2. Main Window

The main window consists of two main parts. The left side of the window contains the physical views of the embryo and the right part either one of the three abstract views or control panels for gene selection or cell selector management . The abstract views are arranged in tabs. The tabs can detached from the main window using the context menu of the tab and re-attached afterwards by closing the window again. The split bar (14) between the left and right side of the window can be moved using the mouse. In this way it is possible to control the size of the different views within the main window.



1 Select a file that has been loaded previously
2 Main menu bar

What is the Point Cloud State?

A Point Cloud State (*.pcstate) file contains a list of genes and for each gene the following information:

Mapping and XMap are only internal used values and not of interesst for the user. Display Weigth is used to control the exposure of the physical views. Display defines if the gene is displayed or not. 

3 File open Open a PointCloud file
4 Tab bar to select the embryo view. In all physical views each cell is represented by a 2D or 3D graphical object which is colored according to expression values measured in the cell it represents. Beside three different 3D physical views of the embryo there are 4 additonal  2D physical views. The 2D embryo views are 2D projections of the Cell View which is described below.

3D Embryo Views:

  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.
  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. Smooth View: Each cell is represented by one point. The surface of the embryo is triangulated and colors are interpolated within the surface triangles. (Not available in PCX-Light)

2D Embryo Views:

  1. Orthographic Views: The embryo is spited into two parts which are projected onto a 2D plane using orthographic projection. The result are 3 different views, one showing the dorsal- and ventral surface of the embryo, a second one showing the anterior and posterior end of embryo, and a third one showing the left and right side of the embryo.
  2. Unrolled Views: 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.
 5   Legend The legend lists all genes and Cell Selectors which are currently displayed in the embryo view. If a 2D embryo view is used then also a list of the displayed expression surfaces is shown. How the legend can be enabled or disable is described in the embryo view properties.
6 Rotate X Rotate the embryo around the x axis.
7 Rotate Y Rotate the embryo around the y axis.
8 Zoom Zoom in and out. To define the zoom speed see the physical view properties.
9 Create Cell Selector Create a new Position Cell Selector. The Create Cell Selector Window is shown in which the color and the name of the new cell selector must be defined. Afterwards a new cell selector is created which can be edited in any embryo view. See the embryo view controls.
10 Show View Properties Display the properties window of the physical views. For more information about the available options see the physical view properties.
11 About this PointCloud Show a window that displays meta data associated with the  currently displayed PointCloud file. See the  physical view properties.
12 Select System Mode Select the system mode of the main canvas where the physical views are displayed. The current mode is marked in green and the mouse cursor is changed accordingly. For more information about the different system modes see the physical view controls.
Select the according window/view by selecting the corresponding tab. The context menu for the current tab can be accessed via "Mouse Left". Via the conext menu all tabs can be detached from the main window and also re-attached afterwards.
If not all tabs can be displayed then additional arrow button to scroll left/right within the tab bar is shown.
14 Split Bar The split bar can be moved using the mouse after it has been selected using the left mouse button. Keep the left mouse button pressed while moving the split bar. By moving the split bar to the left or right edge of the window the physical views or the tabs with all other window can be hidden.