mvh: An R tool to assemble and organize virtual herbaria from openly available specimen images

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences Pub Date : 2025-01-26 DOI:10.1002/aps3.11631

Thais Vasconcelos, James D. Boyko

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引用次数: 0

Abstract

Premise

Recent advances in imaging herbarium specimens have enhanced their use in biodiversity studies. However, user-friendly tools that facilitate the assembly of customized sets of herbarium specimen images on personal devices are still lacking.

Methods and Results

Here we present the R package mvh (“my virtual herbarium”), which includes functions designed to search and download metadata and openly available images associated with herbarium specimens based on taxon or geography. We tested the functionalities of mvh by searching metadata associated with five sets of 10 vascular plant species and five sets of 10 terrestrial coordinates. The download function had a success rate of 99%, downloading 291 out of the 293 images found in the search. Possible reasons for download failure are discussed.

Conclusions

As long as an internet connection is available, mvh simplifies the assembly and organization of virtual herbaria, thereby facilitating the investigation of novel empirical questions as well as trends in digitization efforts.

Abstract Image

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mvh：一个R工具，用于从公开可用的标本图像中组装和组织虚拟植物标本库

植物标本馆标本成像技术的最新进展，增强了其在生物多样性研究中的应用。然而，便于在个人设备上组装定制的植物标本室标本图像集的用户友好工具仍然缺乏。方法和结果本文介绍了R包mvh（“我的虚拟植物标本馆”），它包括基于分类群或地理位置搜索和下载与植物标本馆标本相关的元数据和公开可用图像的功能。我们通过搜索与5组10种维管植物物种和5组10种陆地坐标相关的元数据来测试mvh的功能。下载功能的成功率为99%，下载了293张图片中的291张。讨论了下载失败的可能原因。只要有互联网连接，mvh就简化了虚拟植物标本馆的组装和组织，从而促进了对新的实证问题的研究以及数字化工作的趋势。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Applications in Plant Sciences PLANT SCIENCES-

CiteScore

7.30

自引率

0.00%

发文量

审稿时长

12 weeks

期刊介绍： Applications in Plant Sciences (APPS) is a monthly, peer-reviewed, open access journal promoting the rapid dissemination of newly developed, innovative tools and protocols in all areas of the plant sciences, including genetics, structure, function, development, evolution, systematics, and ecology. Given the rapid progress today in technology and its application in the plant sciences, the goal of APPS is to foster communication within the plant science community to advance scientific research. APPS is a publication of the Botanical Society of America, originating in 2009 as the American Journal of Botany''s online-only section, AJB Primer Notes & Protocols in the Plant Sciences. APPS publishes the following types of articles: (1) Protocol Notes describe new methods and technological advancements; (2) Genomic Resources Articles characterize the development and demonstrate the usefulness of newly developed genomic resources, including transcriptomes; (3) Software Notes detail new software applications; (4) Application Articles illustrate the application of a new protocol, method, or software application within the context of a larger study; (5) Review Articles evaluate available techniques, methods, or protocols; (6) Primer Notes report novel genetic markers with evidence of wide applicability.