Corresponding author: Timothy Mark Jones (
Academic editor: Thomas Couvreur
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
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
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
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.
The data used in this project are primarily derived from an interactive identification program to
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.
This key is designed for use in North America, including Mexico. The original descriptive data was derived from Flora of North America (
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.
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.
New York Botanical Garden Press gave permission to image the plates in K. K. Mackenzie\'s two volume treatment of Carices of North America (
The dataset was derived from an export of CIIK (
.NET Framework (
Visual Studio 2010 / 2012
Silverlight 4 Tools for Visual Studio 2010
Silverlight Software Development Kit (SDK)
Silverlight 4 Toolkit
PivotViewer SDK
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.
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.
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.
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
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.
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.
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.
See \'software technical features\'
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
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
While Silverlight is ideal for this data format, it will be deprecated (see
SLouisiana State University
Scientific Name | Common Name | Rank |
---|---|---|
sedge | genus | |
sedge | genus | |
sedge | genus | |
abruptbeak sedge | species | |
thicket sedge | species | |
lesser brown sedge | species | |
summer sedge | species | |
glomerate sedge | species | |
broadwing sedge | species | |
whitetinge sedge | species | |
blackandwhite sedge | species | |
white bear sedge | species | |
Hawai\'i sedge | species | |
sturdy sedge | species | |
Foxtail sedge | species | |
eastern narrowleaf sedge | species | |
claspbract sedge | species | |
bigleaf sedge | species | |
yellowfruit sedge | species | |
grassyslope arctic sedge | species | |
Columbian sedge | species | |
water sedge | species | |
Arapaho sedge | species | |
northern cluster sedge | species | |
drooping woodland sedge | species | |
sand sedge | species | |
Arkansas sedge | species | |
Assiniboia sedge | species | |
wheat sedge | species | |
slenderbeak sedge | species | |
prickly bog sedge | species | |
black scale sedge | species | |
scrabrous black sedge | species | |
darkbrown sedge | species | |
lesser blackscale sedge | species | |
golden sedge | species | |
southern sedge | species | |
tarheel sedge | species | |
Aztec sedge | species | |
Back\'s sedge | species | |
Bailey\'s sedge | species | |
Baltzell\'s sedge | species | |
Barratt\'s sedge | species | |
Bebb\'s sedge | species | |
southwestern showy sedge | species | |
Bicknell\'s sedge | species | |
two-color sedge | species | |
Bigelow\'s sedge | species | |
stiff sedge | species | |
eastern woodland sedge | species | |
Bolander\'s sedge | species | |
Bolivian sedge | species | |
Brewer\'s sedge | species | |
species | ||
brome-like sedge | species | |
brownish sedge | species | |
button sedge | species | |
Bush\'s sedge | species | |
Buxbaum\'s sedge | species | |
California sedge | species | |
silvery sedge | species | |
hair-like sedge | species | |
capitate sedge | species | |
Carey\'s sedge | species | |
Carolina sedge | species | |
vernal sedge | species | |
chestnut sedge | species | |
thinleaf sedge | species | |
oval-leaf sedge | species | |
Cherokee sedge | species | |
Chihuahuan sedge | species | |
creeping sedge | species | |
coiled sedge | species | |
Collins\' sedge | species | |
fibrousroot sedge | species | |
longhair sedge | species | |
hirsute sedge | species | |
low northern sedge | species | |
northwestern sedge | species | |
soft fox sedge | species | |
openfield sedge | species | |
Crawe\'s sedge | species | |
Craweford\'s sedge | species | |
