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University of Helsinki Institute of Biotechnology
 
MorphoBrowser Alopex lagopus
Open Database
 Selection of teeth
MorphoBrowser
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.

Species List

The list of all species represented in the database appears in the main panel.
Species List

You can select a specific species to view by clicking the SelectRecord button next to the species name. This will send you to the MorphoView pages for that species.

Clicking MorphoViews button 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 Search button 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: Record Next goes to the next page, Record Previous goes to the previous page, Record Last goes to the last page and Record First goes to the first page.

Click Show All button 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:
Navigation Bar

The buttons at the top move between records: Record Next goes to the next record, Record Previous goes to the previous record, Record Last goes to the last record and Record First goes to the first record.

Clicking MorphoViews button will take you back to the complete Species List.

MorphoView

Summary information and the 3D morphology of the sample appear in the main panel.
MorphoView
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

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:
  • hold down 's' + drag mouse up/down: scale view
  • hold down 't' + drag mouse up/down: translate view
  • hold down 'x' + drag window: draw zoom window
  • hold down 'shift' + drag mouse up/down or left/right: rotate around one axis only

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 Search! button button is displayed for each of the three search types available for the MorphoView. Clicking a Search! button button will move you to the Search Results page.

Tooth Row Search

Tooth Row Search

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.


Tooth Row Search
The surface is divided into patches according to the orientation of the surface at each point. The number of discrete patches for the orientation map is the orientation patch count (OPC).


Click  Search! button 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

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.

Tooth Shape Search
Two of the tooth shape descriptors used in the single tooth shape search are the area (AP) and dispersion (DP) profiles. The area and dispersion (perimeter/√area) are measured for each of ten cross-sections at equal intervals down the height of the tooth.

Currently four searches are available:
  • 3_NN_diet_4: search uses the combination of features found to be most accurate at finding the 3 nearest-neighbour teeth according to diet, assuming four dietary classes (vertebrate/invertebrate/graze-foliage/seed-fruit).
  • 7_NN_diet_3: search uses the combination of features found to be most accurate at finding the 7 nearest-neighbour teeth according to diet, assuming three dietary classes (carnivore/omnivore/herbivore).
  • 7_NN_diet_4: search uses the combination of features found to be most accurate at finding the 7 nearest-neighbour teeth according to diet, assuming four dietary classes (vertebrate/invertebrate/graze-foliage/seed-fruit).
  • 7_NN_tax_6: search uses the combination of features found to be most accurate at finding the 7 nearest-neighbour teeth according to taxonomy, assuming six taxonomic orders.

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  Search! button to find the most similar teeth, displayed in Search Results.


Crown Type Search

Crown Type Search

This search routine is based on crown types (Jernvall et al. 1996). Crown typing is a simple scheme that records the number of major buccal and lingual cusps and longitudinal and transverse lophs as a four digit code. A prefix indicates the general shape of cusps (R for round, S for sharp).

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  Search! button to find the most similar teeth, displayed in Search Results.


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.


References
  • Evans AR, Wilson GP, Fortelius M & Jernvall J. (2007). High-level similarity of dentitions in carnivorans and rodents. Nature 445: 78-81.
  • Jernvall J, Hunter JP & Fortelius M. (1996). Molar tooth diversity, disparity, and ecology in Cenozoic ungulate radiations. Science 274: 1489-1492.
  • Pljusnin I, Evans A, Gionis A & Jernvall J. (2006). Data mining phenotypes: dietary prediction as a case study. Journal of Vertebrate Paleontology 26: 110A.