Digitizing microscope slide-based natural history collections: A protocol using slide scanner technology

Natural history collections contain millions of microscope slides documenting global microscopic biodiversity, yet these materials remain largely undigitized and are vulnerable to deterioration and loss. Recent advances in slide scanner technology, originally developed for medical pathology, offer new opportunities for comprehensive digitization of slide-based collections. Here we present an optimized protocol for digitizing diverse microscope slide specimens, using the Hamamatsu NanoZoomer S20 slide scanner, developed while imaging slides at the Smithsonian National Museum of Natural History. We provide specimen-specific recommendations for scanning parameters, including scan area, focal points, Z-stack configuration, and file management workflows. Scanning times range from 41 seconds for small invertebrates to 18 minutes for palynological samples, with final compressed file sizes of 0.15-28 GB. High-resolution images (0.23 μm/pixel) captured diagnostic morphological features across all specimen types, including pollen, diatoms, radiolarians, plant and fungi tissues, and invertebrates. Using this method, we estimated that just the NMNH's paleo-palynology slide collection contains approximately 4.3 billion individual specimens, 30 times more than the current estimated size of the entire NMNH collection. Slide scanning enables 3D data capture, facilitates remote collaboration, improves reproducibility of taxonomic identifications, and creates permanent digital records that mitigate risks of physical deterioration. This protocol provides practical guidance for institutions looking to digitize slide-based collections to preserve and unlock their full research potential.