Abstract Abstract
Images are a critical part of the identification process because they enable direct, immediate and relatively unmediated comparisons between a specimen being identified and one or more reference specimens. The Carices Interactive Visual Identification Key (CIVIK) is a novel tool for identification of North American Carex species, the largest vascular plant genus in North America, and two less numerous closely-related genera, Cymophyllus and Kobresia. CIVIK incorporates 1288 high-resolution tiled image sets that allow users to zoom in to view minute structures that are crucial at times for identification in these genera. Morphological data are derived from the earlier Carex Interactive Identification Key (CIIK) which in turn used data from the Flora of North America treatments. In this new iteration, images can be viewed in a grid or histogram format, allowing multiple representations of data. In both formats the images are fully zoomable.
Keywords: Visual key, identification, Carex, Cymophyllus, Kobresia, interactive identification, sedges
Introduction
The last ten years may be remembered for the rebirth of plant taxonomy and systematics in a new guise, computational biodiversity informatics. For much of the earth, and North America in particular, botanical information that once required substantial effort to acquire is now reliably provided in seconds by such websites as the Global Biodiversity Information Facility (GBIF), Flora of North America, Missouri Botanical Garden's Tropicos, Encyclopedia of Life, United States Plants Database, and emerging regional herbarium networks. Plant biodiversity is now literally at everyone’s fingertips.
State of the art plant identification systems
Traditional biological identification systems today are of two primary types; analytic and gestalt (K. Thiele, pers. comm. 2013). Two forms of analytic keys commonly used today are dichotomous and interactive matrix-based keys. Both are primarily text-based question systems that can yield static images upon the final determination. Conversely, gestalt keys, use an identifiable image of the organism in question. Similar to what is seen in field guides.
Analytic matrix-based keys are considered to be state of the art today The University Of Queensland 2006 due to their ability to scale up across hundreds of taxa. To use, users select characters to achieve a determination of the unknown taxon using a four-panel informational interface. The information panels often represented are 'characters available', 'characters chosen', 'entities available', and entities discarded'. Within this format, it is possible to insert thumbnail-sized, static images to accompany the text if the taxa numbers are relatively small (< 100). But when taxa numbers are higher (>100), their inclusion results in the information panel becoming too long to be usable, e.g. the Carices used here would require copious scrolling across its many meters of length.
Visual keys borrow from both gestalt and analytic methods. They use character matrices for initial pruning of the image set analytically. After a few characters choices the many hundreds of small images are reduced to a manageable set of bigger images. Now gestalt methods take over as the images become larger and truly informative. With this hybrid of functionality, featuring the best of both gestalt and analysis, a novel identification method is created that can cater to the neophyte as well as the expert.
Carex, Kobresia, and Cymophyllous: a model for scalability
Carex is the largest vascular plant genus in North America (Ball and Reznicek 2002). With two closely related genera, Kobresia and Cymophyllus, it forms the Carices of North America; all three are members of the family Cyperaceae, commonly called sedges but often erroneously referred to as grasses. These three genera share a number of basic morphological characteristics including having linear leaves and a fruit enclosed in a bag-like structure called a perigynium. All have small flowers that lack large, colorful petals and sepals. Plus they share one other important characteristic: they are difficult to identify. Nevertheless, they are morphologically distinct and relatively easily recognizable as a group.
The new visual key
The data used in this project are primarily derived from an interactive identification program to Carex that has been online since 2006 at both Utah State University and Louisiana State University (http://www.herbarium.lsu.edu/keys/carex/carex.html). During this time it has been consistently revised and is currently in version 21. (Suppl. materials 3, 4). Web statistics have been tracked from 2007. Data show that numerous individuals worldwide, government agencies, students in classrooms, and participants in identification workshops have repeatedly used the keys. Many users have graciously suggested revisions and clarifications that have increased their usability and performance. The key presented here reflects contributions from several individuals, innumerable field trips, and countless hours in herbaria both identifying and imaging specimens. It is only with such collaboration and effort that an image key to such a large genus can be created.
Goals
My goal in this project was to create an easy to use identification resource that maximized the value of high resolution images while enabling users to explore the distribution of morphological diversity within the genera. Query-able images. For example, to answer questions such as: how are species with trigonous achenes geographically distributed across Canada by province or territory? How common are species with two-sided achenes in species with leaf blades more than 10 mm wide? These sorts of hypotheses are easily answered in histogram mode Fig. 4. Because for the first time, side-by-side image comparisons are possible across species permitting comparative examination and discrimination among closely-related members of any complex, of which there are many, within the Carices. CIVIK is seen here: http://www.herbarium2.lsu.edu/aba/
Figure 4.
An Interactive Visual Identification Key to Carices of North America beta version.
Development of visual identification tool
Study area description
This key is designed for use in North America, including Mexico. The original descriptive data was derived from Flora of North America (Ball and Reznicek 2002) and (Mackenzie 1940). My images come from fieldwork focused in eastern North America while other individuals have contributed images from other locations across North America.
