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

识别花粉的实践具有大量的科学应用，并被用于考古学、生物地层学(岩石测年)和法医科学等领域。花粉和孢子在古生物学中扮演着特别重要的角色，因为它们构成了最丰富和最广泛的植物多样性记录，可以追溯到数亿年前。然而，由于很难从花粉和孢子物质中识别物种，植物生态学和进化中最关键的假说(如植物群落的组装、物种形成和灭绝)不能用花粉数据完全检验。该项目开发了新的方法，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索颗粒的形状和精细的结构和纹理特性，以便将物种鉴定从主观的、附带的程序转变为定量的计算实践。由于尚不知道哪些形态特征具有系统发育意义，人们正在开发新的机器学习技术来在多个尺度上对花粉图像进行建模，识别具有统计信息的形状和纹理方面，并推断它们与潜在的系统发育结构的关系。该项目有一个雄心勃勃的长期目标，即创建一个高通量的花粉数据分析系统，该系统包含对花粉和孢子形态的有意义的描述，提供可验证的生物亲和力假设，并对整个科学界开放和可用。这将使研究人员突破目前花粉鉴定的分类限制，并从多个层面上从根本上改变该学科目前的做法，从鉴定和计数的基本任务，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样化的跨学科团队，包括巴拿马史密森热带研究所的国际合作者，并将在一个新兴的跨学科研究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，其中将包括一个虚拟显微镜网站，使用这项研究产生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