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Imaging the University of Virginia’s Mountain Lake Biological Station Herbarium

Notes from Nature has been a significant undertaking with many people involved, but the transcription work being completed through the project is only a slice of the entire process of increasing access to and use of research collections.  This guest post comes from Christina Deane, Head of Digitization Services in the University of Virginia Library.  Christina was intricately involved with the imaging of the University of Virginia’s Mountain Lake Biological Station Herbarium, which is one of the current featured collections.  Through this post, we hope you’ll gain an understanding of how all of the images in this collection were produced.  If you are interested in seeing more about the University of Virginia Library’s Digitization Services, see this video:  http://www.youtube.com/watch?v=7CRHyj-6syM (look to 3:24 for a photo of a herbarium sheet!).  This story is one of many ways, and we will likely touch on other imaging processes in the future.  – Andrew Sallans


We began a discussion of how this project would be carried out in late summer of 2005.  The conversations included biologists, librarians, and technologists, to make sure that we were covering our bases on _MG_0323technique, metadata, and consistency so we would only have to do this once!  Once we had ironed out some of the metadata issues, we were able to modify our scanning workflow to accommodate the different requirements for the herbarium specimen.   We agreed that we would create archival tiffs and deliverable jpegs at 300 dpi following UVa’s digitization guidelines, and our digital library workflows were already in place to programmatically extract technical metadata from the images.

We hired a student in the spring of 2006 to begin scanning images using our overhead, Hasselblad cameras with PhaseOne P45 Plus digital scan back cameras (capturing at 39 megapixels!).  These cameras are typically used for our rare print materials, including all varieties of rare books, Jefferson letters, and even copies for the Declaration of Independence.  We established a set way to position the ruler and color bar so we could achieve a consistent look for the images, and this was likely influenced by other herbarium digitization projects going on at the time.  It was definitely a different way to work than what we were doing for books and manuscripts.  When we began this work, we didn’t really know how many specimen there were to scan, as the estimates we were provided with were in the thousands.

Our workflow was to barcode the images before scanning them, create a folder name based on the folder the items_MG_0314 were housed in, and name each image based on the barcode.  Our cameras and digital backs were very slow back in 2006, and imaging took a lot longer then than it does now.  Once through the basic quality assurance steps (QA) we were to send jpegs to the librarians in charge of the project so they could facilitate the metadata creation with the team they had assembled to work on this part of the project.  We utilized multiple rounds of QA so at least 3 or 4 people examined each image.

Scanning continued from the spring of 2006 through the spring of 2007, at which point the student working on the project graduated.  Scanning resumed in the spring of 2008.  Over the course of the next year, DS digitized thousands more images.  This _MG_0317process went faster because DS had acquired new camera systems with autofocus lenses and faster digital backs for almost instantaneous capture of the images.  During 2008 we continued scanning specimen as they were delivered to us.  We made a big push in January of 2009 to finish the rest of the collection (over 4000 pieces), and we completed the project that month. Full-time staff involved in the project included Andrew Curley, Kristy Haney, Jeanne Pardee, and Christina Deane.  John Ruscher was the primary student worker in the early part of the project, and many student employees were involved in the second phase of scanning from 2008 to early 2009.  Over the course of the project, we scanned 8,935 images in all.

-Christina Deane, Head of Digitization Services, University of Virginia Library

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Featured Collection: University of Virginia’s Mountain Lake Biological Station Herbarium

Today, I’m pleased to offer another guest post from a colleague here at the University of Virginia, Michelle Prysby.  Michelle supports science education and outreach at UVA, but also has a special place in her heart for herbaria, master naturalist groups, and citizen science, having spent much of her academic career in those areas.  Upon my invitation, she eagerly jumped at the opportunity to help out with sharing the story of Mountain Lake Biological Station as part of UVA’s science education and outreach effort.  – Andrew Sallans


On a remote forested ridge, at 1,160 meters in elevation in the southern Appalachian mountains sits Mountain Lake Biological Station (MLBS), a busy hub for ecological and evolutionary biology research.  As part of the University of Virginia Department of Biology, MLBS serves as a facility for teaching field courses, a research site for scientists from around the country, and, for parts of the year, a home for students and faculty who come there to learn and to study.  Field courses include topics such as Wildlife Disease Ecology and Techniques in Conservation Biology, while research at the station has included studies of high-elevation forest ecology, genetics of various native and non-native plants, and salamander dispersal, to name just a few.