Design description
1. IMAGES
1.1. Contributors
Steve Matson and Tony Reznicek both sent a DVD copy of their Carex field images. Lowell Urbatsch contributed his teaching-microscopy-images (http://www.herbarium.lsu.edu/keys/eee/b52.html). My images were collected from many field sites primarily in the north-eastern United States. The New York Botanical Garden Press granted the use of the plates of both North American Cariceae volumes (Mackenzie 1940). The remaining images were found on the World Wide Web (WWW) and their owners (Forest Starr, Kim Starr, Nhy Nyugen, Ann Debolt) contacted by email to request permission for their use. The remaining image contributor, Robert Mohlenbrock, had made the image used here available on http://www.plants.usda.gov/ so it could be used without seeking permission.
1.2. Processing of images
To manage the large image numbers (e.g., Matson hundreds of images; Jones, many thousands), each set of images from each owner was segregated on a local drive. Predictably, across this many image contributors, naming conventions differed greatly, thus significant renaming of image files was required. The basic convention used was to include the taxon name, type of image, and the author in the file name. Another issue of note was the fact that many of these images had been prepared for delivery via the WWW, and had been re-sized. Larger file sizes were selected for inclusion while those that were originally designed as thumbnails were not used. Rarely, older images that were scanned from slides were either cropped or otherwise manipulated with Photoshop CS 3. Lastly, rotation of images for appropriate orientation was also often required.
1.2.1 Image sizes
Image sizes are variable and range from 40 K to over 13 MB. Line drawings and most images by Jones are at 2848 × 4288 with a maximal bit depth of 24. Matson's images were more variable as some images had been prepared for web use. They range from 2592 × 3888 to 550 × 689 with variable bit depths. Other contributed images are of intermediate sizes.
1.3. Imaging of Mackenzie's plates
New York Botanical Garden Press gave permission to image the plates in K. K. Mackenzie's two volume treatment of Carices of North America (Mackenzie 1940) for use in this project. All plates were imaged with a traditional copy stand, using a Nikon 300D camera with a 1:1 macro lens, and two halogen desk lamps for illumination using JPEG format. All images required batch-processing in Photoshop CS3 for color and a minor defect in skew. Additionally, to limit total file size of the project, the images were reduced to approximately one megabyte from three megabytes by resizing.
2. DATA FOR CXML CREATION
2.1. Primary data via export
The dataset was derived from an export of CIIK (http://www.herbarium.lsu.edu/keys/carex/carex.html) in comma separated values (CSV) from LUCID 3.4 Identification Software (The University Of Queensland 2006). These data were the template for the new secondary dataset (Fig. 1). The exported data were imported into Excel 2010 and the Excel PivotViewer plug-in generated the Commerce eXtensible Markup Language (CXML) version of the data (Suppl. material 1). This plugin has since been deprecated in favor of a command line tool, Pauthor (Microsoft 2010a, Microsoft 2010b).
Figure 1.
Workflow of project
2.2. Dependent software
.NET Framework (Microsoft 2007)
Visual Studio 2010 / 2012
Silverlight 4 Tools for Visual Studio 2010
Silverlight Software Development Kit (SDK)
Silverlight 4 Toolkit
PivotViewer SDK
2.3. Interface considerations in a micro-ontology
In Pivot Viewer with the Silverlight 4 format, the characters and states (C&S) are located in the searchable information pane on left, with the displayable information pane on right. This left pane is of a fixed width, lacking word-wrapping functions (Fig. 2). If all C&S information data mined were used, extensive scrolling would be required and thereby reduce the usability of the key. For this reason, long text strings in the C&S were edited for brevity. A 'less is more' approach was taken, with C&S being restricted to those that would be appropriate in an ontology.
Figure 2.
The Visual Carices of North America upon instantiation in default grid setting.
2.4. Clustering issues in the graphical mode require a “normalization character state”
*Visual keys require a normalization character state; or the image numbers must be standardized for graphical display*
If image numbers between species are not consistent, a representative or semantic image is required. This leading image permits true one-to-one comparisons over any number of taxa. Without it, accurate representations of the data would be obscured due to clustering. For this reason, only those taxa with a line drawing are presented here to allow for a one-to-one comparison across taxa. It was done early in development as a work-around to the differing number of images per taxon problem. Later unpublished works of this type deal with this issue in multiple ways (see 'Additional information').
To use this normalization feature, select ‘Image by’ at the base of the left information pane, then select ‘Mackenzie, K. K.’ from the information panel. Now, only grey scale images are used in a portrait format with an attention to the aspect ratio. All images are presented in the same fashion and uniformity in a grey scale that is easy to visually interpret. This ad-hoc commitment to Mackenzie's species list was done for this reason.
2.5. Data and images together
Images were added in small batches in a new Excel file. Character data were copy-pasted from the secondary spreadsheet to the third instance of Excel to form the final building file across multiple monitors.
2.6. Tertiary data
The completed third spreadsheet is now run using the 'New collection tool' by selecting its icon in the ribbon panel of Excel. It generates two primary products; image tiles in numerous folders and a CXML file (Suppl. material 1). The control leverages Deepzoom technology (Microsoft 2008) to create a deep zoom image library (DZI) and deep zoom collection files (DZC) like those seen on Google or Bing maps (Fig. 3). This geometric series of images supports the zoom-ability of images. As the user zooms in, things get geometrically resolved without the penalty associated with a large image download. As users pan through a collection, they can see only what they desire.
Figure 3.
