Collaborative Research: CoralReef3D - An open-source toolkit for underwater 3D ecosystem modeling and analysis

珊瑚礁是地球上最多样化的生态系统之一，拥有至少30%的海洋物种。它们每年在全球产生近10万亿美元的收入，为超过5%的人类提供蛋白质和收入。不幸的是，由于气候变化和当地的压力，大多数珊瑚礁都在严重衰退。然而，有些珊瑚礁似乎比其他珊瑚礁更有弹性。 我们需要迅速找到并识别这些珊瑚礁，以阐明赋予这种恢复力的因素。 从历史上看，定位和展示复原力所需的各种调查一直是缓慢的，昂贵的，并依赖于训练有素的科学家。这些传统的方法太慢，太繁琐，无法为我们21世纪的挑战提供21世纪的解决方案。在该项目中，先进的3D计算机视觉和摄影测量技术将被组装成一个名为CoralReef 3D的新型计算工具集，该工具集将提供给世界各地的潜水员和海岸测量员。 这个共享软件将允许非专家创建地理参考（因此可重复）3D珊瑚礁蒙太奇，可以很容易地评估珊瑚生长和生存的基准研究。 这项研究的影响将通过开源软件、在线研讨会、学生培训以及涉及博物馆和公众的外联活动来扩大。CoralReef 3D预计将在水下3D测量方面取得重大进展。在这项研究中，新的水折射校正方法将被开发并纳入CoralReef 3D。在相机/水界面的水折射失真的校正将允许生产的海景蒙太奇的准确测量。 例如，该程序的先进的目标识别和语义分割功能将允许它生成线性或体积测量的图像尺度。 这也将有助于精确计算被调查地区的生态系统粗糙度（拓扑复杂性）和地貌。 通过在所有图像上提供GPS信息，CoralReef 3D可以追踪单个殖民地的命运，并量化生态系统随时间的变化。 将进行受控实验室验证和现场验证。 受控实验室确认将在Reef Systems Coral Farm维护的深海水箱中进行。 将在夏威夷和佛罗里达群岛沿着深度梯度进行现场验证。为了缩短通常与复杂图像分析程序相关的学习曲线，CoralReef 3D将使用文本和图片说明进行广泛记录。这些技术进步将为水中复杂物体的3D建模提供基准方法。CoralReef 3D将使专家和非专家能够对快速变化的海洋生态系统进行负担得起的，大规模的和准确的评估。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。

Coral reefs are one of the most diverse ecosystems on Earth, hosting at least 30% of all marine species. They generate almost $10 trillion USD per year globally and provide protein and income for more than 5% of humanity. Unfortunately, most coral reefs are in severe decline due to the climate change and local stressors. Some reefs, however, appear to be more resilient than others. We need to find and identify these reefs quickly to elucidate the factors that confer this resilience. Historically, the kinds of surveys required to locate and demonstrate resilience have been slow, expensive, and reliant on highly trained scientists. These traditional methods are too slow and too cumbersome to provide 21st Century solutions for our 21st Century challenges. In this project, advanced 3D computer vision and photogrammetric techniques will be assembled into a novel computational toolset called CoralReef3D, which will be made available to divers and coastal surveyors all over the world. This shareware will allow non-experts to create georeferenced (and therefore repeatable) 3D reef montages that can easily be assessed for benchmark studies on coral growth and survival. The impact of this research will be broadened by open-source software, online workshops, student training, and outreach activities involving museums and the general public.CoralReef3D is expected to bring forth significant advancements in underwater 3D measurements. During this research, novel water-refraction correction methods will be developed and incorporated into CoralReef3D. Correction for water-refraction distortions at the camera/water interface will allow production of accurate measurements of seascape montages. For instance, the program’s advanced capabilities for object-recognition and semantic-segmentation will allow it to generate on-image scales for linear or volumetric measurements. This will also enable precise calculations of ecosystem rugosity (topological complexity) and geomorphology in surveyed areas. By providing GPS information on all images, CoralReef3D can fate-track individual colonies and quantify ecosystem changes over time. Both controlled laboratory validation and in situ field validation will be conducted. Controlled laboratory validations will be performed in deep seawater tanks maintained by Reef Systems Coral Farm. In situ field validations will be performed in Hawaii and the Florida Keys along depth gradients. To shorten the learning curve normally associated with sophisticated image analysis programs, CoralReef3D will be extensively documented using both text and pictorial instructions. These technological advances will produce a benchmark method for 3D modeling of complex objects in water. CoralReef3D will empower both experts and non-specialists to make affordable, large-scale, and accurate assessments of rapidly-changing marine ecosystems.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.