Biodiversity Data Journal 1: e984 OO)
doi: 10.3897/BDJ.1.e984

open access

Interactive key

A visual identification key utilizing both gestalt
and analytic approaches to identification of
Carices present in North America (Plantae,
Cyperaceae)

Timothy Mark Jones T

t+ Louisiana State University, Baton Rouge, United States of America

Corresponding author: Timothy Mark Jones (tione54@tigers.Isu.edu)
Academic editor: Thomas Couvreur
Received: 07 Aug 2013 | Accepted: 13 Sep 2013 | Published: 16 Sep 2013

Citation: Jones T (2013) A visual identification key utilizing both gestalt and analytic approaches to identification
of Carices present in North America (Plantae, Cyperaceae). Biodiversity Data Journal 1: e984. doi: 10.3897/
BDJ.1.e984

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

© Jones T. This is an open access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC-BY), which
permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

2 Jones T

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-

A visual identification key utilizing both gestalt and analytic approaches t ... 3

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.|su.edu/aba/

Project description

Title: 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.

4 Jones T

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.|su.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 hitp://
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 x 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 x
3888 to 550 x 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.

A visual identification key utilizing both gestalt and analytic approaches t ... 5

2. DATA FOR CXML CREATION
2.1. Primary data via export

The dataset was derived from an export of CIIK (http:/Awww.herbarium.|su.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).

Images for gestalt Data for analytic Combined

‘ fiir
to pare
internal data External data Precere Herage farvar r

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

6 Jones T

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.

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Pie =— ¥ ORGE =f Sn ee ee ee

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tne BY’ FEOR 18 Neh ofr eengy Fae ee eof adie d oe f =
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ce] + ae BoB oe Ne 6 = |) a ge a oman

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<n ee Gk Ban sD ie
rare wa DE-Q0ecfewe=s = ffi =sefRRE= ~ — 270 see§ oe oo
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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.

A visual identification key utilizing both gestalt and analytic approaches t ... 7

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.

256 pixels
SS aoe

512 pixels

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 CKML

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).

8 Jones T

Figure 4.

An Interactive Visual Identification Key to Carices of North America beta version.

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

A visual identification key utilizing both gestalt and analytic approaches t ... 9

6. History of Use

ClViKhas 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 hitip://
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 hittp://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

Taxa included:

Rank Scientific Name Common Name
genus Carex sedge

genus Kobresia sedge

genus Cymophyllus sedge

species 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

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Carex albicans Willd. ex Spreng.
Carex albonigra Mack.

Carex albursina E. Sheld.

Carex alligata Boott

Carex alma L.H. Bailey

Carex alopecoidea Tuck.

Carex amphibola Steud.

Carex amplectens Mack.

Carex amplifolia Boott

Carex annectens (E.P. Bicknell) E.P. Bicknell

Carex anthoxanthea J. Presl & C. Presl
Carex aperta Boott

Carex aquatilis Wahlenb.

Carex arapahoensis Clokey

Carex arcta Boott

Carex arctata Boott

Carex arenaria L.

Carex arkansana (L.H. Bailey) L.H. Bailey
Carex assiniboinensis W. Boott
Carex atherodes Spreng.

Carex athrostachya Olney

Carex atlantica L. H. Bailey

Carex atrata L.

Carex atratiformis Britton

Carex atrofusca Schkuhr

Carex atrosquama Mack.

Carex aurea Nutt.

Carex austrina Mack.

Carex austrocaroliniana L.H. Bailey
Carex aztecica Mack.

Carex backii Boott

Carex baileyi Britton

Carex baltzellii Chapm.

Carex barrattii Torr. ex Schwein.

Carex bebbii (L. H. Bailey) Olney ex Fernald

Carex bella L.H. Bailey

Carex bicknellii Britton & A.Br.
Carex bicolor Bellardi ex All.
Carex bigelowii Torr. ex Schwein.
Carex biltmoreana Mack.