Tiled image set illustrating the change in file size as well as number of images by creating a geometric series of images
2.6.1 Issues completing tertiary data for image tiles and CXML
Hardware and software issues were experienced at all stages. Testing revealed that while tiling a few hundred high resolution images with PivotViewer is manageable, using over a thousand high-resolution images made Excel unstable. Memory allocation as well as the processor spiking issues - limited development time and resulted in extended periods of waiting for test builds overnight or on a build across many days. The creation of the image tiles is best attempted with a state-of-the-art computer with a solid state drive. CIVIK total tile-set and cxml build-time was approximately 12 hours for the final presented build (Fig. 4).
3. Deployable image tiles sizes
The DZI files are nearly four gigabytes in file size and comprise over 250,000 image-tile files in over 18,000 folders with an associated CXML of 3.3 megabytes in size. A Silverlight application package (XAP) file is also required to drive the application.
4. Compile with Visual Studio
To compile with Visual Studio, open a new instance of a Silverlight application for the web in Visual Studio. Now add the references to PivotViewer on the main Extensible Application Markup Language (XAML) page in UserControl. Then add the URL to the CXML file to the XAML.CS code behind file. Then, build or compile the deployment package for placement on the server.
4.1 XAML and XAML.CS Code behind Files
See 'software technical features'
5. Deploy to web server
Ensure that the following Multipurpose Internet Mail Extensions (MIME) types are configured on server; significant development time was lost due to one of these settings not being in place.
• CXML - text/xml
• DZC - text/xml
• DZI - text/xml
6. History of Use
CIVIKhas been tracked via Google Analytics with the other later works of visual types. These combined works reveal that 13,933 visits occurred from 116 countries in 2464 cities over a three year period. An average dwell time of two minutes across the three works of type is seen here. (See Additional information and Suppl. material 6).
7. Considerations and discussion
While Silverlight is ideal for this data format, it will be deprecated (see http://support.microsoft.com/gp/lifean45) as no future versions are scheduled for release. It will, however, be supported for ten years which will aid future works of this kind. Thankfully, HTML 5 versions are also now available for PivotViewer that enable the CXML format across all devices in a device agnostic fashion. This cross platform capability is exciting as it does not require the Silverlight runtime, so phone and tablets are enabled as well with HTML 5. HTML 5 versions have one other important advantage - a Google translate function is easily added in minutes to over 70 languages (see http://translate.google.com/about/). Opening the door to future iterations of high-resolution images supported by text that is translatable.
Funding
SLouisiana State University
Geographic coverage
Description: The identification key can be used for species occurring in United States, Canada, and Mexico. Several species have a much wider distribution, hence the key has some value in other regions as well.
Coordinates: 90 and 15 Latitude; -180 and -45 Longitude.
Taxonomic coverage
| Scientific Name | Common Name | Rank |
|---|---|---|
| Carex | sedge | genus |
| Kobresia | sedge | genus |
| Cymophyllus | sedge | genus |
| Carex abrupta Mack. | abruptbeak sedge | species |
| Carex abscondita Mack. | thicket sedge | species |
| Carex adusta Boott | lesser brown sedge | species |
| Carex aestivalis M.A. Curtis ex A. Gray | summer sedge | species |
| Carex aggregata Mack. | glomerate sedge | species |
| Carex alata Torr. | broadwing sedge | species |
| Carex albicans Willd. ex Spreng. | whitetinge sedge | species |
| Carex albonigra Mack. | blackandwhite sedge | species |
| Carex albursina E. Sheld. | white bear sedge | species |
| Carex alligata Boott | Hawai'i sedge | species |
| Carex alma L.H. Bailey | sturdy sedge | species |
| Carex alopecoidea Tuck. | Foxtail sedge | species |
| Carex amphibola Steud. | eastern narrowleaf sedge | species |
| Carex amplectens Mack. | claspbract sedge | species |
| Carex amplifolia Boott | bigleaf sedge | species |
| Carex annectens (E.P. Bicknell) E.P. Bicknell | yellowfruit sedge | species |
| Carex anthoxanthea J. Presl & C. Presl | grassyslope arctic sedge | species |
| Carex aperta Boott | Columbian sedge | species |
| Carex aquatilis Wahlenb. | water sedge | species |
| Carex arapahoensis Clokey | Arapaho sedge | species |
| Carex arcta Boott | northern cluster sedge | species |
| Carex arctata Boott | drooping woodland sedge | species |