Courtesy of Special Collections, University of Virginia Library, Charlottesville, Va. Item RG-30/1/10.011

The station has some high tech research facilities, including a DNA extraction lab and chambers for growing organisms in controlled environments.  The first stop, however, for a scientist interested in studying plants in the area would likely be the much less high tech herbarium.  The MLBS herbarium houses more than 9000 plant specimen from the Mountain Lake area, the surrounding Giles County, and a smattering of other locations in Virginia and the Southeast.  It’s a great resource that gets used by many scientists studying plants at Mountain Lake.  Visiting scientists starting a new research study, for example, might comb through the herbarium to locate possible study populations of a particular plant.  A new graduate student might use the herbarium to help formulate research questions and choose a study system.  It’s also used for education, particularly during MLBS courses on plant conservation and diversity.

The herbarium has been assembled over time through collections by U.Va. scientists and through the acquisition of other scientists’ collections over time.   It has become a fairly extensive collection for the region, with significant contributions made by many different researchers.  It’s a region that is quite biologically diverse, too, with varying topography and microclimates.  Walking out from the station atop Salt Pond Mountain, one can find several forest types, rock outcrops, bogs, streams, meadows, and one of only two natural freshwater lakes in Virginia.

MLBSHerbarium

Photo of UVA Mountain Lake Biological Station Herbarium cabinet, taken by Andrew Sallans

The herbarium grows every year, particularly through the efforts of students taking the plant diversity course in the summers.  It contains some very old specimens—more than 100 years old.  Some of these species may no longer even exist in the locations where they were originally collected.  That’s one reason herbaria like the one at Mountain Lake are so important as both a reference collection and historical record.

The MLBS Herbarium is cared for by Eric Nagy, Associate Director of MLBS and Assistant Research Professor of Biology at U.Va., and by Zack Murrell, Associate Professor of Biology at Appalachian State University and instructor for the MLBS Plant Conservation and Diversity summer undergraduate field course.

“The herbarium is one of Mountain Lake Biological Station’s greatest assets,” says Nagy.  “Other field stations drool when they see what we have for our users.”  The digitization of the collections and the database of specimen information transcribed through Notes from Nature will make it even more valuable.

Mountain Lake Biological Station invites the public to its Open House event, July 13.  If you happen to be nearby, stop in to learn more about the research at the station and visit the herbarium in person.

-Michelle Prysby, Director of Science Education and Public Outreach, University of Virginia

Profile of Notes from Nature Team Member: Andrew Sallans

Name:  Andrew Sallans

Title:  Head of Strategic Data InitiativesAndrew

Where do you work primarily?  University of Virginia Library

What you do in your day job?  Unlike most of my Notes from Nature colleagues, I am not in a research or teaching position, and instead focus my energy on building services to support data-intensive research, working with researchers on data management problems, and facilitating the management, access, use, and preservation of research data with UVA researchers.  

What’s your role with NfN and what do you hope to gain from it?  If relevant, how will your research benefit?  I’ve been involved with Notes from Nature from its inception, having been the lead PI on a proposal to Zooniverse on behalf of SERNEC.  I’ve been working with SERNEC for around 6 years now, with an eye towards digitizing the local UVA biological collections and providing a proper, broader long-term home for the digital data output.  The opportunity to partner with the Essig Museum and Natural History Museum teams has been a real pleasure and opportunity to see other approaches for increasing access to biological collections, digitization methods, metadata standards, cataloging approaches, and general collection challenges.  I believe that these experiences will all be beneficial as we continue to develop and evolve research collection management strategies here at UVA.

