5.1.1 Gene Controls
  5.1.2 Gene Expression Histogram
  5.1.3 Color Mapping

This window summarizes the main controls of the Physical Views. In PointCloudXplore this window consists of two tabs, the "Genes" tab and the "Cell Selectors" tab. The "Genes" tab contains the main controls to define visual properties of genes as well as for definition of Expression Surfaces. The "Cell Selectors" tab provides basic functionality for the management of Position Cell Selectors which can be edited in the physical views.

5.1.1 Gene Controls:

The "Genes" tab consists of three main parts: Gene Selection Table, Selected Gene List, and Global Options.

In Gene Selection Table, each row represents a gene and each column a developmental stage. Gene names are sorted case-insensitively by their alphabetical order. In the case that the user loads an atlas file, which contains expression values in several stages for a gene, each column in the Gene Selection Table represents an individual stage. The stage name is shown in a stage:percentage format. For example, 5:4-8 means 4% to 8% in stage 5. If there is no data for a specific stage of a gene, there will be no check box shown in the corresponding cell in the table. When the user check a check box in the Gene Selection Table, the channel (gene/stage combination) will be selected, turned on (shown in all visualization), and shown in the Selected Gene List; when the channel is unchecked, it will be unselected, tuned off (hide in all visualization), and removed from the Selected Gene List.

The order of channels shown in the Selected Gene List depends on when they are selected. The Selected Gene List provides major visualization controls of selected channels. Here, the user can turn a channel on/off(show/hide), change a channel's color,min/max displayed values (see the gene expression histogram),  and define the color scheme and opacity for a channel's expression surface. There is also a Smart Coloring button in the section. When the user click this button, the program will assign distinctive colors for selected channels automatically.

The Global Options section of the window provides functionality to define the overall brightness of the created visualization and allows one to reset the minimum- and maximum displayed values.

 

Name

Function
1 Gene Selection Table  Select a channel (gene/stage combination) by checking the corresponding check box.
2 Separator
The user can drag this separator to adjust the sizes of Gene Selection Table and Selected Gene List. 
3 Selected Gene List Single click here will show/hide(check/uncheck) a selected channel in all visualization.
4 Color The user can change channel's color by single-clicking here.
 5 Min~Max Single click here allows the user to see the histogram of the channel. The user can change min/max in the histogram window.
6 Surface Show an Expression Surface for the according channel. An Expression Surface is created as soon as a color scheme(mapping) has been selected. The following options are available:
  1. Hidden: Do not display an Expression Surface for the according gene.
  2. Single Color: Color the Expression Surface of the gene using the user defined basic color of the gene (see 4)
  3. Gene Color: Color the Expression Surface according to the expression values of the corresponding gene.
  4. Embryo Color: Map the colors defined in underlying 2D Physical View onto the Expression surface. An expression surface can in this way be colored according to the expression values of different genes.

For more detailed information see the color mapping of Expression Surfaces.

7 Opacity The user can define the opacity of the expression surface by single-clicking here. 1.0 = full opacity ; 0.0 = completely transparent
8 Smart Coloring Automatically assign distinctive colors for selected channels.
9 Exposure Define a global brightness value for all channels. Lower or increase the global brightness of cell colors in the  Physical Views. This brightness value is used in the color mapping of the Physical Views to avoid colors adding up to white. In PointCloudXplore either a user defined global brightness value is used(Manual Exposure), or automatically defined gene weights using the auto weight function(Automatic Exposure).
10 Manual Exposure Slider When Manual Exposure(see 9) is selected, the user can change the global brightness value by dragging this slider.
11 Reset Min/Max Reset the minimum- and maximum displayed values(see 5) of all genes back to default. The default values are the minimum- and maximum expression value of the genes.
12 Use cell positions in stage Define which cell postions from which stage of embryo development should be used in the Physical Views. Cells move within the embryo during development. Using this option one can view the morphology of the embryo at different time-points. Expression patterns from any time-point can be mapped onto the embryo using cell positions from any time-point.

5.1.2 Gene Expression Histogram:

 

Name

Function
1 Percentage smaller than min The percentage of cells which express the according gene on a lower level than the user defined  minimum displayed value (see 8).
2 Percentage between min/max The percentage of cells which express the according gene on a level that is larger than or equal to the minimum displayed value and smaller than or equal to the maximum displayed value.
3 Percentage larger than max The percentage of cells which express the according gene on a higher level than the user defined maximum displayed value (see 9).
4 Maximum histogram value The value of the highest peak in the histogram.
5 Minimum histogram value The smallest possible value in the histogram (always 0 ).
 6 Minimum value The smallest measured expression value of the gene (fluorescence).
7 Maximum value The largest measured expression value of the gene (fluorescence).
8 Minimum displayed value The blue line shows the value of the user defined minimum displayed value in the histogram. The blue number aside of the blue line shows the value of the minimum displayed value. The minimum displayed value is used in the color mapping. This value allows one to manually erase background noise from the visualization.
9 Maximum displayed value The red line shows the value of the user defined maximum displayed value in the histogram. The red number aside of the red line shows the value of the maximum displayed value. The maximum displayed value is used in the color mapping. This value allows one to manually correct background for outliers.

5.1.3 Color Mapping:

The HSV (hue , saturation , value)  color model is used to map expression values to color. The user can define for each gene the basic color H. Saturation, S, of color is always 1.0. The expression values are then mapped the color brightness V. For each gene a minimum (blue line in the figure below) and a maximum (red line the figure below) value can be defined. All expression values smaller then the minimum value are mapped to black and all expression values which are larger then the maximum value are mapped to full color brightness. All expression values between the minimum and maximum value are mapped linearly to color brightness V. The color mapping for cell selector is quite similar but here the brightness of color is in general 1.0 or 0.0, i.e cell is selected or cell is not selected. In this way in each cell one color value is defined for each displayed gene and each displayed cell selector. These color values are then added up in RGB space while each color value is first multiplied with the according user defined display weight (the user defined brightness value in the GUI) of the corresponding gene (or cell selector). The display weights can be used to avoid colors adding up to white if the expression patterns of genes with non independent basic colors, H, overlap. The color mapping is inverted if the minimum displayed value is set to a larger value then the maximum displayed value. Inverting the color mapping means that then low expression value are mapped to full color and high expression values to darker color. The same mapping strategy is also used in the height mapping of Expression Surfaces.

The following figure shows a histogram of the expression levels of an example gene. The blue line shows the user defined minimum value and the red line the user defined maximum value. The percentage values displayed above the histogram are the percentage of values which are smaller than the minimum value, the percentage of values between the minimum and maximum value, and the percentage of values which are larger than the user defined maximum. The resulting color mapping is illustrated below the histogram.