| Carex arenaria L. | sand sedge | species |
| Carex arkansana (L.H. Bailey) L.H. Bailey | Arkansas sedge | species |
| Carex assiniboinensis W. Boott | Assiniboia sedge | species |
| Carex atherodes Spreng. | wheat sedge | species |
| Carex athrostachya Olney | slenderbeak sedge | species |
| Carex atlantica L. H. Bailey | prickly bog sedge | species |
| Carex atrata L. | black scale sedge | species |
| Carex atratiformis Britton | scrabrous black sedge | species |
| Carex atrofusca Schkuhr | darkbrown sedge | species |
| Carex atrosquama Mack. | lesser blackscale sedge | species |
| Carex aurea Nutt. | golden sedge | species |
| Carex austrina Mack. | southern sedge | species |
| Carex austrocaroliniana L.H. Bailey | tarheel sedge | species |
| Carex aztecica Mack. | Aztec sedge | species |
| Carex backii Boott | Back's sedge | species |
| Carex baileyi Britton | Bailey's sedge | species |
| Carex baltzellii Chapm. | Baltzell's sedge | species |
| Carex barrattii Torr. ex Schwein. | Barratt's sedge | species |
| Carex bebbii (L. H. Bailey) Olney ex Fernald | Bebb's sedge | species |
| Carex bella L.H. Bailey | southwestern showy sedge | species |
| Carex bicknellii Britton & A.Br. | Bicknell's sedge | species |
| Carex bicolor Bellardi ex All. | two-color sedge | species |
| Carex bigelowii Torr. ex Schwein. | Bigelow's sedge | species |
| Carex biltmoreana Mack. | stiff sedge | species |
| Carex blanda Dewey | eastern woodland sedge | species |
| Carex bolanderi Olney | Bolander's sedge | species |
| Carex boliviensis Van Heurck & Müll. Arg. | Bolivian sedge | species |
| Carex breweri Boott | Brewer's sedge | species |
| Carex brizoides L. | species | |
| Carex bromoides Willd. | brome-like sedge | species |
| Carex brunnescens (Pers.) Poir. | brownish sedge | species |
| Carex bullata Willd. | button sedge | species |
| Carex bushii Mack. | Bush's sedge | species |
| Carex buxbaumii Wahlenb. | Buxbaum's sedge | species |
| Carex californica L.H. Bailey | California sedge | species |
| Carex canescens L. | silvery sedge | species |
| Carex capillaris L. | hair-like sedge | species |
| Carex capitata Sol. | capitate sedge | species |
| Carex careyana Torr. ex Dewey | Carey's sedge | species |
| Carex caroliniana Schwein. | Carolina sedge | species |
| Carex caryophyllea Latourr. | vernal sedge | species |
| Carex castanea Wahlenb. | chestnut sedge | species |
| Carex cephaloidea (Dewey) Dewey ex Boott | thinleaf sedge | species |
| Carex cephalophora Muhl. ex Willd. | oval-leaf sedge | species |
| Carex cherokeensis Schwein. | Cherokee sedge | species |
| Carex chihuahuensis Mack. | Chihuahuan sedge | species |
| Carex chordorrhiza L. | creeping sedge | species |
| Carex circinnata C.A.Mey. | coiled sedge | species |
| Carex collinsii Nutt. | Collins' sedge | species |
| Carex communis L.H. Bailey | fibrousroot sedge | species |
| Carex comosa Boott | longhair sedge | species |
| Carex complanata Torr. & Hook. | hirsute sedge | species |
| Carex concinna R. Br. | low northern sedge | species |
| Carex concinnoides Mack. | northwestern sedge | species |
| Carex conjuncta Boott | soft fox sedge | species |
| Carex conoidea Willd. | openfield sedge | species |
| Carex crawei Dewey ex Torr. | Crawe's sedge | species |
| Carex crawfordii Fernald | Craweford's sedge | species |
| Carex crebriflora Wiegand | coastal plain sedge | species |
| Carex crinita Lam. | fringed sedge | species |
| Carex cristatella Britton & A.Br. | crested sedge | species |
| Carex crus-corvi Shuttlew. ex Kunze | ravenfoot sedge | species |
| Carex cryptolepis Mack. | northeastern sedge | species |
| Carex cumulata (L.H. Bailey) Mack. | clustered sedge | species |
| Carex cusickii Mack. | Cusick's sedge | species |
| Carex dasycarpa Muhl. | sandywoods sedge | species |
| Carex davisii Schwein. & Torr. | Davis' sedge | species |
| Carex davyi Mack. | Davy's sedge | species |
| Carex debilis Michx. | white edge sedge | species |
| Carex decomposita Muhl. | cypressknee sedge | species |
| Carex deflexa Hornem. | northern sedge | species |
| Carex densa (L.H. Bailey) L.H. Bailey | dense sedge | species |
| Carex deweyana Schwein. | Dewey's sedge | species |
| Carex diandra Schrank | lesser panicled sedge | species |
| Carex digitalis Willd. | slender woodland sedge | species |
| Carex donnell-smithii L.H. Bailey | Donell's sedge | species |
| Carex douglasii Boott | Douglas' sedge | species |
| Carex ebenea Rydb. | ebony sedge | species |
| Carex eburnea Boott | bristleleaf sedge | species |
| Carex egglestonii Mack. | Eggleston's sedge | species |
| Carex elliottii Schwein. & Torr. | Elliott's sedge | species |
| Carex elynoides Holm | blackroot sedge | species |
| Carex emoryi Dewey | Emory's sedge | species |
| Carex engelmannii L.H. Bailey | Engelmann's sedge | species |
| Carex exilis Dewey | coastal sedge | species |
