4.1.1 What is the Cell Magnifier?
  4.1.2 What is Seed Cell Selection?
  4.1.3 How to use the Cell Magnifier?

4.1.1  What is the Cell Magnifier?

In a difference to all other Physical and Abstract Views currently available in the PointCloudXplore, the Cell Magnifier concentrates not on comparing gene expression values in different cells but on expression values in just one cell. In this view, it is not the expression values in other cells that provide the surrounding context but all expression values measured in the current cell itself. In the Cell Magnifier, gene expression values are visualized using a bar graph, one bar for each gene. The individual bars are colored according to colors the user has defined in the Gene Selection Control Panel  (see Gene Selection Control Panel). Since exact expression values can only be roughly estimated from the size of the bar, the exact measured gene expression value is also displayed beside each bar. The cell to be displayed in the Cell Magnifier can be selected in any Physical Views(see Physical View controls).

       

4.1.2 What is Seed Cell Selection?

Seed cell selection means that one cell is used as a starting point for selection. The user first defines the cell which shall be used as the seed. Next, Cell Magnifier is used to display the levels of expression of all genes in that cell. The user then selects for one or more genes  a range in gene expression space. A recursive flood fill algorithm is then used to execute cell selection in which cells connected to the seed that share the chosen gene expression values are identified. Simplified this algorithm can be described as follows:

  1. Calculate all neighbors of all cell which are in the current list of selected cells

  2. Check which neighbors have an expression profile that fits the user defined expression ranges

  3. Add the neighbors which follow the user defined expression criteria to the list of currently selected cells

  4. If new selected cells have been calculated go back to 1) else end.

In the example shown below, all cells in the posterior of the embryo showing high hb expression have been selected automatically. First a cell is manually selected by the user in the region of interest. Afterwards the genes of interest (here only hb) and a range in expression for each of these genes is defined (here a range of 35-100 for hb). Afterwards all cells which are connected to the selected seed cell and which have the according expression profile are selected automatically.

4.1.3 How to use the Cell Magnifier?

Usage of the Cell Magnifier is quite simple. The current cell to be displayed in the Cell Magnifier can be selected in any physical view (beside the Sphere View). After switching into the "Select Mode" (see the physical view controls) it is possible to define the current cell using "SHIFT+MOUSE LEFT".  The current cell is marked in gray in the physical views when the "Select Mode" is enabled. After selection of the current cell all expression values of the current cell are shown as bar graph in the Cell Magnifier. The genes in the bar graph view can either be sorted after stage and then by name, or first after name and then by stage (1). The Cell Magnifier supports two work modes, the "Magnifier Mode" and the "Seed Cell Selection Mode". In the "Magnifier Mode" only the bar graph of the gene expression values is shown. By selecting the "Enable Seed Cell Selection" check box (2) the "Seed Cell Selection Mode" can be enabled. In this mode seed cell selection can be executed.  Using the according check boxes shown beside each gene name (3) one can define which gene dimensions shall be used for seed cell selection. After a gene has been selected one needs to define a minimum and maximum value in the now enabled boxes shown aside of each gene bar (4). After selecting the "Search" button (5) the Create Cell Selector Window is shown. Seed cell selection is then executed after the color and name of the new Cell Selector have been defined and confirmed in the "Create Cell Selector Window". The new created Cell Selector is a so called "Position Cell Selector"  (POS) which can be edited in the physical views of the embryo.



Name Function
1 Gene Sort
Define how the genes should be sorted in the bar graph view:
  1. Sort by stage/name:  Sort genes first by stage and then by name, i.e., show all genes of stage one sorted by name, then all genes of stage two sorted by name and so on.
  2. Sort by name/stage: Sort genes first by name and then by stage, i.e., show all values of gene A sorted by stage, then all values of gene B sorted by stage and so on.
2 Enable Seed Cell Selection Switch between "Magnifier Mode" and "Seed Cell Selection Mode"
  1. Magnifier Mode: Display only the bar graph showing the expression for all genes in the current cell.
  1. Seed Cell Selection Mode: Show additional controls to perform seed cell selection.
3 Gene Select Select which genes should be used for seed cell selection. Controls displayed only in "Seed Cell Selection Mode"
4 Expression Range Select Define the range in expression for the selected genes that should be used when performing seed cell selection. Controls displayed only in "Seed Cell Selection Mode"
5 Search Show the Create Cell Selector Window. Then define name and color for the new Cell Selector. Seed cell selection is the performed after the new name and color for the cell selector have been confirmed by selecting the "Create Cell Selector" button in the Create Cell Selector Window.