Carex blanda Dewey

Carex bolanderi Olney

Carex boliviensis Van Heurck & Mull. Arg.

whitetinge sedge
blackandwhite sedge
white bear sedge
Hawai'i sedge

sturdy sedge

Foxtail sedge

eastern narrowleaf sedge
claspbract sedge

bigleaf sedge

yellowfruit sedge
grassyslope arctic sedge
Columbian sedge

water sedge

Arapaho sedge

northern cluster sedge
drooping woodland sedge
sand sedge

Arkansas sedge
Assiniboia sedge

wheat sedge
slenderbeak sedge
prickly bog sedge

black scale sedge
scrabrous black sedge
darkbrown sedge

lesser blackscale sedge
golden sedge

southern sedge

tarheel sedge

Aztec sedge

Back's sedge

Bailey's sedge

Baltzell's sedge

Barratt's sedge

Bebb's sedge
southwestern showy sedge
Bicknell's sedge
two-color sedge
Bigelow's sedge

stiff sedge

eastern woodland sedge
Bolander's sedge

Bolivian sedge

species
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Carex breweri Boott

Carex brizoides L.

Carex bromoides Willd.

Carex brunnescens (Pers.) Poir.
Carex bullata Willd.

Carex bushii Mack.

Carex buxbaumii Wahlenb.
Carex californica L.H. Bailey
Carex canescens L.

Carex capillaris L.

Carex capitata Sol.

Carex careyana Torr. ex Dewey
Carex caroliniana Schwein.
Carex caryophyllea Latourr.
Carex castanea Wahlenb.
Carex cephaloidea (Dewey) Dewey ex Boott
Carex cephalophora Muhl. ex Willd.
Carex cherokeensis Schwein.
Carex chihuahuensis Mack.
Carex chordorrhiza L.

Carex circinnata C.A.Mey.
Carex collinsii Nutt.

Carex communis L.H. Bailey
Carex comosa Boott

Carex complanata Torr. & Hook.
Carex concinna R. Br.

Carex concinnoides Mack.
Carex conjuncta Boott

Carex conoidea Willd.

Carex crawei Dewey ex Torr.
Carex crawfordii Fernald

Carex crebriflora Wiegand
Carex crinita Lam.

Carex cristatella Britton & A.Br.
Carex crus-corvi Shuttlew. ex Kunze
Carex cryptolepis Mack.

Carex cumulata (L.H. Bailey) Mack.
Carex cusickii Mack.

Carex dasycarpa Muhl.

Carex davisii Schwein. & Torr.
Carex davyi Mack.

Carex debilis Michx.

Carex decomposita Muhl.

Brewer's sedge

brome-like sedge
brownish sedge
button sedge
Bush's sedge
Buxbaum's sedge
California sedge
silvery sedge
hair-like sedge
capitate sedge
Carey's sedge
Carolina sedge
vernal sedge
chestnut sedge
thinleaf sedge
oval-leaf sedge
Cherokee sedge
Chihuahuan sedge
creeping sedge
coiled sedge
Collins' sedge
fibrousroot sedge
longhair sedge
hirsute sedge

low northern sedge
northwestern sedge
soft fox sedge
openfield sedge
Crawe's sedge
Craweford's sedge
coastal plain sedge
fringed sedge
crested sedge
ravenfoot sedge
northeastern sedge
clustered sedge
Cusick's sedge
sandywoods sedge
Davis' sedge
Davy's sedge
white edge sedge

cypressknee sedge

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Carex deflexa Hornem.

Carex densa (L.H. Bailey) L.H. Bailey
Carex deweyana Schwein.
Carex diandra Schrank

Carex digitalis Willd.

Carex donnell-smithii L.H. Bailey
Carex douglasii Boott

Carex ebenea Rydb.

Carex eburnea Boott

Carex egglestonii Mack.

Carex elliottii Schwein. & Torr.
Carex elynoides Holm

Carex emoryi Dewey

Carex engelmannii L.H. Bailey
Carex exilis Dewey

Carex exsiccata L.H. Bailey
Carex festucacea Schkuhr ex Willd.
Carex feta L. H. Bailey

Carex filifolia Nutt.

Carex fissa Mack.

Carex flacca Schreb.

Carex flaccosperma Dewey
Carex flava L.

Carex floridana Schwein.

Carex foenea Willd.

Carex folliculata L.

Carex formosa Dewey

Carex fracta Mack.

