Bringing the phenomics of aquatic embryos to key challenges in aquaculture

表型组学是对描述生物体可观察特征的高维数据的获取，可以被认为是21世纪测量表型的技术支持方法。表型组学有可能改变生物学的理解，并使表型组在学术界和工业界都可以应用，但缺乏必要的技术，除了特定的模式物种之外，仍然是实现这一潜力的严重瓶颈。该项目团队开发了两种新的仪器，用于水生物种在胚胎发育期间（生命最活跃的时期）的表型组学，用于实验室（LabEP）和动态（FieldEP）环境。这两种仪器都使用显微镜和自动化来捕捉这段时间内快速的时间、空间和功能变化，并使用计算机视觉来测量高维度的现象组，包括生长、生理性能、行为和团队开创的测量现象组的新方法，作为像素波动内能值的光谱。水产养殖是一个快速增长的部门，具有战略经济和卫生重要性。在该项目期间，我们将与水产养殖部门就技术和业务发展开展合作，促进知识交流，并为该部门的表型学确定关键战略方向，以支持其复原力、可持续性和增长。在与水产养殖项目合作伙伴（国家龙虾孵化场，RSP/LumpFish Dorset和Guernsey SeaFarms）的初始项目会议期间，我们将展示技术，为不同项目合作伙伴建立技术开发和优化仪器硬件和软件配置的战略方向，具体取决于设施要求，解决关键运营挑战，物种，发育阶段和特定的生物学终点感兴趣。软件（包括计算机视觉管道，包括人工智能训练的预测模型）和硬件（包括相机、镜头、照明和电机）将在团队的实验室中进行测试，然后在主要项目合作伙伴的设施中安装仪器，同时对这些合作伙伴的工作人员进行培训，为双方的知识交流提供机会。我们将与合作伙伴合作，协助他们在工作流程的同时测试这些技术。该团队将得到来自科学仪器部门（Indigo scientific）的项目合作伙伴的支持，该合作伙伴将告知组件的采购和团队的业务发展计划。通过随后与水产养殖项目伙伴的会议，该小组将编写一份白皮书，从项目伙伴的经验和反馈中了解这些工具的主要优势和机会。这将分发给项目伙伴、水产养殖网络和特定部门的出版物。在项目结束时，团队将制定业务发展计划，以支持确定和实现战略计划，以最大限度地发挥这些技术在该部门的影响。

Phenomics is the acquisition of high-dimensional data describing an organisms' observable characteristics and can be considered a technology-enabled 21st century approach to measuring the phenotype. Phenomics has the potential to transform biological understanding and to make the phenome accessible to applications within both academia to industry, but a lack of necessary technologies beyond particular model species remains a serious bottleneck to realising this potential. The project team have developed two new instruments for phenomics of aquatic species during embryonic development - the most dynamic period of life, for use in laboratory (LabEP) and dynamic (FieldEP) environments. Both instruments use microscopy and automation to capture this period of rapid temporal, spatial and functional change, and employ computer vision to measure the phenome with high dimensionality, including growth, physiological performance, behaviour and new approaches pioneered by the team for measuring the phenome as spectra of energy values within pixel fluctuations. Aquaculture is a rapidly growing sector and one of strategic economic and health importance. During this project we will work with the aquaculture sector on both technical and business development for knowledge exchange and to establish key strategic directions for phenomics in the sector to support its resilience, sustainability, and growth. During an initial project meeting with aquaculture project partners (National Lobster Hatchery, RSP/LumpFish Dorset and Guernsey SeaFarms) we will showcase the technologies to establish strategic directions for the technical development and optimisation of the hardware and software configuration of the instruments for different project partners, depending on factors including facility requirements, addressing key operational challenges, species, developmental stages and particular biological endpoints of interest. Software (incl. computer vision pipelines including AI-trained predictive models) and hardware (incl. cameras, lenses, lighting and motorisation) will be tested in the team's laboratories prior to installation of the instruments in the facilities of key project partners, accompanied with the training of these partners' staff, providing opportunities for knowledge exchange in both directions. We will work with partners in assisting them to test the technologies alongside their workflows. The team will be supported by a project partner from the scientific instrumentation sector (Indigo Scientific) who will inform the sourcing of components and the team's business development plan.Via subsequent meetings with the aquaculture project partners, the team will write a whitepaper capturing the key strengths and opportunities of the instruments informed from the experiences and feedback of project partners. This will be circulated to both project partners, aquaculture networks and sector-specific publications. A business development plan will be produced by the team towards the conclusion of the project to support the identification and realisation of a strategic plan towards maximising the impact of these technologies within the sector.