Abstract
The world’s natural history collections constitute an enormous evidence base for scientific research on the natural world. To facilitate these studies and improve access to collections, many organisations are embarking on major programmes of digitization. This requires automated approaches to mass-digitization that support rapid imaging of specimens and associated data capture, in order to process the tens of millions of specimens common to most natural history collections. In this paper we present Inselect—a modular, easy-to-use, cross-platform suite of open-source software tools that supports the semi-automated processing of specimen images generated by natural history digitization programmes. The software is made up of a Windows, Mac OS X, and Linux desktop application, together with command-line tools that are designed for unattended operation on batches of images. Blending image visualisation algorithms that automatically recognise specimens together with workflows to support post-processing tasks such as barcode reading, label transcription and metadata capture, Inselect fills a critical gap to increase the rate of specimen digitization.
Highlights
There are an estimated two billion specimens stored in natural history collections worldwide [1]
Museum specimens have been used to estimate the regional species richness of tropical insects [6], to develop novel species-distribution models [7], to reveal the historical spread of a fungal pathogen linked to declines of amphibians [8] and to examine historical responses of butterflies to climate change [9]
We evaluated the performance of the software using 804 multi-specimen Tagged Image File Format (TIFF) images of specimens from the NHM’s collections
Summary
There are an estimated two billion specimens stored in natural history collections worldwide [1]. These botanical, zoological, anthropological, geological, mineralogical, and paleontological collections represent the largest and most significant part of the available scientific evidence base of the planet’s biosphere. These specimens form a global research infrastructure for tackling major scientific challenges such as environmental change, biodiversity loss, human health, sustainable agriculture, and the exploration of scarce minerals [2,3,4,5]. The public and private institutions that manage collections cover practically all-geographic areas with increasing levels of sampling density and taxonomic coverage
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