What’s the most exciting aspect of citizen science work from your point-of-view?  This project has been exciting in many, many ways.  Although I’m not in the role of a scientist, I’ve had the privilege of interacting directly with many collections over the past decade in order to help manage and preserve those collections.  I’ve always loved being able to closely examine, understand, interpret, and contextualize items in collections, but this is something most people are never exposed to.  Even with many new programs to increase STEM research and education, it’s sometimes hard to develop enthusiasm when direct contact with science is sometimes too dangerous or costly for the student or scientific object; I’ve seen the same be true in libraries (ie. lack of interest in history because it’s all behind glass).  Zooniverse projects like Notes from Nature offer an excellent opportunity to make a meaningful contribution to scientific progress by completing critical tasks at a massive scale, while simultaneously having an opportunity to interact quite closely (ie. high-quality images are almost as good as the real thing!) with many specimen and the expert scientists and managers who work with them each day.  I’m hopeful that we’ll inspire new researchers and research projects and create some great conversations between those who are passionate about science.

A sampling of Notes from Nature

If you haven’t yet joined in on the Notes from Nature transcription effort, there’s still plenty of time.  We’ll be adding new collections in coming days, and there will be many more exciting specimen to see.

Here’s a sampling of some of the fascinating specimen that have appeared already.  Which are your favorite?

Featured Collection: FSU’s Robert K. Godfrey Herbarium

As you may have noticed, many of the herbarium images currently featured in Notes from Nature come from FSU’s Robert K. Godfrey Herbarium.  To peak your interest, we are happy to share this guest post from the herbarium’s director, Austin Mast.  Enjoy!  – Andrew Sallans


Florida State University’s Robert K. Godfrey Herbarium is a biodiversity research collection of about 210,000 plant and microalgae specimens. These primarily document the distribution and natural variation of the roughly 2,800 species of flowering plants, ferns, conifers, and cycads found in the East Gulf Coastal Plain (EGCP) ecoregion—a North American biotic hotspot—and the microalgae of Florida’s Gulf and Atlantic coasts. A secondary strength of the collection is tropical Central America. The herbarium grows at a rate of about 2,000 specimens each year.

White-top Pitcher Plant

White-top Pitcher Plant

Stretching across the Florida panhandle to eastern Louisiana along the coast, the EGCP is home to 125 endemic plant taxa (species and varieties found nowhere else), including the White-top Pitcher Plant (left).  A large number of the regional endemics are restricted to pine-dominated wetlands and uplands, two communities that have dwindled to less than 5% of their original extent and are now considered among the most endangered ecosystems in North America. Loss of longleaf pine-dominated communities and fire suppression has left many endemics critically imperiled, and the EGCP is also considered a “species endangerment hotspot,” with many of its counties within the top 95th percentile of US counties when ranked by the number of threatened and endangered species in each. The Robert K. Godfrey Herbarium is the most extensive collection of plants from the eastern part of the EGCP.

The herbarium was established in 1940 by Herman Kurz (1886–1966), a professor of botany at what was then the Florida State College for Women. It is named for Kurz’s successor, Robert K. Godfrey (1911–2000), who collected about one-third of the specimens currently in the collection, named many plant species himself, and had 12 plant species or varieties named for him (such as Hymenocallis godfreyi, an endangered spiderlily restricted to one county in Florida; below right). The FSU botanists Loran Anderson, Gil Nelson, and Austin Mast (the herbarium director) currently use the specimens onsite for research and education, as do Florida’s natural resource managers. Through an active loan program, biologists from around the world borrow specimens from the Robert K. Godfrey Herbarium for studies of plant and microalgae systematics, ecology, evolution, biogeography, conservation biology, anatomy, and morphology.FSU image

About a third of the Robert K. Godfrey Herbarium’s specimens have been digitally imaged, databased, and georeferenced since 2003, thanks to support from the National Science Foundation, the Florida Department of Environmental Protection, and the Florida Fish and Wildlife Conservation Commission and the (typically) short-term efforts of about 75 students and staff members. This third of the collection is searchable at http://herbarium.bio.fsu.edu/search-specimens.php, allowing anyone with access to the web to sort result tables, browse through images, and generate distribution maps.

The Robert K. Godfrey Herbarium would like to complete the digitization of the remaining two-thirds of the collection in the next 10 years. This parallels the broader goal of the US biodiversity research community to digitize the roughly 90% of the 1 billion biodiversity research specimens yet to be digitized in US collections in the next decade. This ambitious community goal can be reached with greater coordination and standardization within the digitization community, more efficient workflows, technological innovation, and broader participation—ESPECIALLY public participation. For more information on how the public can contribute, see the report on iDigBio’s Public Participation in Digitization of Biodiversity Specimens Workshop organized by the Robert K. Godfrey Herbarium’s director, Austin Mast.

