Approximately 145 million: That’s the number of specimens – including plants, animals, minerals and human artifacts – curators estimate are held in the Smithsonian National Museum of Natural History. However, these estimates do not reflect the billions of tiny individual specimens contained on microscope slides – thin pieces of glass that fix objects in place for observation – each representing a record of a species at a specific place and time.
Microscope slide collections are an underused part of natural history collections because they are small, fragile and generally not well cataloged. One slide is usually recorded as a single specimen, even though it may contain hundreds of thousands of identifiable samples. They play a significant role in documenting life both present and past, and they are also a core educational resource for training future scientists.
Our team of plant paleontologists and evolutionary biologists use microscopy techniques to extract the full potential of natural history collections. In our recently published research in the journal PLoS One, we developed a way to digitally image whole microscope slides and make the specimens they contain available to scientists and students around the world.
Unseen troves of specimens
The Denver Pollen Collection contains about 70,000 slides of fossilized pollen extracted from rocks of many geological ages. The collection, now housed at the Smithsonian National Museum of Natural History, represents over 60 years of effort by scores of geologists and paleontologists working for the U.S. Geological Survey, gathering specimens from all over the continental U.S., Alaska and many other parts of the world.
Presented with one of the most complete fossil records of plant life in existence, scientists have used this collection to understand how vegetation and climate changed over geological time.
Ingrid C. Romero, CC BY-ND
For example, through studying the Denver Pollen Collection, researchers discovered that the North Slope of Alaska had a temperate to subtropical climate about 50 to 56 million years ago that allowed palm trees to grow north of the Arctic Circle.
The collection was also critical in determining how quickly vegetation recovered from the asteroid impact that caused mass extinctions 66 million years ago.
Despite its scientific value, the number of specimens in the Denver Pollen Collection had never been estimated. When the Smithsonian received the collection in 2021, our team began digitally imaging some of these slides over the course of several years.
We estimate this collection holds approximately 4.3 billion microfossils – four times more specimens than were previously estimated to exist in all the collections of the world’s 73 largest natural history museums combined.
Preserving specimens through digitization
Digitizing microscope slides is important for preserving the information they contain. Many slides are deteriorating – the mounting medium that holds the cover slips can yellow and crack with time, obscuring the specimens from view.
In our study, we show how using up-to-date microscope slide scanners can help researchers digitize and preserve microspecimens – including pollen, diatoms and radiolarians – as well as small insects and various plant and fungal tissues. These scanners can digitize full slides at high resolution. Each scan takes seconds to a few minutes, depending on the size of the specimen. They can also capture 3D images of organs and features within specimens.
Traditionally, natural history studies relied on the expertise of a single specialist. An expert might spend dozens of hours manually analyzing a microscope slide and find only a fraction of the thousands of specimens present. Additionally, other researchers can verify their findings only if they have access to the same slide.
With slide scanning and digital imaging, researchers can use AI models to detect most of the specimens in a slide and record where they’re located on a slide. This makes it easier to not only relocate individual specimens but also access them remotely across the web, thus improving researchers’ ability to replicate and verify the accuracy of studies.
Digitizing specimens on microscope slides not only preserves information as the slides themselves deteriorate, but it also makes it more accessible for researchers, students and the public.
Digital slide images give students in botany, entomology, micropaleontology and other fields access to vast reference collections that may not be available in their home countries. This enlarges the talent pool in these fields by allowing students from all over the globe to participate in original research, such as on how climate change is affecting extinction and the migration of different species.
Open-access databases of digital microscopy also make scientific collaboration easier. Researchers can examine and measure images at any location at any time, without needing to handle the physical slide. This reduces barriers to sharing science as well as the risk of damaging slides during transportation or handling.
Future of microscope slide collections
Digitizing microscope slides in natural history museums and automating how microfossils are labeled opens up more opportunities for researchers to share and study hundreds of billions of specimens in collections around the globe.
However, digitization is not without cost. We estimate that fully digitizing the Denver Pollen Collection would require almost five years of continuous work and about 3.5 petabytes of storage. But we believe these efforts will return a massive dataset that captures changes in the Earth’s flora and climate over geological time.
Digital microscopy opens new horizons for fields such as micropaleontology to explore the biodiversity of the planet. There is a whole galaxy of nature waiting to be seen … and it is already stored in museums and universities around the world.
Ingrid C. Romero has received funding from the Smithsonian Institution Climate Change Fellowship, the National Museum of Natural History Office of the Associated Director for Science, and the Smithsonian Office of the Undersecretary for Science.
She is affiliated with The Micropaleontological Society, and currently she is the Palynology Group Chair.
Scott L. Wing receives funding from the Smithsonian Institution (Life on a Sustainable Planet Program and the Smithsonian National Museum of Natural History).
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