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

Area of Science:

• Biodiversity research
• Digital specimen preservation
• Natural history collections

Background:

• Millions of microscope slides in natural history collections are undigitized, risking data loss and deterioration.
• Microscopic biodiversity documentation is crucial but limited by current accessibility.
• Advances in slide scanner technology present opportunities for large-scale digitization.

Purpose of the Study:

• To present an optimized protocol for digitizing diverse microscope slide specimens using the Hamamatsu NanoZoomer S20.
• To provide specimen-specific recommendations for scanning parameters and file management.
• To enable comprehensive digitization of slide-based collections for research and preservation.

Main Methods:

• Utilized the Hamamatsu NanoZoomer S20 slide scanner for digitizing various specimens.
• Developed specimen-specific recommendations for scan area, focal points, and Z-stack configuration.
• Implemented file management workflows for compressed file sizes ranging from 0.15-28 GB.

Main Results:

• Achieved high-resolution images (0.23 μm/pixel) capturing diagnostic features across pollen, diatoms, radiolarians, tissues, and invertebrates.
• Scanning times varied from 41 seconds to 18 minutes per slide.
• Estimated the Smithsonian NMNH's paleo-palynology collection alone contains ~4.3 billion specimens.

Conclusions:

• Slide scanning facilitates 3D data capture, remote collaboration, and reproducible taxonomic identification.
• Digitization creates permanent digital records, mitigating risks of physical specimen deterioration.
• The protocol offers practical guidance for institutions to unlock the research potential of slide collections.