Digitizing microscope slides is transforming how researchers access and study the vast holdings of natural history museums. Curators at the Smithsonian National Museum of Natural History estimate the institution houses about 148 million specimens. That total does not capture the billions of individual items mounted on glass slides, each documenting a species at a particular place and time.
Slide collections remain underused because they are delicate, compact and often poorly cataloged. A single slide is commonly logged as one specimen even when it contains hundreds of thousands of identifiable particles. These materials are essential for reconstructing past and present biodiversity and serve as core teaching tools for training new scientists.
Plant paleontologists and evolutionary biologists reported in PLoS One that whole-slide digital imaging can unlock this hidden trove. Their team developed a workflow to scan complete slides and share the contents online for scientists and students worldwide.
Digitizing microscope slides reveals unseen troves
The Denver Pollen Collection includes roughly 70,000 slides of fossil pollen extracted from rocks spanning many geological periods. Now held at the Smithsonian National Museum of Natural History, it reflects more than six decades of work by U.S. Geological Survey geologists and paleontologists who sampled across the continental United States, Alaska and other regions.
Because it represents one of the most complete plant fossil records available, researchers have used the collection to trace long-term shifts in vegetation and climate. Findings from this resource showed that Alaska’s North Slope experienced temperate to subtropical conditions about 50 to 56 million years ago, supporting palm trees north of the Arctic Circle. The slides also helped determine how rapidly plant communities recovered after the asteroid impact 66 million years ago that triggered mass extinctions.
Until recently, no one had estimated the number of individual specimens contained in the Denver Pollen Collection. After the Smithsonian received the material in 2021, the research team began scanning slides over several years. They estimate the archive holds about 4.3 billion microfossils, or roughly four times more than prior estimates for all specimens within the 73 largest natural history museums combined.
Digitizing microscope slides preserves fragile records
Digitization also safeguards information as slides age. Mounting media can yellow and crack, obscuring specimens. The study outlines how modern slide scanners can capture entire slides at high resolution, imaging pollen, diatoms, radiolarians, small insects and plant and fungal tissues. Scans typically require seconds to a few minutes and can include 3D renderings that reveal internal structures.
Traditional slide studies often relied on a single expert spending dozens of hours to locate and identify only a fraction of what is present. Verification by other researchers depended on access to the same physical slide. High-throughput imaging changes that. With slide scans, AI models can detect and map most specimens on a slide, streamlining relocation, enabling remote access and improving the reproducibility of studies.
Digitized images broaden access for students in botany, entomology, micropaleontology and related fields, especially in places without large reference collections. This expanded access can accelerate research on issues such as how climate change influences extinction and migration. Open-access microscopy databases also facilitate collaboration by allowing scientists to examine and measure images anywhere, reducing handling risks and shipping needs.
The future of digitizing microscope slides
Scaling up slide digitization and automating microfossil labeling could open hundreds of billions of specimens to wider study. The researchers estimate that fully scanning the Denver Pollen Collection would take nearly five years of continuous work and require about 3.5 petabytes of storage. They argue the result would be a comprehensive dataset documenting changes in Earth’s flora and climate over deep time.
Digital microscopy is expanding the horizons of micropaleontology and related disciplines. A vast record of life is already preserved in museums and universities, and making it digitally accessible will help reveal what those slides have held in plain sight.
This article has been updated to reflect that the Smithsonian National Museum of Natural History houses 148 million specimens. For more on how emerging tools are reshaping scientific research, see how tech that animates lifelike creatures is transforming visual effects.