This section provides a step-by-step introduction to the visualization of MECE hierarchy of
zebrafish, defined by
Owen Randlet. Often it is
difficult to grasp knowledge
about anatomy due to the complex shapes and their complex spatial relationships. Semantic
information like ontologies support anatomical
understanding and ontological viewers enable flexible and interactive exploration of anatomical
structures.
Owen et al have performed
a new MECE (Mutually Exclusive and Collectively Exhaustive) segmentation, which allows for unambiguous and
quantitative anatomical analyses, and fits with standard anatomical nomenclature.
To demonstrate the explore and search functionality of the MECE hierarchy, we consider Maunther
cells.
To explore the ontology, follow the steps mentioned below:
Start FishExplorer newly, by hitting the refresh button of the browser. Then the 3D viewer is
started as default window,
as shown in the image below.
Click the “MECE” tab (highlighted as red in the image above). Then a
ontological tree, like the one shown in the image below, appears on the screen.
Each node in the ontological tree, representing an anatomical region or a group of anatomical
regions, is displayed as an item of the tree. The minus symbol is shown in front of the region
when the hierarchy below the node is expanded; it is denoted by the plus symbol when their exists a hierarchy below, which is not expanded.
For example, there is a plus symbol in the front of hindbrain,
as it is an intermediate node in the ontological tree and its sub-hierarchy is not expanded. Whereas
there is no sign in front of spinal cord, as it is a leaf node in the ontology currently used.
Exploration of the ontological tree is possible by clicking plus and minus symbols in the front of nodes. This unfolds or collapses the sub-hierarchy
of that node. As we are interested in Maunther cells, we first click on the plus symbol in front of the
hindbrain and then the plus symbol of rhombomere 4.
You can also search the Maunther cells in the search box, as shown in the image below. click the search button, The ontological tree will be automatically unfolded and the
nodes matching the search criteria will appear as red.
If you would like to load this anatomical region in the 2D and 3D viewer, click the checkbox in front of region name as shown below.
The regions can be removed from the viewer by deselecting the checkbox.
