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IU Herbarium’s preserved plant collection enters new era with massive digitization project

Feb. 22, 2017

On the far east side of the IU Bloomington campus in a low-slung structure near 10th and the Bypass, one of the university’s greatest hidden treasures is undergoing a transformation.

Paul Rothrock looking into a microscope at the plants

Paul Rothrock is a reasearch scientist at IU and associate curator of the collection at the IU Herbarium. | PHOTO COURTESY OF EMILY STERNEMAN

The keepers of the IU Herbarium -- a sprawling collection of 150,000 painstakingly preserved and cataloged flowers, grasses, leaves and other plant life -- are overseeing a complete digitization of the vast collection.

Founded at IU in 1885, the IU Herbarium is in the Smith Research Building, Room 130. The director of the IU Herbarium is Eric Knox, a senior scientist in the IU Bloomington College of Arts and Sciences’ Department of Biology.

“This effort will bring the herbarium into the 21st century so everything in the collection is available to scientists across the globe,” Knox said. “Every new specimen that enters the collection contains digital information, so right now we’re focused on making a big, one-time push that reaches back over the past 130 years.” 

Knox has served as a director and curator at the IU Herbarium since 2004. Other keepers of the collection are associate curator Paul E. Rothrock, a research scientist at IU since 2014, and assistant curator Walter Fertig, who joined IU last year to lead a large team of undergraduate assistants who are photographing every specimen and compiling the collection for an online database. 

The IU Herbarium Digitization Project is supported by the IU Bloomington Department of Biology, College of Arts and Sciences, Center for Biological Research Collections, Vice Provost for Research, Vice President for Research, UITS and IU Libraries.

Although known to researchers at IU, Knox said, the herbarium and its history aren't as familiar to other members of the university community. Founded over 130 years ago, the IU Herbarium grew dramatically in the early 1900s after it began to house the personal collection of Charles Deam, an Indiana pharmacist-turned-botanist who amassed a collection of 78,000 plant specimens while working on the “Flora of Indiana,” a meticulously cataloged collection of the state’s plant life published in 1940.

Over the years, the contributions of IU students and faculty doubled the collection’s size in ways that reflect the expertise of the people who’ve left their mark on the university. The collection contains one of the largest samples of sunflowers, for example, due to the work of Charles Bixler Heiser, a renowned ethnobotanist and leading authority on the plant. Knox’s own area of expertise -- the lobelia family -- is reflected in the collection’s specimens of giant lobelias that grow on equatorial mountains of Africa. Altogether, the collection contains plants from at least 85 countries. 

keepers of the collection posing for a group photo

The digitization group includes three curators and five graduate assistants. Back from left: Tomas Fuentes-Rohwer, Paul Rothrock, Eric Knox, Walter Fertig, Rowan Mitton, Kamila Czebotar; front from left: Allie McKinzie and Maggie Vincent. | PHOTO COURTESY OF EMILY STERNEMAN

“Every single specimen in the herbarium is unique,” Rothrock said. “A common misperception is that herbaria are like a stamp or coin collections. Except there are millions of exact copies of those (stamps or coins); no two plants are exactly alike.”

The herbarium’s long history has also left its mark on the collection. Hidden among the rows upon rows of metal shelves that house the collection’s specimens -- each mounted on sheets of acid-free paper -- are a small cluster of antique wooden cabinets, the personal property of Deam. Portraits of famous botanists and antique microscopes also reflect the history of the collection. The oldest plant in the collection dates back to 1867, two years after the end of the Civil War.

The collection is not a static museum, however, but a vital source of data for modern research.

“You can do new science with old samples because, essentially, you can preserve plants forever in an herbarium,” Knox said. “And not just details like the veins in leaves or structures in cells, but all the chemical and genetic information too.” 

For example, an IU Ph.D. student recently shed light on plant evolution by using scanning electron microscopy to study tiny pollen samples in the collection. Another traced the spread of psychedelic ergot fungus through hundreds of morning glory species by applying modern chemical analysis to preserved seeds. Knox’s own work has used next-generation DNA sequencing to extract the complete chloroplast genome of an extinct species of lobelia.

In addition to working with IU researchers and visiting scientists, Fertig said the herbarium has provided information to environmental consultants with the I-69 Project, who needed to know where endangered plants might be located along the road’s construction route. 

There are several major milestones in the digitization of the collection, estimated to be completed a year before the university’s bicentennial in 2020. The first step -- a complete inventory of the collection -- took two years. The second, which is ongoing, is photographing every specimen with a high-resolution camera and assigning them barcodes. The written information accompanying each sample must also be scanned into the system and manually checked to ensure no errors occurred during the input process. 

Assisting with data entry are 13 IU undergraduates, whose work is vital to the project, Knox said. He estimates the first step in the process alone would have required a single person -- working nonstop at the impossible pace of one sample a minute -- thousands of hours to complete.

a faculty member aiding a student in digitization process

Eric Knox, the director of the IU herbarium, works with graduate assistant Maggie Vincent to compile material for the project. | PHOTO COURTESY OF EMILY STERNEMAN

The penultimate step is extracting modern geographic data from the collection’s pen-and-paper notations, a skill that requires enough historical knowledge to recognize whether a local landmark has shifted over the years. After this data is integrated into the collection, Fertig said researchers will be able to run analyses that show where certain rare plants in the state face risk of extinction, among other projects. 

The digitization project will be complete once the last plant has been archived on the Consortium of Midwest Herbaria, a data portal for herbaria across the region. Users can also check out the project’s progress on the website right now, or even use the resource to identify plants in their own backyard. But the last of the IU information, such as the geolocation data, won’t be available until 2019.

“Scanning the plants is important, but it’s the data that makes the collection special,” Knox said. “I like to say the only difference between an herbarium and a bunch of dead flat plants is the scientific information on those labels.”

The IU Herbarium digitization project aligns with several priorities in the university's Bicentennial Strategic Plan, including celebrating a vibrant community of scholars, a commitment to student success and global engagement.

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