3D Views
  3.1.1 Cell View
  3.1.2 Sphere View
  3.1.3 Smooth View
2D Views
  3.1.4 Orthographic Views
  3.1.5 Unrolled View

3D Views:

In the 3D views each cell is represented by one 3D graphical object which is positioned in space according to the physical position of the cell it represents. Each 3D graphical object is then colored according to the gene expression values of the according cell while the user can define which genes shall be displayed (see Gene Selection). All physical views 2D or 3D ones use the same color mapping which is described below. The different 3D views defer mainly in the 3D graphical representations of the cells i.e. polygons in the Cell View, spheres in the Sphere View, and points in the Smooth View. The Cell- and the Smooth View have also in common that the whole embryo is represented  by a closed surface while in the Sphere View each cell is represented by an independent3D



3.1.1 Cell View:

Each cell is represented by a polygon on the embryo surface. The size of the cells depends on the distribution of the cells whereas the shape of the cells has no direct meaning.



3.1.2 Sphere View:

Each cell is represented by a sphere. The spheres are scaled according to the nuclear volume of the cell they represent.


3.1.3 Smooth View:

Each cell is represented by one point. The surface of the embryo is triangulated and colors are interpolated within the surface triangles. The EigenCrust method is used to calculate the triangulation. This view is not available in PointCloudXplore-Light.


2D Views:

All 2D views of the embryo are projections of the 3D Cell View embryo model. The 2D views defer in the projection which is used to create a 2D view from the 3D model. The main properties of the resulting 2D views are described below. The color mapping in the 2D Views is the same as in the 3D Views.



3.1.4 Orthographic Views:

The embryo is spited into two parts which are projected onto a 2D plane using orthographic projection. The result is 3 different views, one showing the dorsal- and ventral surfaces of the embryo, a second one showing the anterior and posterior ends of embryo, and a third one showing the left and right sides of the embryo. The shape of the embryo is preserved in all three orthographic views. The high curviture of the embryo in combination with the used orthographic projection leads to high cell densities on the projection borders. These high cell densities provide a notion of depth but it can be hard to determine the exact expression pattern on the projection borders. Therefore the user needs to switch between the three views in order gain a complete overview of all cells.

3.1.5 Unrolled View:

The 3D Cell View embryo model is first projected onto a cylinder which is then unrolled into a 2D rectangular plane. Relative cell positions along the AP- and DV-axis of the embryo are preserved but not the shape of the embryo. The Unrolled View provides a complete overview of all cells of the embryo while the spatial expression pattern of the genes are preserved.