Carex frankii Kunth

Carex garberi Fernald

Carex geophila Mack.

Carex geyeri Boott

Carex gigantea Rudge

Carex glacialis Mack.

Carex glareosa Schkuhr ex Wahlenb.
Carex glaucescens Elliott

Carex glaucodea Tuck. ex Olney
Carex globosa Boott

Carex gmelinii Hook. & Arn.
Carex gracillima Schwein.

Carex granularis Muhl. ex Willd.
Carex gravida L.H. Bailey

Carex grayi J. Carey

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northern sedge

dense sedge

Dewey's sedge

lesser panicled sedge
slender woodland sedge
Donell's sedge
Douglas' sedge

ebony sedge
bristleleaf sedge
Eggleston's sedge
Elliott's sedge
blackroot sedge
Emory's sedge
Engelmann's sedge
coastal sedge
western inflated sedge
fescue sedge
greensheath sedge
threadleaf sedge
hammock sedge
heath sedge

thinfruit sedge

yellow sedge

Florida sedge
dry-spike sedge
norther long sedge
handsome sedge
fragile sheath sedge
Frank's sedge

elk sedge

White Mountain sedge
Geyer's sedge

giant sedge

glacial sedge

lesser salt marsh sedge
southern waxy sedge
blue sedge

roundfruit sedge
Gmelin's sedge
graceful sedge
limestone meadow sedge
heavy sedge

Gray's sedge

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A visual identification key utilizing both gestalt and analytic approaches t ... 13

Carex grisea Wahlenb.
Carex gynandra Schwein.
Carex gynocrates Wormsk.
Carex gynodynama Olney
Carex halliana L.H. Bailey
Carex hallii Olney

Carex harfordii Mack.

Carex hassei L.H. Bailey
Carex haydenii Dewey
Carex helleri Mack.

Carex hendersonii L. H. Bailey
Carex heteroneura S.Watson
Carex hirsutella Mack.
Carex hirta L.

Carex hirtifolia Mack.

Carex hirtissima W. Boott
Carex hitchcockiana Dewey
Carex holostoma Drejer
Carex hoodii Boott

Carex hookeriana Dewey
Carex hormathodes Fernald
Carex houghtoniana Torr. ex Dewey
Carex hyalina Boott

Carex hyalinolepis Steud
Carex hystericina Muhl. ex Willd.
Carex idahoa L. H. Bailey
Carex illota L. H. Bailey
Carex incurviformis Mack.
Carex inops L. H. Bailey
Carex integra Mack.

Carex interior L. H. Bailey
Carex interrupta Boeckeler
Carex intumescens Rudge
Carex jamesii Schwein.
Carex jonesii L.H. Bailey
Carex joorii L.H. Bailey
Carex lacustris Willd.

Carex laeviculmis Meinsh.
Carex laxiculmis Schwein.
Carex laxiflora Lam.

Carex leavenworthii Dewey
Carex lemmonii W. Boott

Carex lenticularis Michx.

inflated narrow-leaf sedge
nodding sedge
northern bog sedge
Olney's hairy sedge
Hall's sedge

deer sedge

Harford's sedge

salt sedge

Hayden's sedge
Heller's sedge
Henderson's sedge
different-nerve sedge
fuzzy sedge

hammer sedge
pubescent sedge
fuzzy sedge
Hitchcock's sedge
arctic marsh sedge
Hood's sedge
Hooker's sedge
marsh straw sedge
Houghton's sedge
tissue sedge
shoreline sedge
bottlebrush sedge
Idaho sedge

sheep sedge

coastal sand sedge
long-stolon sedge
smoothbeak sedge
inland sedge
greenfruit sedge
greater bladder sedge
James' sedge

Jones' sedge

cypress swamp sedge
hairy sedge? (lake sedge)
smoothstem sedge
spreading sedge
broad looseflower sedge
Leavenworth's sedge
Lemmon's sedge

lakeshore sedge

14

species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species

species

Carex leporinella Mack.

Carex leptalea Wahlenb.

Carex leptonervia (Fernald) Fernald

Carex limosa L.
Carex livida (Wahlenb.) Willd.

Carex loliacea L.

Carex lonchocarpa Willd. ex Spreng.

