Florida Museum of Natural History

University of Florida Herbarium (FLAS)

Computerization and Digitization
of the University of Florida Herbarium (FLAS)

UF / Institute of Food and Agricultural Sciences / United States Department of Agriculture CRIS - Hatch Project FLAS-HRB-04170

ACCESSION NO: 0199077 SUBFILE: CRIS
PROJ NO: FLA-HRB-04170 AGENCY: CSREES FLA
PROJ TYPE: HATCH PROJ STATUS: EXTENDED
START: 01 JAN 2004 TERM: 30 SEP 2009 FY: 2007

INVESTIGATOR: Williams, N. H.

PERFORMING INSTITUTION:
HERBARIUM
UNIVERSITY OF FLORIDA
GAINESVILLE, FLORIDA 32610

COMPUTERIZATION AND DIGITIZATION OF THE UNIVERSITY OF FLORIDA HERBARIUM

NON-TECHNICAL SUMMARY: Requests for information on plants in the University of Florida Herbarium centers on type specimens, poisonous plants, edible and medicinal plants, and general info on vascular plants. Much of this information could be available to the general public as well as the scientific public by a searchable, web accessible database with digitized images. This project will provide a searchable, web accessible database with digitized images for use by scientists and the lay public.

OBJECTIVES: Objectives: 1. We propose to computerize the vascular plant and bryophyte herbarium of the University of Florida, which consists of the vascular plant herbarium of approximately 250,000 specimens and the bryophyte herbarium of approximately 250,000 specimens. To date we have developed a computerized database of approximately 30,000 specimens. 2. We will organize the database so that information can be recovered on a) poisonous plants, b) irritant plants, c) other harmful plants, d) edible plants and useful plants, and e) all other plants in the collection. 3. We will digitize a significant portion of the specimens in the above five categories to provide a web based resource. 4. We will provide a web searchable database of label data using Microsoft SQL Server as a database that will be a valuable tool for the research community.

APPROACH: Approach: 1) Computerization of the collections. Our database is a special application developed in MicroSoft Visual FoxPro. The database is upsized to MicroSoft SQL Server and deployed on the web through Active Server Pages. Priority criteria used for selecting specimens for data entry: 1) type specimens; 2) new specimen sets of University of Florida Herbarium affiliated collectors with label data prepared in accordance with our data standards; 3) historic collections of J.K. Small, A.P. Garber, etc. as encountered in loan preparation; and 4) specimen data requests from researchers. This system has been an opportunistic system of computerizing the herbarium collections. 2) Digital Imaging. The digital images available in the University of Florida Herbarium Collections Catalog and Type Specimens web sites are prepared using several types of scanners and digital cameras. This work is facilitated by the collaboration of the Florida Museum of Natural History / University of Florida Herbarium, University of Florida Libraries Digital Library Center and the Florida Center for Library Automation. The highest resolution images are prepared by the staff of the George A. Smathers Libraries Digital Library Center. These images are acquired using a ZBE Satellite large format stationary camera equipped with a PowerPhase ARI cameraback, 135mm Rodenstock lens and daylight filter. Computer support is currently a Macintosh (PowerMac G4) computer system with 17 gigabytes of storage and ~ 800 megabytes of active memory. Camera images are matched with a 1.8 gamma monitor, relative colorimetrics and the "BEST" quality for rendering profiles. Colorimetrics are calibrated using Kodak Q-60R1 target per ANSI IT8.7/2-1993(1999:04). Intermediate processing of digital herbarium images is achieved with Adobe Photoshop 5.0. Staff and volunteers in the University of Florida Herbarium are acquiring images of selected specimens on a flatbed scanner, Microtek Scanmaker 9600XL. Specimens are scanned at 400 ppi and saved in tif format (.tif). Most of the specimens available in the Floristic Inventory of Kanapaha Botanical Gardens project are prepared by this method. Digital images of plant materials taken with consumer model digital cameras prior to pressing are being added to compliment the specimens. All images are converted to SID format by the Digital Library Center. The images are made available on the Internet via the Lizardtech viewing source Mr. SID from the Florida Center for Library Automation web server.