| Carex exsiccata L.H. Bailey | western inflated sedge | species |
| Carex festucacea Schkuhr ex Willd. | fescue sedge | species |
| Carex feta L. H. Bailey | greensheath sedge | species |
| Carex filifolia Nutt. | threadleaf sedge | species |
| Carex fissa Mack. | hammock sedge | species |
| Carex flacca Schreb. | heath sedge | species |
| Carex flaccosperma Dewey | thinfruit sedge | species |
| Carex flava L. | yellow sedge | species |
| Carex floridana Schwein. | Florida sedge | species |
| Carex foenea Willd. | dry-spike sedge | species |
| Carex folliculata L. | norther long sedge | species |
| Carex formosa Dewey | handsome sedge | species |
| Carex fracta Mack. | fragile sheath sedge | species |
| Carex frankii Kunth | Frank's sedge | species |
| Carex garberi Fernald | elk sedge | species |
| Carex geophila Mack. | White Mountain sedge | species |
| Carex geyeri Boott | Geyer's sedge | species |
| Carex gigantea Rudge | giant sedge | species |
| Carex glacialis Mack. | glacial sedge | species |
| Carex glareosa Schkuhr ex Wahlenb. | lesser salt marsh sedge | species |
| Carex glaucescens Elliott | southern waxy sedge | species |
| Carex glaucodea Tuck. ex Olney | blue sedge | species |
| Carex globosa Boott | roundfruit sedge | species |
| Carex gmelinii Hook. & Arn. | Gmelin's sedge | species |
| Carex gracillima Schwein. | graceful sedge | species |
| Carex granularis Muhl. ex Willd. | limestone meadow sedge | species |
| Carex gravida L.H. Bailey | heavy sedge | species |
| Carex grayi J. Carey | Gray's sedge | species |
| Carex grisea Wahlenb. | inflated narrow-leaf sedge | species |
| Carex gynandra Schwein. | nodding sedge | species |
| Carex gynocrates Wormsk. | northern bog sedge | species |
| Carex gynodynama Olney | Olney's hairy sedge | species |
| Carex halliana L.H. Bailey | Hall's sedge | species |
| Carex hallii Olney | deer sedge | species |
| Carex harfordii Mack. | Harford's sedge | species |
| Carex hassei L.H. Bailey | salt sedge | species |
| Carex haydenii Dewey | Hayden's sedge | species |
| Carex helleri Mack. | Heller's sedge | species |
| Carex hendersonii L. H. Bailey | Henderson's sedge | species |
| Carex heteroneura S.Watson | different-nerve sedge | species |
| Carex hirsutella Mack. | fuzzy sedge | species |
| Carex hirta L. | hammer sedge | species |
| Carex hirtifolia Mack. | pubescent sedge | species |
| Carex hirtissima W. Boott | fuzzy sedge | species |
| Carex hitchcockiana Dewey | Hitchcock's sedge | species |
| Carex holostoma Drejer | arctic marsh sedge | species |
| Carex hoodii Boott | Hood's sedge | species |
| Carex hookeriana Dewey | Hooker's sedge | species |
| Carex hormathodes Fernald | marsh straw sedge | species |
| Carex houghtoniana Torr. ex Dewey | Houghton's sedge | species |
| Carex hyalina Boott | tissue sedge | species |
| Carex hyalinolepis Steud | shoreline sedge | species |
| Carex hystericina Muhl. ex Willd. | bottlebrush sedge | species |
| Carex idahoa L. H. Bailey | Idaho sedge | species |
| Carex illota L. H. Bailey | sheep sedge | species |
| Carex incurviformis Mack. | coastal sand sedge | species |
| Carex inops L. H. Bailey | long-stolon sedge | species |
| Carex integra Mack. | smoothbeak sedge | species |
| Carex interior L. H. Bailey | inland sedge | species |
| Carex interrupta Boeckeler | greenfruit sedge | species |
| Carex intumescens Rudge | greater bladder sedge | species |
| Carex jamesii Schwein. | James' sedge | species |
| Carex jonesii L.H. Bailey | Jones' sedge | species |
| Carex joorii L.H. Bailey | cypress swamp sedge | species |
| Carex lacustris Willd. | hairy sedge? (lake sedge) | species |
| Carex laeviculmis Meinsh. | smoothstem sedge | species |
| Carex laxiculmis Schwein. | spreading sedge | species |
| Carex laxiflora Lam. | broad looseflower sedge | species |
| Carex leavenworthii Dewey | Leavenworth's sedge | species |
| Carex lemmonii W. Boott | Lemmon's sedge | species |
| Carex lenticularis Michx. | lakeshore sedge | species |
| Carex leporinella Mack. | Sierra hare sedge | species |
| Carex leptalea Wahlenb. | bristlystalked sedge | species |
| Carex leptonervia (Fernald) Fernald | nerveless woodland sedge | species |
| Carex limosa L. | mud sedge | species |
| Carex livida (Wahlenb.) Willd. | livid sedge | species |
| Carex loliacea L. | ryegrass sedge | species |
| Carex lonchocarpa Willd. ex Spreng. | southern long sedge | species |
| Carex longii Mack. | Long's sedge | species |
| Carex louisianica L. H. Bailey | Louisiana sedge | species |
| Carex lucorum Willd. | Blue Ridge sedge | species |
| Carex lupuliformis Sartwell ex Dewey | false hop sedge | species |
| Carex lupulina Muhl. ex Willd. | hop sedge | species |
| Carex lurida Wahlenb. | shallow sedge | species |
| Carex luzulina Olney | woodrush sedge | species |