coastal plain sedge | species | |
fringed sedge | species | |
crested sedge | species | |
ravenfoot sedge | species | |
northeastern sedge | species | |
clustered sedge | species | |
Cusick\'s sedge | species | |
sandywoods sedge | species | |
Davis\' sedge | species | |
Davy\'s sedge | species | |
white edge sedge | species | |
cypressknee sedge | species | |
northern sedge | species | |
dense sedge | species | |
Dewey\'s sedge | species | |
lesser panicled sedge | species | |
slender woodland sedge | species | |
Donell\'s sedge | species | |
Douglas\' sedge | species | |
ebony sedge | species | |
bristleleaf sedge | species | |
Eggleston\'s sedge | species | |
Elliott\'s sedge | species | |
blackroot sedge | species | |
Emory\'s sedge | species | |
Engelmann\'s sedge | species | |
coastal sedge | species | |
western inflated sedge | species | |
fescue sedge | species | |
greensheath sedge | species | |
threadleaf sedge | species | |
hammock sedge | species | |
heath sedge | species | |
thinfruit sedge | species | |
yellow sedge | species | |
Florida sedge | species | |
dry-spike sedge | species | |
norther long sedge | species | |
handsome sedge | species | |
fragile sheath sedge | species | |
Frank\'s sedge | species | |
elk sedge | species | |
White Mountain sedge | species | |
Geyer\'s sedge | species | |
giant sedge | species | |
glacial sedge | species | |
lesser salt marsh sedge | species | |
southern waxy sedge | species | |
blue sedge | species | |
roundfruit sedge | species | |
Gmelin\'s sedge | species | |
graceful sedge | species | |
limestone meadow sedge | species | |
heavy sedge | species | |
Gray\'s sedge | species | |
inflated narrow-leaf sedge | species | |
nodding sedge | species | |
northern bog sedge | species | |
Olney\'s hairy sedge | species | |
Hall\'s sedge | species | |
deer sedge | species | |
Harford\'s sedge | species | |
salt sedge | species | |
Hayden\'s sedge | species | |
Heller\'s sedge | species | |
Henderson\'s sedge | species | |
different-nerve sedge | species | |
fuzzy sedge | species | |
hammer sedge | species | |
pubescent sedge | species | |
fuzzy sedge | species | |
Hitchcock\'s sedge | species | |
arctic marsh sedge | species | |
Hood\'s sedge | species | |
Hooker\'s sedge | species | |
marsh straw sedge | species | |
Houghton\'s sedge | species | |
tissue sedge | species | |
shoreline sedge | species | |
bottlebrush sedge | species | |
Idaho sedge | species | |
sheep sedge | species | |
coastal sand sedge | species | |
long-stolon sedge | species | |
smoothbeak sedge | species | |
inland sedge | species | |
greenfruit sedge | species | |
greater bladder sedge | species | |
James\' sedge | species | |
Jones\' sedge | species | |
cypress swamp sedge | species | |
hairy sedge? (lake sedge) | species | |
smoothstem sedge | species | |
spreading sedge | species | |
broad looseflower sedge | species | |
Leavenworth\'s sedge | species | |
Lemmon\'s sedge | species | |
lakeshore sedge | species | |
Sierra hare sedge | species | |
bristlystalked sedge | species | |
nerveless woodland sedge | species | |
mud sedge | species | |
livid sedge | species | |
ryegrass sedge | species | |
southern long sedge | species | |
Long\'s sedge | species | |
Louisiana sedge | species | |
Blue Ridge sedge | species | |
false hop sedge | species | |
hop sedge | species | |
shallow sedge | species | |
woodrush sedge | species | |
Lyngbye\'s sedge | species | |
thickhead sedge | species | |
largehead sedge | species | |
longawn sedge | species | |
sea sedge | species | |
Mariposa sedge | species | |
Mead\'s sedge | species | |
fragile sedge | species | |
Fernald\'s sedge | species | |
Mertens\' sedge | species | |
Michaux\'s sedge | species | |
littletooth sedge | species | |
fewseeded bog sedge | species | |
species | ||
small wing sedge | species | |
wretched sedge | species | |
Mitchell\'s sedge | species | |
troublesome sedge | species | |
Muehlenberg\'s sedge | species | |
manystem sedge | species | |
manyrib sedge | species | |
rough sedge | species | |
Muskingum sedge | species | |
Nebraska sedge | species | |
Sierra sedge | species | |
alpine nerve sedge | species | |