PROGRESS: 2007/10 TO 2008/09
OUTPUTS: The herbarium's collection catalog (http://www.flmnh.ufl.edu/herbarium/cat/) grew by 4243 entries between 1 October 2007 and 30 September 2008 to a total of 48851 catalogued accessions. Major specimen sets added include: vouchers for Kristen Porter Utley's M.S. Thesis, 'Santeria : an ethnobotanical study in Miami, Florida, USA,' Walter Judd's 2006 Dominican Republic field trip, Erinn Koch's flora of an unnamed spring in Lafayette County, Florida, Heather Hill's flora of Riverview Pointe Reserve, Manatee County, Florida, Dan Skean's 1989 Haitian field trip collections and J.R. Abbott's miscellaneous Florida collections targeting under-documented counties. All specimens of selected species were added to the collection catalog for a project by Dr. Betsy VonHolle of the University of Central Florida to look at flowering phenologies of specific nonnative plant species in Florida over time. Cataloging and imaging of representative Florida endangered and threatened species continued. During this reporting period 150 species (1243 specimens, 1249 images) were photographed and posted. The image library included 439 E&T species depicting 2409 specimens in 2475 images as of 30 September 2008. Other specimens imaged include 507 accessions being utilized in the NSF grant, 'AToL: collaborative research: resolving the trunk of the Angiosperm tree and twelve of its thorniest branches.' These images will also be included in the Tree of Life Knowledge and Information Network (tolkin.org) database with links back to our catalog. As of 30 September 2008 there were 8621 images of 7573 specimens and 2955 species available through our web site, an increase of 2361 images for the period. Images are acquired with a Microtek 9800XL flatbed scanner at 400 ppi resolution. After quality and efficiency research and with collaborative funding from the Museum we have purchased a TTI Repro-graphic Workstation with a Sinarback eVolution 75H camera. This system provides sharper images with better depth of field and hardly any of the shadowing common in the scans. The equipment was being set up and tested in August and September 2007. Our testing indicates that we should be able to more than triple our imaging speed from 15 to 50 or more per hour. A new PowerMac Workstation and 3TB of managed, backed up, data space were purchased with special CRIS funding. New images are posted on the Florida Museum of Natural History servers in Zoomify / Adobe Flash format. Images posted prior to 2006 (ca. 2465) are hosted on the MrSid Server at the Florida Center for Library Automation. Since plans are being made to shut down this server we are encoding those images for display both as part of the UF Herbarium's web site in Zoomify format and the UF Libraries Digital Collections in JPEG 2000 format. Kent Perkins attended the Latin American Plants Initiative Meeting in Panama City, Panama from 23 to 25 October 2007. The meeting was fully funded by the Mellon Foundation to encourage participation in this new project. The University of Florida Herbarium will participate as part of the Caribbean group and a proposal for funding has been submitted to the Mellon Foundation. PARTICIPANTS: * Individuals: Norris H. Williams - P.I. (paid on Florida Museum of Natural History salary line); Kent D. Perkins - project management, computer programming, web site, data entry, image creation and processing (paid on IFAS Extension salary line); Marc Frank - specimen preparation and nomenclature research; Joshua Robinson - data entry and specimen organization; Johann Souss - data entry and specimen organization; Kathleen Davis - image creation and processing, specimen data entry. * Partner Organizations, Collaborators: Florida Museum Associates - provides salary support for image creation specialist, Kathleen Davis. University of Central Florida (Dr. Betsy VonHolle) - salary reimbursement for data entry of selected nonnative species. TARGET AUDIENCES: Plant systematic, environmental and ecological researchers are using our web site's collection catalog and images to mine data for project work. We also provide downloaded MS-Excel spreadsheets to researchers for use in studies. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

IMPACT: 2007/10 TO 2008/09
Recognition of endangered and threatened species is crucial for the protection of populations from inadvertent damage or destruction and for the discovery of new populations. The rapidly increasing development of Florida's natural habitats heightens concerns about species loss within the state. The label data and images in the University of Florida Herbarium collection catalog provide sufficient detail to assist citizens in recognizing endangered, threatened and invasive species and provide locally initiated government and NGO programs with good, reliable, research quality information. Herbarium specimens are fundamental research elements in plant systematics. Type specimens are crucial in nomenclatural work as plant names are tied to these specimens. The availability of data and images for specimens facilitates research and collaboration.