Carex longii Mack.
Carex louisianica L. H. Bailey

Carex lucorum Willd.

Carex lupuliformis Sartwell ex Dewey

Carex lupulina Muhl. ex Willd.
Carex lurida Wahlenb.

Carex luzulina Olney

Carex lyngbyei Hornem.

Carex macloviana d'Urv.

Carex macrocephala Willd. ex Spreng.

Carex macrochaeta C. A. Mey.

Carex marina Dewey

Carex mariposana L.H. Bailey ex Mack.

Carex meadii Dewey

Carex membranacea Hook.
Carex merritt-fernaldii Mack.
Carex mertensii Prescott ex Bong.
Carex michauxiana Boeckeler
Carex microdonta Torr.

Carex microglochin Wahlenb.
Carex micropoda C. A. Mey.
Carex microptera Mack.

Carex misera Buckley

Carex mitchelliana M. A. Curtis
Carex molesta Mack.

Carex muehlenbergii Willd.
Carex multicaulis L.H. Bailey
Carex multicostata Mack.
Carex muricata L.

Carex muskingumensis Schwein.
Carex nebraskensis Dewey
Carex nervina L.H. Bailey
Carex neurophora Mack.

Carex nigromarginata Schwein.
Carex normalis Mack.

Carex norvegica Retz.

Jones T

Sierra hare sedge

bristlystalked sedge

nerveless woodland sedge

mud sedge

livid sedge
ryegrass sedge
southern long sedge
Long's sedge
Louisiana sedge
Blue Ridge sedge
false hop sedge
hop sedge
shallow sedge
woodrush sedge
Lyngbye's sedge
thickhead sedge
largehead sedge
longawn sedge
sea sedge
Mariposa sedge
Mead's sedge
fragile sedge
Fernald's sedge
Mertens' sedge
Michaux's sedge
littletooth sedge

fewseeded bog sedge

small wing sedge
wretched sedge
Mitchell's sedge
troublesome sedge
Muehlenberg's sedge
manystem sedge
manyrib sedge
rough sedge
Muskingum sedge
Nebraska sedge
Sierra sedge

alpine nerve sedge
black edge sedge
greater straw sedge

Norway sedge

species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species

species

A visual identification key utilizing both gestalt and analytic approaches t ...

Carex nudata W. Boott

Carex obnupta L. H. Bailey

Carex obtusata Lilj.

Carex occidentalis L. H. Bailey
Carex oligosperma Michx.

Carex oreocharis Holm

Carex ormostachya Wiegand
Carex oxylepis Torr. & Hook.
Carex paleacea Schreb. ex Wahlenb.
Carex pallescens L.

Carex panicea L.

Carex pansa L.H. Bailey

Carex pauciflora Lightf.

Carex peckii Howe

Carex pedunculata Muhl. ex Willd.
Carex pellita Muhl ex Willd.

Carex pensylvanica Lam.

Carex perglobosa Mack.

Carex petricosa Dewey

Carex phaeocephala Piper

Carex picta Steud.

Carex pityophila Mack.

Carex planostachys Kunze

Carex plantaginea Lam.

Carex platyphylla J. Carey

Carex podocarpa R. Br.

Carex polystachya Sw. ex Wahlenb.
Carex praeceptorium Mack.

Carex praegracilis W. Boott

Carex prairea Dewey ex Alph.Wood
Carex prasina Wahlenb.

Carex praticola Rydb.

Carex preslii Steud.

Carex projecta Mack.

Carex proposita Mack.

Carex pseudocyperus L.

Carex purpurifera Mack.

Carex radiata (Wahlenb.) Small
Carex rariflora (Wahlenb.) Sm.
Carex raynoldsii Dewey

Carex recta Boott

Carex reniformis (L.H. Bailey) Small

Carex retroflexa Muhl. ex Willd.

naked sedge
slough sedge
obtuse sedge
western sedge
fewseed sedge

grassyslope sedge

necklace spike sedge

sharpscale sedge
chaffy sedge

pale sedge
grass-like sedge
Payson's sedge
fewflower sedge
Peck's sedge
longstalk sedge
wooly sedge
Pensylvania sedge
globe sedge
rockdwelling sedge
dunhead sedge
Boott's sedge
loving sedge
cedar sedge
plantainleaf sedge
broadleaf sedge
shortstalk sedge
Caribbean sedge
early sedge
clustered field sedge
prairie sedge
drooping sedge
meadow sedge
Presl's sedge

necklace sedge

Great Smoky Mountain sedge

cypress-like sedge
purple sedge

eastern star sedge

looseflower alpine sedge

Raynolds' sedge
estuary sedge
kidneyshape sedge

reflexed sedge

15

16

species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species
species

species

Jones T

Carex rosea Willd.

