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MorphoBrowser
Contact Jukka Jernvall jukka.jernvall -at- helsinki.fi Institute of Biotechnology |
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Instructions
 To view the database, click here
or click the button above. The database interface will
open in a
separate browser window. Click 'Enter MorphoBrowser
database' to enter the database, which will take you to the species
list. On all pages in the database, click the MorphoBrowser logo in the
top left of the page to return to the start page.
The list of all species represented in the database appears in the main
panel.
 You can select a specific species to view by clicking the 
button next to the
species name. This will send you to the MorphoView
pages for that species. Clicking  in
the
left panel will send you to the the MorphoView
pages for all of the species that are currently listed on the Species
List page. If you want to view a subset of the species, then you can
use
the boxes
at the top of each column to enter search terms, then hit  or 'Enter'. A
wildcard is automatically entered at the end of entries, so you need
only enter the beginning of
words. For example, entering 'car' under Order and hitting 'Enter'
will
find all taxa in the order Carnivora. If you also enter 'can' under
Family, you will find all taxa in the family Canidae. You can insert
your own wildcard ('%') anywhere else if
needed, for example typing '%dactyla' under Order will find all
all taxa in the families Artiodactyla and Perissodactyla. The search is
not case sensitive.
Click on a column header to sort the records by that field, or
to
toggle
between ascending and descending. The buttons at the topof the left panel move between pages of records:  goes to the next page,  goes to the previous
page,  goes to the last page and  goes to the first page. Click  in the left panel
to clear the search
and show all
records.The number of species records found is displayed at the bottom left of the page, and the number of pages of records at the bottom right. Navigation Bar On the MorphoView and Search Results pages, a navigation bar appears on the left:  The buttons at the top move between records: goes to the next record, goes to the previous
record, goes to the last record
and goes to the first record.
Clicking  will take you back
to the complete Species List.Summary information and the 3D morphology of the sample appear in the main panel.  The top of the record displays the binomial name, with the unique identifier and common name below. On the right are the higher taxonomic fields. Unique identifier is used to identify subspecies or genetic strains/mutants. In the left column is shown summary information about the sample. The teeth represented in the sample are listed, and below each tooth the corresponding crown type. For a description of crown type, see Crown Type Search below. In the right column the 3D morphology of the sample is viewable in the Morphoview Window. Below the 3D viewing window, possible shape searches for the current tooth or tooth row are displayed. Only some of the teeth in the database have values stored for the different search types. MorphoView Window  Clicking and dragging on the tooth image will rotate it. The orientation axes in the bottom left corner of the 3D representation indicate the occlusal (occl), buccal/lingual (bucc or ling) and posterior (post) directions of the tooth. Some useful navigation buttons are:
Below the MorphoView window is a drop-down box with five pre-set views: occlusal, anterior, lateral 1, posterior, and lateral 2. Select a view from the list to display it. Right-clicking on the viewing area brings up additional options; to open a new viewing window with the current tooth in it, click 'New Display'. For more detailed instructions on how to use JavaView, see the Shortcuts page on the JavaView website. Shape Searching In addition to a text-based search for teeth according to taxonomy, the user can search for similar teeth based on tooth shape. This can be done using simple classifications of tooth shape, or shape descriptors generated directly from the 3D data. Three types of shape searches have been implemented based on: • shape of tooth row • shape of single tooth • crown type classification A separate  button is displayed
for each of the three search
types available for the MorphoView. Clicking a button
will move you to the Search Results page. The shape search for a tooth row is based on the orientation
patch count (OPC) method of Evans et
al. (2007). OPC is a measure of dental complexity. Briefly,
it
is the total number
of individual patches found when the tooth surface is divided into
patches which are oriented in specific directions. OPC has
been found to be a good indicator of the general dietary category
(ranging from hypercarnivore to herbivore) of
carnivorans and rodents.
Click to find the tooth
rows with the most similar OPC value, displayed in Search Results. Note that upper tooth row
OPCs
tend to be
higher than lower tooth row OPCs for the same diet.Tooth Shape Search  The shape search for a single tooth is based on the data mining method of Pljusnin et al. (2006). Multiple shape variables, including area and dispersion profiles (see below), orientation patch count (see above) and surface relief, were automatically measured from the 3D scans. Common data mining algorithms were employed to search for combinations of features that were best able to predict diet or taxonomy. In the database, four of these combinations of features are used in nearest-neighbour searches to find the most similar teeth.
Currently four searches are available:
Select from the list of available searches in the first drop-down box, and select from the list of available teeth in the second drop-down box, and click to find the most similar teeth, displayed in Search Results.Crown Type Search  The search compares the current tooth with all other teeth in the database by comparing each digit in the code and returning the sum of the differences. Select from the list of available crown types in the first drop-down box, and select the the maximum distance between crown types in the second drop-down box (range 0-2), and click to find the most
similar teeth, displayed in Search
Results.Search Results  On the Search Results page, the search type appears at the top. The original MorphoView is displayed on the top half of the screen, and the search results can be scrolled through on the bottom half. Search results are presented in rank order. In the search results, Distance listed for each tooth indicates the extent of the difference between this tooth and the original search tooth, i.e. 0 = no difference.
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