Collaborative Research: ABI Innovation: Breaking through the taxonomic barrier of the fossil pollen record using bioimage informatics

花粉鉴定的实践具有大量的科学应用，并应用于考古学、生物地层学（岩石年代测定）和法医学等多个领域。花粉和孢子在古生物学中发挥着特别重要的作用，因为它们形成了最丰富、最广泛的植物多样性记录，其历史可以追溯到数亿年前。然而，由于从花粉和孢子材料中识别物种极其困难，植物生态学和进化中最关键的假设（例如植物群落的组装、物种形成和灭绝）无法用花粉数据进行充分检验。该项目开发了新方法，使用高通量、超分辨率结构照明显微镜和自动图像分析来探测谷物的形状、精细结构和质地特性，以便将物种识别从主观的肉眼程序转变为定量的计算实践。由于事先不知道哪些形态特征在系统发育上有意义，因此正在开发新的机器学习技术来对多个尺度的花粉图像进行建模，识别具有统计信息的形状和纹理方面，并推断它们与潜在系统发育结构的关系。该项目有一个雄心勃勃的长期目标，即创建一个用于分析花粉数据的高通量系统，该系统结合了花粉和孢子形态的有意义的特征，提供了可测试的生物亲和力假设，并向整个科学界开放和可用。这将使研究人员能够突破当前花粉识别的分类学限制，并从根本上改变该学科在许多层面上的当前实践，从识别和计数的基本任务到在全球气候植被模型中解释和使用这些数据。该项目汇集了一个多元化的跨学科团队，其中包括巴拿马史密森尼热带研究所的国际合作者，并将在跨学科研究的新兴领域培训来自多个科学学科和背景的研究生和本科生。一个公共推广部分正在开发中，其中包括一个虚拟显微镜网站，该网站使用本研究生成的图像向非专家介绍花粉形态的美丽、复杂性和相关性。有关该项目的更多信息，请访问：http://www.life.illinois.edu/punyasena

The practice of identifying pollen has a large number of scientific applications and is used in fields as diverse as archaeology, biostratigraphy (the dating of rocks), and forensic science. Pollen and spores play a particularly important role in paleontology, because they form the most abundant and extensive record of plant diversity, dating back hundreds of millions of years. However, the most critical hypotheses in plant ecology and evolution (e.g. the assembly of plant communities, speciation and extinction) cannot be fully tested with pollen data due to the extreme difficulty of recognizing species from pollen and spore material. This project develops new methods to probe the shape and fine structural and textural properties of the grains using high-throughput, super-resolution structured illumination microscopy and automated image analysis in order to transform species identification from a subjective, by-eye procedure to a quantitative, computational practice. Since it is not known a priori which morphological features are phylogenetically meaningful, new machine learning techniques are being developed to model pollen images at multiple scales, identify aspects of shape and texture that are statistically informative, and infer their relation to the underlying phylogenetic structure. The project has the ambitious long-term goal of creating a high-throughput system for analyzing pollen data that incorporates meaningful characterizations of pollen and spore morphology, provides testable hypotheses of biological affinity, and is open and available to the entire scientific community. This will allow researchers to break through the current taxonomic limitations of pollen identification and fundamentally change current practices in the discipline on many levels, from the basic task of identification and counting to the interpretation and use of these data in global climate-vegetation models. The project brings together a diverse, interdisciplinary team including international collaborators at the Smithsonian Tropical Research Institute in Panama and will train graduate and undergraduate students from multiple scientific disciplines and backgrounds in an emerging area of interdisciplinary research. A public outreach component is in development that will include a virtual microscopy web site using images generated by this research to introduce non-experts to the beauty, complexity, and relevance of pollen morphology. Additional information about this project can be found at: http://www.life.illinois.edu/punyasena