Carex rossii Boott

Carex rostrata Stokes

Carex rufina Drejer

Carex rupestris All.

Carex sartwellii Dewey

Carex saxatilis L.

Carex scabrata Schwein.

Carex scabriuscula Mack.

Carex schweinitzii Dewey ex Schwein.
Carex scirpoidea Michx.

Carex scoparia Willd.

Carex scopulorum Holm

Carex senta Boott

Carex seorsa Howe

Carex shortiana Dewey & Torr.
Carex simulata Mack.

Carex socialis Mohlenbr. & Schwegman
Carex sparganioides Muhl. ex Willd.
Carex specifica L.H. Bailey

Carex spectabilis Dewey

Carex spicata Huds.

Carex spissa L.H.Bailey ex Hemsl.
Carex sprengelii Dewey ex Spreng.
Carex squarrosa L.

Carex sterilis Willd.

Carex stipata Muhl. ex Willd.
Carex straminea Willd. ex Schkuhr
Carex striata Michx.

Carex striatula Michx.

Carex stricta Lam.

Carex styloflexa Buckley

Carex stylosa C. A. Mey.

Carex subbracteata Mack.

Carex supina Willd. ex Wahlenb.
Carex swanii (Fernald) Mack.
Carex sylvatica Huds.

Carex tenera Dewey

Carex tetanica Schkuhr

Carex torreyi Tuck.

Carex tribuloides Wahlenb.

Carex tuckermanii Boott

Carex turgescens Torr.

rosy sedge

Ross' sedge
beaked sedge
snowbed sedge
curly sedge
Sartwell's sedge
rock sedge

eastern rough sedge
Siskiyou sedge
Schweinitz's sedge
northern singlespike sedge
broom sedge
mountain sedge
swamp carex

weak stellate sedge
Short's sedge
analogue sedge
low woodland sedge
bur-reed sedge
narrowfruit sedge
showy sedge
prickly sedge

San Diego sedge
Sprengel's sedge
squarrose sedge
dioecious sedge
awlfruit sedge
straw sedge
Walter's sedge
lined sedge

upright sedge

bent sedge
variegated sedge
smallbract sedge
weak arctic sedge
Swan's sedge
European woodland sedge
quill sedge

rigid sedge

Torrey's sedge
blunt broom sedge
Tuckerman's sedge

pine barren sedge

species
species
species
species
species
species
species
species
species
species
species

species

A visual identification key utilizing both gestalt and analytic approaches t ...

Carex typhina Michx.
Carex umbellata Willd.
Carex verrucosa Muhl.
Carex vesicaria L.

Carex viridula Michx.
Carex vulpina L.

Carex vulpinoidea Michx.
Carex willdenowii Willd.
Carex woodii Dewey

Carex xerantica L.H. Bailey
Cymophyllus fraseri (Ker Gawl.) Kartesz & Gandhi

Kobresia simpliciuscula (Wahlenb.) Mack.

Usage rights

Use license: Open Data Commons Attribution License

Characters used in the key

—
DS. ONO CLE NS

11.

