Large–scale digitization of herbarium specimens: Development and usage of an automated, high–throughput conveyor system

Abstract

The billions of specimens housed in natural science collections provide a tremendous source of under–utilized data that are useful for scientific research, conservation, commerce, and education. Digitization and mobilization of specimen data and images promises to greatly accelerate their utilization. While digitization of natural science collection specimens has been occurring for decades, the vast majority of specimens remain un–digitized. If the digitization task is to be completed in the near future, innovative, high–throughput approaches are needed. To create a dataset for the study of global change in New England, we designed and implemented an industrial–scale, conveyor–based digitization workflow for herbarium specimen sheets. The workflow is a variation of an object–to–image–to–data workflow that prioritizes imaging and the capture of storage container–level data. The workflow utilizes a novel conveyor system developed specifically for the task of imaging flattened herbarium specimens. Using our workflow, we imaged and transcribed specimen–level data for almost 350,000 specimens over a 131–week period; an additional 56 weeks was required for storage container–level data capture. Our project has demonstrated that it is possible to capture both an image of a specimen and a core database record in 35 seconds per herbarium sheet (for intervals between images of 30 minutes or less) plus some additional overhead for container–level data capture. This rate was in line with the pre–project expectations for our approach. Our throughput rates are comparable with some other similar, high–throughput approaches focused on digitizing herbarium sheets and is as much as three times faster than rates achieved with more conventional non–automated approaches used during the project. We report on challenges encountered during development and use of our system and discuss ways in which our workflow could be improved. The conveyor apparatus software, database schema, configuration files, hardware list, and conveyor schematics are available for download on GitHub.

Advances in the systematics and evolution of western Mediterranean representative species of the Pentanema conyzae clade through genetic fingerprinting

“…) showed that the genetic variation of the samples is organized into seven groups, which correspond to traditionally well‐established species. These species were recovered as being monophyletic according to the AFLP data treated with phenetic reconstruction methods, which is consistent with findings by Gutiérrez‐Larruscain et al () based on phylogenetic reconstructions using DNA sequence data.…”

“…et al The species P. aschersonianum and P. verbascifolium belong to a complex of species distributed in the Balkan Peninsula and Anatolia, and are characterized by a lanate indument that gives them an ashen appearance. In the reconstruction presented in Gutiérrez‐Larruscain et al (), this species was recovered in a basal position within the Pentanema montanum clade as a sister group to the rest of the species included within this clade, which are characterized as being endemic to the western Mediterranean area. In the case of Pentanema langeanum , endemic to the C and N of the Iberian Peninsula, the taxonomic status of this species has been controversial due to its morphological similarity with P. conyzae , since both have short ray florets.…”

“…The analyses by Gutiérrez‐Larruscain et al () based on nuclear ribosomal DNA internal transcribed spacer (ITS) sequences have defined two lineages within the genus Pentanema : the clade D1 or “ Pentanema salicinum clade”, and the clade D2 or “ Pentanema conyzae clade” (Fig. ).…”

“…The lack of information on the interpopulation genetic variability of the species included in the Pentanema conyzae clade, distributed in the western Mediterranean area, together with the aforementioned taxonomic complications (i.e., identification of P. britannicum as opposed to P. heleniodes , the lack of diagnostic value of the morphological characters used in the identification keys available, and the persisting doubts on the taxonomic status of P. langeanum ) call for a more detailed study. For this, and taking into account the low levels of variation found within the group in prior phylogenetic analyses that used plastidial and ribosomal DNA sequences (Gutiérrez‐Larruscain et al, ), we conducted an amplified fragment length polymorphism (AFLP) fingerprinting analysis. This analysis includes all the species belonging to the Pentanema conyzae clade distributed in the western Mediterranean.…”

Notulae to the Italian native vascular flora: 5

“…Nomenclature and distribution updates according to Meve and Liede (2002), Barbaro and Kreutz (2007), Crespo et al (2015), Ardenghi and Polani (2016), Wilson (2016), Lazzeri (2017), Banfi (2018), Baum and Johnson (2018), Di Gristina et al (2018), Gutiérrez-Larruscain et al (2018), Nardi et al (2018), Madhani et al (2018), Selvaggi et al (2018) and corrections to Bartolucci et al (2018) are provided in Supplementary material 1. F. Bartolucci…”