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设计一个具有内置图像质量管理功能的植物标本数字化工作流程。

Designing an Herbarium Digitisation Workflow with Built-In Image Quality Management.

作者信息

Nieva de la Hidalga Abraham, Rosin Paul L, Sun Xianfang, Bogaerts Ann, De Meeter Niko, De Smedt Sofie, Strack van Schijndel Maarten, Van Wambeke Paul, Groom Quentin

机构信息

School of Computer Science and Informatics - Cardiff University, Cardiff, United Kingdom School of Computer Science and Informatics - Cardiff University Cardiff United Kingdom.

Meise Botanic Garden, Meise, Belgium Meise Botanic Garden Meise Belgium.

出版信息

Biodivers Data J. 2020 Mar 26;8:e47051. doi: 10.3897/BDJ.8.e47051. eCollection 2020.

Abstract

Digitisation of natural history collections has evolved from creating databases for the recording of specimens' catalogue and label data to include digital images of specimens. This has been driven by several important factors, such as a need to increase global accessibility to specimens and to preserve the original specimens by limiting their manual handling. The size of the collections pointed to the need of high throughput digitisation workflows. However, digital imaging of large numbers of fragile specimens is an expensive and time-consuming process that should be performed only once. To achieve this, the digital images produced need to be useful for the largest set of applications possible and have a potentially unlimited shelf life. The constraints on digitisation speed need to be balanced against the applicability and longevity of the images, which, in turn, depend directly on the quality of those images. As a result, the quality criteria that specimen images need to fulfil influence the design, implementation and execution of digitisation workflows. Different standards and guidelines for producing quality research images from specimens have been proposed; however, their actual adaptation to suit the needs of different types of specimens requires further analysis. This paper presents the digitisation workflow implemented by Meise Botanic Garden (MBG). This workflow is relevant because of its modular design, its strong focus on image quality assessment, its flexibility that allows combining in-house and outsourced digitisation, processing, preservation and publishing facilities and its capacity to evolve for integrating alternative components from different sources. The design and operation of the digitisation workflow is provided to showcase how it was derived, with particular attention to the built-in audit trail within the workflow, which ensures the scalable production of high-quality specimen images and how this audit trail ensures that new modules do not affect either the speed of imaging or the quality of the images produced.

摘要

自然历史馆藏的数字化已从创建用于记录标本目录和标签数据的数据库发展到纳入标本的数字图像。这一发展受到了几个重要因素的推动,比如需要提高全球对标本的可获取性,以及通过限制人工处理来保护原始标本。馆藏的规模表明需要高通量的数字化工作流程。然而,对大量易碎标本进行数字成像既昂贵又耗时,而且应该只进行一次。为实现这一点,所生成的数字图像需要对尽可能多的应用有用,并且具有潜在无限的保存期限。数字化速度的限制需要与图像的适用性和寿命相平衡,而这又直接取决于这些图像的质量。因此,标本图像需要满足的质量标准会影响数字化工作流程的设计、实施和执行。已经提出了不同的标准和指南来从标本中生成高质量的研究图像;然而,它们实际适应不同类型标本需求的情况还需要进一步分析。本文介绍了梅斯植物园(MBG)实施的数字化工作流程。这个工作流程具有相关性,因为它采用模块化设计,高度注重图像质量评估,具有灵活性,允许结合内部和外包的数字化、处理、保存和发布设施,并且有能力不断发展以整合来自不同来源的替代组件。文中提供了数字化工作流程的设计和操作,以展示其推导过程,特别关注工作流程中内置的审计跟踪,它确保了高质量标本图像的可扩展生产,以及这个审计跟踪如何确保新模块不会影响成像速度或所生成图像的质量。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6756/7125238/2fc68567f939/bdj-08-e47051-g001.jpg

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