The Robert K. Godfrey Herbarium (and all of the world’s biodiversity research collections) need your help to make our specimens broadly discoverable and potentially useful to everyone. Thank you, Notes from Nature community members!

-Austin R. Mast, Director of FSU Robert K. Godfrey Herbarium

Why do we need so many collections of the same plant?!

F3.largeCrop

Figure from a paper by C. Lavoie and D. Lachance showing a shift toward earlier flowering time for coltsfoot (Tussilago farfara). Image used by permission of the Botanical Society of America.

When people first get a look inside of a herbarium cabinet they often ask: “why do you need so many specimens of the same plant species?” Well there are a few reasons for this. People who study plants don’t just want to see one example of a species. They may want to see multiple collections so that they can understand the variation in characters for the species. For example, the leaf shape may be highly variable so we would need to see different specimens to understand this. It may also be important to get an idea of all the places where a certain plant can be found. We would need several specimens from different locations to understand the geography. We may also want to know how characteristics of a plant, or its geographic distribution, might be changing over time. In this case, we would need collections from multiple years.

The change in when plants bloom (aka phenological shift) has received a lot of attention over the past few years. It is now well established that changes in the climate have caused many species to shift the timing of when the leaves emerge in the spring (leaf out) and when the flowers open. This shift has major implications. One example is that a plant might bloom before its pollinators are available. If pollination does not occur, this could result in the plant not being able to produce fruits and seeds, which are important for the future success of the species.

Herbarium specimens can be used in a relatively simple way to study phenological shifts.

Carpinus.caroliniana

American Hornbeam (Carpinus caroliniana) flowering in March 2007.

Using the date information provided on the specimen label, we can record the day of the year that different plant collections were made (e.g., collections showing flowers in bloom) and graph these values against the year. What is commonly found is that plants are blooming earlier as a response to a warmer climate. For example, the graphic at the right shows how a plant is blooming earlier. The collections made in the year 2000 bloomed several days earlier than the ones collected in 1920. The full article can be read here.

I am interested in knowing the date that plants were collected for a different reason.

For exotic species, or species that are relatively newly introduced into an area, it is valuable to know when they first arrived in a new place and how fast they are spreading. If we can locate the earliest museum records of a species in the United States for example, we can then trace its expansion to new areas over time using additional museum records (subsequent collections). We can then examine where the exotic species has spread and how fast. There are many factors that influence the spread of exotic species, but describing the basic aspects of their spread in space and time is a first important step in our efforts to understand this process.

The Notes From Nature projects asks citizen scientists to transcribe specimen labels in order to help record this kind of information that is important in ecological research. The date is a simple but extremely important piece of information. Phenological shifts and the spread of exotic species are two important issues that can be addressed using this information.

-Michael Denslow

What is an herbarium?

students and folder low

Researchers working in the herbarium at Appalachian State University

An herbarium is a place that houses plant specimens. Many people expect that an herbarium will be filled with living plants. However, these plant specimens are pressed, dried and glued to sheets of paper. They are dead. The sheets of paper are typically stored inside of cabinets for safekeeping and organizational purposes. An herbarium is similar to a library in that both house artifacts (specimens or books) in a safe and organized way that allows them to be found and used by researchers. If plant specimens are stored properly they will last hundreds of years with little sign of degradation.

If you think about it, it makes sense to store plant specimens in this way (as dead samples). Logistically you can fit and care for many more pressed specimens than living plants in the collection. In addition, an herbarium often contains plants from all over the world including plants from diverse habitats such as deserts and alpine tundra. It would be tough to grow all of these different plants in one place.

Herbaria are sometimes part of natural history museums, associated with botanic gardens or academic institutions. The largest herbarium collections in the world are housed in Paris and New York. These large collections contain millions of specimens. However most herbarium collections are much smaller. There are more than 3500 herbaria scattered across the world. In fact, you likely have a local herbarium that contains specimens of the plants that occur in your area. To learn more about the herbaria in your area you can search Index Herbariorum, a global directory of herbaria.

-Michael Denslow

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