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

cattail sedge
parasol sedge
warty sedge
blister sedge

little green sedge
true-fox sedge

fox sedge
Willdenow's sedge
Wood's sedge
whitescale sedge
Fraser's cymophyllous

simple bog sedge

is

18 Jones T

Platform: Silverlight runtime

Web location: http:/Avww.herbarium2.lsu.edu/aba/

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/xaml1"

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.Ling;
using System.Net;
using System.Windows;
using System.Windows.Controls;
using System.Windows.Documents;
using System.Windows.Media;
using System.Windows.Media.Animation;

using System.Windows.Shapes;

using System.Windows.Pivot;

m
m
m
m
m
m
using System.Windows.Input;
m
m
m
m
1

namespace Al10

{

public partial class MainPage: UserControl

{
public MainPage ()

{

InitializeComponent ();

Pivot .LoadCollection ("http://www.herbarium2.1lsu.edu/aba/Al0.cxml", string.Empty);
}
private void UserControl_Loaded(object sender, RoutedEventArgs e)

{

A visual identification key utilizing both gestalt and analytic approaches t ... 19

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 hittp://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, | wish to thank W. Thomas and K. Thiele, for
editorial commentary provided for this manuscript.

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, Reznicek A (Ed.) (2002) Flora of North America. Magnoliophyta: Commelinidae (in part);
Cyperaceae. Vol. 23. 23. Oxford University Press, New York, 608 pp. [In English]. URL: http://
www.efloras.org/florataxon.aspx?flora_id=1&taxon_ id=10246 [ISBN 0-19-515207-7].

* Mackenzie K (1940) North American Cariceae. 1 & 2. New York Botanical Garden Press, New
York, 539 pp.

* Microsoft (2007) .NET Framework. 3.5. Microsoft. Release date: 2007 11 20. URL: http://
www.microsoft.com/en-us/download/details.aspx?id=21

20 Jones T

* Microsoft (2008) Deep Zoom. 0.9.000.5. Microsoft. Release date: 2008 10 13. URL: hittp://

msdn.microsoft.com/en-us/library/cc645050%28VS.95%29.aspx
* Microsoft (2010a) Microsoft Silverlight PivotViewer. Microsoft. Release date: 2010 8 09. URL:

http:/Awww.microsoft.com/en-us/download/details.aspx?id=17747
* Microsoft (2010b) Pivot Collection Tool for the Command Line. 1.2. Microsoft. Release date: 2010

7 13. URL: http://pauthor.codeplex.com/
* The University Of Queensland (2006) Lucid Software 3.4. URL: http://www.lucidcentral.com/

Supplementary materials

Suppl. material 1: Tertiary file structure for Carices CXML file

Authors: Jones, T. M.

Data type: occurences, morphological,

Filename: A10.cxml - Download file (4.19 MB)
Suppl. material 2: Secondary Carex morphology data; cleaned and truncated for
building CKML

Authors: Jones, T. M.

Data type: occurrences, morphological, images

Brief description: This file is an example of a build file for the creation of the CXML file.

Filename: 957am fixed scirpoidea space issue.xlsx - Download file (483.24 kb)

Suppl. material 3: Website data from Utah State University
Authors: Google Analytics
Data type: PDF
Brief description: Data sheet for visitiation to CIIK by country
Filename: Analytics utc.usu.edu_keys_Carex_Carex.html Location 20060531-20130630.pdf -
Download file (180.01 kb)
Suppl. material 4: Website data from Louisiana State University
Authors: Google Analytics
Data type: PDF
Brief description: Data sheet for visitiation to CIIK by country

Filename: Analytics Carex key LSU Location 20060531-20130630.pdf - Download file (178.08 kb)

Suppl. material 5: Primary Carex morphology data from Lucid 3.4

Authors: Jones, T. M.

A visual identification key utilizing both gestalt and analytic approaches t ... 21

Data type: XLSX
Brief description: Export from CIIK 2013 in CSV format

Filename: Carex-all-CSV.xlsx - Download file (732.82 kb)

Suppl. material 6: CIVIK usage 2011 - 2013
Authors: Google Analytics
Data type: PDF

Brief description: This includes all visual keys developed. Here CIVIK is represented by both /
aba/ and /aaa/ and iteratives.

Filename: Analytics www.herbarium2.lsu.edu_aaa_A5TestPage.html Pages
20100531-20130630.pdf - Download file (168.54 kb)
Suppl. material 7: Visual keys usage with Google Analytics
Authors: Google
Data type: analytics
Brief description: Compilation of all visual keys using Google Analytics

Filename: Analytics www.herbarium2.lsu.edu-aaa-A5 TestPage.html Language
20100809-20130908.pdf - Download file (189.65 kb)