 9 ] and movement analysis of numerous species of aquatic embryos [ 10 , 11 ].…”

“…Targeted analyses within EPT datasets have proven effective at extracting and quantifying signals from specific ‘traditional’ components of an embryo’s developmental physiology, including lethal end points, and heart rate in aquatic invertebrates with very different heart architectures (i.e. molluscs and amphipods [ 5 ]). Indeed, aquatic embryos and larvae are emerging as scalable models for the use of HDOP, with technologies and methodologies increasingly becoming available [ 2 , 5 , 12 ].…”

“…molluscs and amphipods [ 5 ]). Indeed, aquatic embryos and larvae are emerging as scalable models for the use of HDOP, with technologies and methodologies increasingly becoming available [ 2 , 5 , 12 ]. Early use of EPTs in aquatic embryos has found that they are sensitive to different environmental conditions [ 5 ], but their mechanistic underpinning and biological relevance remains unclear.…”