| Carex lyngbyei Hornem. | Lyngbye's sedge | species |
| Carex macloviana d'Urv. | thickhead sedge | species |
| Carex macrocephala Willd. ex Spreng. | largehead sedge | species |
| Carex macrochaeta C. A. Mey. | longawn sedge | species |
| Carex marina Dewey | sea sedge | species |
| Carex mariposana L.H. Bailey ex Mack. | Mariposa sedge | species |
| Carex meadii Dewey | Mead's sedge | species |
| Carex membranacea Hook. | fragile sedge | species |
| Carex merritt-fernaldii Mack. | Fernald's sedge | species |
| Carex mertensii Prescott ex Bong. | Mertens' sedge | species |
| Carex michauxiana Boeckeler | Michaux's sedge | species |
| Carex microdonta Torr. | littletooth sedge | species |
| Carex microglochin Wahlenb. | fewseeded bog sedge | species |
| Carex micropoda C. A. Mey. | species | |
| Carex microptera Mack. | small wing sedge | species |
| Carex misera Buckley | wretched sedge | species |
| Carex mitchelliana M. A. Curtis | Mitchell's sedge | species |
| Carex molesta Mack. | troublesome sedge | species |
| Carex muehlenbergii Willd. | Muehlenberg's sedge | species |
| Carex multicaulis L.H. Bailey | manystem sedge | species |
| Carex multicostata Mack. | manyrib sedge | species |
| Carex muricata L. | rough sedge | species |
| Carex muskingumensis Schwein. | Muskingum sedge | species |
| Carex nebraskensis Dewey | Nebraska sedge | species |
| Carex nervina L.H. Bailey | Sierra sedge | species |
| Carex neurophora Mack. | alpine nerve sedge | species |
| Carex nigromarginata Schwein. | black edge sedge | species |
| Carex normalis Mack. | greater straw sedge | species |
| Carex norvegica Retz. | Norway sedge | species |
| Carex nudata W. Boott | naked sedge | species |
| Carex obnupta L. H. Bailey | slough sedge | species |
| Carex obtusata Lilj. | obtuse sedge | species |
| Carex occidentalis L. H. Bailey | western sedge | species |
| Carex oligosperma Michx. | fewseed sedge | species |
| Carex oreocharis Holm | grassyslope sedge | species |
| Carex ormostachya Wiegand | necklace spike sedge | species |
| Carex oxylepis Torr. & Hook. | sharpscale sedge | species |
| Carex paleacea Schreb. ex Wahlenb. | chaffy sedge | species |
| Carex pallescens L. | pale sedge | species |
| Carex panicea L. | grass-like sedge | species |
| Carex pansa L.H. Bailey | Payson's sedge | species |
| Carex pauciflora Lightf. | fewflower sedge | species |
| Carex peckii Howe | Peck's sedge | species |
| Carex pedunculata Muhl. ex Willd. | longstalk sedge | species |
| Carex pellita Muhl ex Willd. | wooly sedge | species |
| Carex pensylvanica Lam. | Pensylvania sedge | species |
| Carex perglobosa Mack. | globe sedge | species |
| Carex petricosa Dewey | rockdwelling sedge | species |
| Carex phaeocephala Piper | dunhead sedge | species |
| Carex picta Steud. | Boott's sedge | species |
| Carex pityophila Mack. | loving sedge | species |
| Carex planostachys Kunze | cedar sedge | species |
| Carex plantaginea Lam. | plantainleaf sedge | species |
| Carex platyphylla J. Carey | broadleaf sedge | species |
| Carex podocarpa R. Br. | shortstalk sedge | species |
| Carex polystachya Sw. ex Wahlenb. | Caribbean sedge | species |
| Carex praeceptorium Mack. | early sedge | species |
| Carex praegracilis W. Boott | clustered field sedge | species |
| Carex prairea Dewey ex Alph.Wood | prairie sedge | species |
| Carex prasina Wahlenb. | drooping sedge | species |
| Carex praticola Rydb. | meadow sedge | species |
| Carex preslii Steud. | Presl's sedge | species |
| Carex projecta Mack. | necklace sedge | species |
| Carex proposita Mack. | Great Smoky Mountain sedge | species |
| Carex pseudocyperus L. | cypress-like sedge | species |
| Carex purpurifera Mack. | purple sedge | species |
| Carex radiata (Wahlenb.) Small | eastern star sedge | species |
| Carex rariflora (Wahlenb.) Sm. | looseflower alpine sedge | species |
| Carex raynoldsii Dewey | Raynolds' sedge | species |
| Carex recta Boott | estuary sedge | species |
| Carex reniformis (L.H. Bailey) Small | kidneyshape sedge | species |
| Carex retroflexa Muhl. ex Willd. | reflexed sedge | species |
| Carex rosea Willd. | rosy sedge | species |
| Carex rossii Boott | Ross' sedge | species |
| Carex rostrata Stokes | beaked sedge | species |
| Carex rufina Drejer | snowbed sedge | species |
| Carex rupestris All. | curly sedge | species |
| Carex sartwellii Dewey | Sartwell's sedge | species |
| Carex saxatilis L. | rock sedge | species |
| Carex scabrata Schwein. | eastern rough sedge | species |
| Carex scabriuscula Mack. | Siskiyou sedge | species |
| Carex schweinitzii Dewey ex Schwein. | Schweinitz's sedge | species |
| Carex scirpoidea Michx. | northern singlespike sedge | species |
| Carex scoparia Willd. | broom sedge | species |
| Carex scopulorum Holm | mountain sedge | species |
| Carex senta Boott | swamp carex | species |