black edge sedge | species | |
greater straw sedge | species | |
Norway sedge | species | |
naked sedge | species | |
slough sedge | species | |
obtuse sedge | species | |
western sedge | species | |
fewseed sedge | species | |
grassyslope sedge | species | |
necklace spike sedge | species | |
sharpscale sedge | species | |
chaffy sedge | species | |
pale sedge | species | |
grass-like sedge | species | |
Payson\'s sedge | species | |
fewflower sedge | species | |
Peck\'s sedge | species | |
longstalk sedge | species | |
wooly sedge | species | |
Pensylvania sedge | species | |
globe sedge | species | |
rockdwelling sedge | species | |
dunhead sedge | species | |
Boott\'s sedge | species | |
loving sedge | species | |
cedar sedge | species | |
plantainleaf sedge | species | |
broadleaf sedge | species | |
shortstalk sedge | species | |
Caribbean sedge | species | |
early sedge | species | |
clustered field sedge | species | |
prairie sedge | species | |
drooping sedge | species | |
meadow sedge | species | |
Presl\'s sedge | species | |
necklace sedge | species | |
Great Smoky Mountain sedge | species | |
cypress-like sedge | species | |
purple sedge | species | |
eastern star sedge | species | |
looseflower alpine sedge | species | |
Raynolds\' sedge | species | |
estuary sedge | species | |
kidneyshape sedge | species | |
reflexed sedge | species | |
rosy sedge | species | |
Ross\' sedge | species | |
beaked sedge | species | |
snowbed sedge | species | |
curly sedge | species | |
Sartwell\'s sedge | species | |
rock sedge | species | |
eastern rough sedge | species | |
Siskiyou sedge | species | |
Schweinitz\'s sedge | species | |
northern singlespike sedge | species | |
broom sedge | species | |
mountain sedge | species | |
swamp carex | species | |
weak stellate sedge | species | |
Short\'s sedge | species | |
analogue sedge | species | |
low woodland sedge | species | |
bur-reed sedge | species | |
narrowfruit sedge | species | |
showy sedge | species | |
prickly sedge | species | |
San Diego sedge | species | |
Sprengel\'s sedge | species | |
squarrose sedge | species | |
dioecious sedge | species | |
awlfruit sedge | species | |
straw sedge | species | |
Walter\'s sedge | species | |
lined sedge | species | |
upright sedge | species | |
bent sedge | species | |
variegated sedge | species | |
smallbract sedge | species | |
weak arctic sedge | species | |
Swan\'s sedge | species | |
European woodland sedge | species | |
quill sedge | species | |
rigid sedge | species | |
Torrey\'s sedge | species | |
blunt broom sedge | species | |
Tuckerman\'s sedge | species | |
pine barren sedge | species | |
cattail sedge | species | |
parasol sedge | species | |
warty sedge | species | |
blister sedge | species | |
little green sedge | species | |
true-fox sedge | species | |
fox sedge | species | |
Willdenow\'s sedge | species | |
Wood\'s sedge | species | |
whitescale sedge | species | |
Fraser\'s cymophyllous | species | |
simple bog sedge | species |
Open Data Commons Attribution License
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
Carices Interactive Visual Identification Key
1.1
English
Silverlight runtime
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>
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(
"
, string.Empty);
}
private void UserControl_Loaded(object sender, RoutedEventArgs e)
{
}
}
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
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.
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
This file is an example of a build file for the creation of the CXML file.
Data sheet for visitiation to CIIK by country
Data sheet for visitiation to CIIK by country
Export from CIIK 2013 in CSV format
This includes all visual keys developed. Here CIVIK is represented by both /aba/ and /aaa/ and iteratives.
Compilation of all visual keys using Google Analytics
Workflow of project
The Visual Carices of North America upon instantiation in default grid setting.
Tiled image set illustrating the change in file size as well as number of images by creating a geometric series of images
An Interactive Visual Identification Key to Carices of North America beta version.