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Two basic types of preparation are used to visualize specimens with a light microscope: wet mounts and fixed specimens.
The simplest type of preparation is the wet mount, in which the specimen is placed in a drop of liquid on the slide. A liquid specimen can be directly deposited on the slide using a dropper. Solid specimens, such as skin scraping, can be placed on the slide before adding a drop of liquid to prepare the wet mount. Sometimes the liquid is simply water, but stains are often added...
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Digitizing microscope slide-based natural history collections: A protocol using slide scanner technology.

Ingrid C Romero1,2, Scott L Wing1, Carlos A Jaramillo2

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Digitizing natural history microscope slides with advanced scanners preserves biodiversity data. This protocol optimizes high-resolution imaging for millions of specimens, safeguarding them for future research.

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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.