| Carex seorsa Howe | weak stellate sedge | species |
| Carex shortiana Dewey & Torr. | Short's sedge | species |
| Carex simulata Mack. | analogue sedge | species |
| Carex socialis Mohlenbr. & Schwegman | low woodland sedge | species |
| Carex sparganioides Muhl. ex Willd. | bur-reed sedge | species |
| Carex specifica L.H. Bailey | narrowfruit sedge | species |
| Carex spectabilis Dewey | showy sedge | species |
| Carex spicata Huds. | prickly sedge | species |
| Carex spissa L.H.Bailey ex Hemsl. | San Diego sedge | species |
| Carex sprengelii Dewey ex Spreng. | Sprengel's sedge | species |
| Carex squarrosa L. | squarrose sedge | species |
| Carex sterilis Willd. | dioecious sedge | species |
| Carex stipata Muhl. ex Willd. | awlfruit sedge | species |
| Carex straminea Willd. ex Schkuhr | straw sedge | species |
| Carex striata Michx. | Walter's sedge | species |
| Carex striatula Michx. | lined sedge | species |
| Carex stricta Lam. | upright sedge | species |
| Carex styloflexa Buckley | bent sedge | species |
| Carex stylosa C. A. Mey. | variegated sedge | species |
| Carex subbracteata Mack. | smallbract sedge | species |
| Carex supina Willd. ex Wahlenb. | weak arctic sedge | species |
| Carex swanii (Fernald) Mack. | Swan's sedge | species |
| Carex sylvatica Huds. | European woodland sedge | species |
| Carex tenera Dewey | quill sedge | species |
| Carex tetanica Schkuhr | rigid sedge | species |
| Carex torreyi Tuck. | Torrey's sedge | species |
| Carex tribuloides Wahlenb. | blunt broom sedge | species |
| Carex tuckermanii Boott | Tuckerman's sedge | species |
| Carex turgescens Torr. | pine barren sedge | species |
| Carex typhina Michx. | cattail sedge | species |
| Carex umbellata Willd. | parasol sedge | species |
| Carex verrucosa Muhl. | warty sedge | species |
| Carex vesicaria L. | blister sedge | species |
| Carex viridula Michx. | little green sedge | species |
| Carex vulpina L. | true-fox sedge | species |
| Carex vulpinoidea Michx. | fox sedge | species |
| Carex willdenowii Willd. | Willdenow's sedge | species |
| Carex woodii Dewey | Wood's sedge | species |
| Carex xerantica L.H. Bailey | whitescale sedge | species |
| Cymophyllus fraseri (Ker Gawl.) Kartesz & Gandhi | Fraser's cymophyllous | species |
| Kobresia simpliciuscula (Wahlenb.) Mack. | simple bog sedge | species |
Usage rights
Use license
Open Data Commons Attribution License
Characters used in the key
Species
Country
U.S. state
Canadian province or territory
Section within Carex
Culm height
Blade width
Inflorescence type
Proximal spike sexuality
Terminal spike sexuality
Stigma branch number
Perigynium length
Perigynium width
Perigynium cross-section shape
Achene length
Achene width
Achene cross-section shape
Style: whether deciduous or persistent
Image author
Image type
Software specification
Name
Carices Interactive Visual Identification Key
Version
1.1
Interface language
English
Platform
Silverlight runtime
Web location
Software technical features
Main XAML page
<UserControl x:Class="A5.MainPage"
xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
xmlns:d="http://schemas.microsoft.com/expression/blend/2008"
xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006"
xmlns:local="clr-namespace:System.Windows.Pivot;assembly=System.Windows.Pivot"
mc:Ignorable="d" d:DesignHeight="300" d:DesignWidth="400" Loaded="UserControl_Loaded">
<Grid x:Name="LayoutRoot" Background="Black">
<local:PivotViewer x:Name="Pivot"/>
</Grid>
</UserControl>
XAML.CS or Code behind
using System;
using System.Collections.Generic;
using System.Linq;
using System.Net;
using System.Windows;
using System.Windows.Controls;
using System.Windows.Documents;
using System.Windows.Input;
using System.Windows.Media;
using System.Windows.Media.Animation;
using System.Windows.Shapes;
using System.Windows.Pivot;
namespace A10
{
public partial class MainPage: UserControl
{
public MainPage()
{
InitializeComponent();
Pivot.LoadCollection("http://www.herbarium2.lsu.edu/aba/A10.cxml", string.Empty);
}
private void UserControl_Loaded(object sender, RoutedEventArgs e)
{
}
}
}
Additional information
Later examples of visual keys deal with the clustering problem differently. Both Silverlight and HTML 5 based grass genera of Louisiana keys use existing herbarium specimen images to normalize, one herbarium specimen per taxon. Leveraging recent physical and vetted sources. This normalization character is select-able as 'one-to-one comparisons' at the bottom of character information panel http://www.herbarium2.lsu.edu/grass2/. Secondly, Kingdom Plantae in HTML 5 is normalized by image number only, without a selectable character state, across divisions http://www.herbarium2.lsu.edu/aca/. Magnoliophyta is taken at a log value due to its disparate taxa value when compared to the other divisions.
