A Novel Automated Mass Digitisation Workflow for Natural History Microscope Slides

Abstract

The Natural History Museum, London (NHM) has embarked on an ambitious programme to digitise its collections. One aim of the programme has been to improve the workflows and infrastructure needed to support high-throughput digitisation and create comprehensive digital inventories of large scientific collections. This paper presents the workflow developed to digitise the entire Phthiraptera (parasitic lice) microscope slide collection (70,663 slides). Here we describe a novel process of semi-automated mass digitisation using both temporary and permanent barcode labels applied before and during slide imaging. By using a series of barcodes encoding information associated with each slide (i.e. unique identifier, location in the collection and taxonomic name), we can run a series of automated processes, including file renaming, image processing and bulk import into the NHM's collection management system. We provide data on the comparative efficiency of these processes, illustrating how simple activities, like automated file renaming, reduces image post-processing time, minimises human error and can be applied across multiple collection types.

Keywords: Phthiraptera; Data Matrix barcodes; automation; mass digitisation; microscope slides; natural history collections.

Figure 1.

Examples of natural history microscope slides that are damaged or non-standard in size and mountant thickness.

Figure 2.

For the previous slide digitisation pilot batches of up to 100 slides were placed in a template and imaged using the SatScan^TM.

Figure 3.

High throughput slide digitisation workflow using multiple barcodes to encode metadata to enable automated file renaming and bulk ingestion into a collection management system (CMS).

Figure 4.

(a) An example of the temporary location and taxon primary key label, encoding these values in two machine-readable Data Matrix barcodes. (b) Temporary location and taxon labels inserted into a slide collection. This label was designed for vertical slide collections but can be adapted for other collection types.

Figure 5.

(a) Imaging setup consisting of a vertically mounted DSLR camera, a custom-built lightbox and a slide imaging template fixed in place. (b) Slide imaging template consisting of a raised ‘L-shaped’ edge, where the slide is positioned and a grooved area where the temporary location and taxon primary key label is placed within the field of view.

Figure 6.

Folder structure and file processing using automated file renaming and image processing. Legend: Dashed lines - folder structure; green lines - automated steps; blue lines - manual steps; orange ovals - processes.

Figure 7.

Example of the final specimen image, rotated and cropped using XnConvert, ready for ingestion into the collection management system.