Acknowledgements
The author sincerely appreciates the ground-breaking work completed by others before this project even began. Without these prior efforts, this current project could not have been completed in this same time-frame. A sincere thank you to all the editors of Flora of North America, Volume 23, and the image contributors. To G. Wilder, J. Bissell, M. Barkworth, A. Reznicek, K. Niklas, and my Ph.D. advisor, L. Urbatsch, thank you for sharing your wisdom and support. Also, I wish to thank W. Thomas and K. Thiele, for editorial commentary provided for this manuscript.
Supplementary files
Tertiary file structure for Carices CXML file
Authors: Jones, T. M.
Data type: occurences, morphological,
File: A10.cxml
Secondary Carex morphology data; cleaned and truncated for building CXML
Authors: Jones, T. M.
Data type: occurrences, morphological, images
This file is an example of a build file for the creation of the CXML file.
File: 957am fixed scirpoidea space issue.xlsx
Website data from Utah State University
Authors: Google Analytics
Data type: PDF
Data sheet for visitiation to CIIK by country
File: Analytics utc.usu.edu_keys_Carex_Carex.html Location 20060531-20130630.pdf
Website data from Louisiana State University
Authors: Google Analytics
Data type: PDF
Data sheet for visitiation to CIIK by country
File: Analytics Carex key LSU Location 20060531-20130630.pdf
Primary Carex morphology data from Lucid 3.4
Authors: Jones, T. M.
Data type: XLSX
Export from CIIK 2013 in CSV format
File: Carex-all-CSV.xlsx
CIVIK usage 2011 - 2013
Authors: Google Analytics
Data type: PDF
This includes all visual keys developed. Here CIVIK is represented by both /aba/ and /aaa/ and iteratives.
File: Analytics www.herbarium2.lsu.edu_aaa_A5TestPage.html Pages 20100531-20130630.pdf
Visual keys usage with Google Analytics
Authors: Google
Data type: analytics
Compilation of all visual keys using Google Analytics
File: Analytics www.herbarium2.lsu.edu-aaa-A5TestPage.html Language 20100809-20130908.pdf
Author contributions
Jones developed the project, and contacted the other contibutors for images. S. Matson and T. Reznicek both mailed a DVD copy of their Carex field images. L. Urbatsch's teaching-microscopy-images were copied and saved to USB thumbdrives. New York Botanical Garden Press permitted the use of the images of both North American Cariceae volumes by Mackenzie, K.K. Remaining image owners were found on the WWW and contacted by email. Thankfully, they granted permission for usage, including; F. Starr & K. Starr, N. Nyugen, and A. Debolt. R. Mohlenbrock's image was gathered from Plants.gov.
References
- Ball P. W., Reznicek A. A. Vol. 23. Oxford University Press; New York: 2002. Flora of North America. Magnoliophyta: Commelinidae (in part); Cyperaceae. Vol. 23.608. [in English] [Google Scholar]
- Mackenzie K. K. 1 & 2. New York Botanical Garden Press; New York: 1940. North American Cariceae.539 [Google Scholar]
- Microsoft . Microsoft; 2007. [2007-11-20T00:00:00+02:00]. .NET Framework. Version: 3.5. [Google Scholar]
- Microsoft . Microsoft; 2008. [2008-10-13T00:00:00+03:00]. Deep Zoom. Version: 0.9.000.5. [Google Scholar]
- Microsoft . Microsoft; 2010. [2010-08-09T00:00:00+03:00]. Microsoft Silverlight PivotViewer. [Google Scholar]
- Microsoft . Microsoft; 2010. [2010-07-13T00:00:00+03:00]. Pivot Collection Tool for the Command Line. Version: 1.2. [Google Scholar]
- Queensland The University Of. Lucid Software 3.4. http://www.lucidcentral.com/ 2006
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Authors: Jones, T. M.
Data type: occurences, morphological,
File: A10.cxml
Authors: Jones, T. M.
Data type: occurrences, morphological, images
This file is an example of a build file for the creation of the CXML file.
File: 957am fixed scirpoidea space issue.xlsx
Authors: Google Analytics
Data type: PDF
Data sheet for visitiation to CIIK by country
File: Analytics utc.usu.edu_keys_Carex_Carex.html Location 20060531-20130630.pdf
Authors: Google Analytics
Data type: PDF
Data sheet for visitiation to CIIK by country
File: Analytics Carex key LSU Location 20060531-20130630.pdf
Authors: Jones, T. M.
Data type: XLSX
Export from CIIK 2013 in CSV format
File: Carex-all-CSV.xlsx
Authors: Google Analytics
Data type: PDF
This includes all visual keys developed. Here CIVIK is represented by both /aba/ and /aaa/ and iteratives.
File: Analytics www.herbarium2.lsu.edu_aaa_A5TestPage.html Pages 20100531-20130630.pdf
Authors: Google
Data type: analytics
Compilation of all visual keys using Google Analytics
File: Analytics www.herbarium2.lsu.edu-aaa-A5TestPage.html Language 20100809-20130908.pdf