5.2.1 What is a Cell Selector?
  5.2.2 What is the Current Cell Selector?
  5.2.3 Overview of Cell Selector Management
  5.2.4 Central Cell Selector Management
    5.2.4.1 Cell Selector Management Tab
    5.2.4.2 Management Operations
    5.2.4.3 Cell Selector Editor Window
  5.2.5 Distributed Cell Selector Management
5.2.6 Create Cell Selector Window
  5.2.7 Logical Operators and Cell Selector Combinations

5.2.1 What is a Cell Selector?

A Cell Selector is an object that can be used for cell selection. In literature the term "brush" is often used to refer to an object for data selection but in the context of PointCloudXplore the term Cell Selector is used instead as it is found to be more intuitive. Depending on how cell selection is executed different types of Cell Selectors can be used which are described below.

All Cell Selectors define for each cell a value which defines whether the cell is selected or not. In PointCloudXplore-Lite these Cell Selector Values are either 0 (=cell not selected) or 1 (=cell selected). All Cell Selectors can be visualized in any data display (e.g. Physical Views, or Scatterplot). The different Cell Selector types differ only in the parameter that is used for cell selection and the way they can be edited.  PointCloudXplore supports currently four different main types of Cell Selectors:
  1. Position Cell Selector: This Cell Selector type is used for selection of cells in Physical Views. Cells are selected manually by the user according to cell position by drawing on the embryo surface. Position Cell Selectors can also be defined automatically when using Seed Cell Selection which is available in the Cell Magnifier. All Position Cell Selectors can be edited in any Physical View (beside Smooth View). In PointCloudXplore Position Cell Selectors are defined for one specific PointCloud only i.e. the selection defined by a Position Cell Selector can not be transferred between different PointCloud files. Between different Virtual Embryos however, a transfer of Position Cell Selectors is however often possible since the number of cells and the ID's of cells are here usually identical.
  2. Data Cell Selector: This Cell Selector type is mainly used for selection of cells in scatter plots but is also supported by parallel coordinates. Cells are selected according to ranges in expression of three user defined genes. In 3D parallel coordinates it is also possible to also perform selection of cells with respect to AP/DV cell positions using this cell selector type. Higher order selections can be defined by combining several Data Cell Selectors using the AND operator (see 5.2 and 5.4).
  3. Pattern Cell Selector: This Cell Selector type used for selection of cells in parallel coordinates. Cells are selected according to ranges in expression in n user defined genes.
  4. Logical Operators: Logical Operators are used to define logical combinations of Cell Selectors. Available operators are AND, OR, and NOT. The logical operators are itself Cell Selectors that can be displayed in any data display but the selection which they define can not be directly edited by the user. In fact the logical operators are defined by the selection of other Cell Selectors. Logical operators take the selection defined by other Cell Selectors and define a new selection based on logical rules. A NOT is a unary operator and is used to invert the selection of another Cell Selector. The AND and the OR operator are binary operators meaning they combine the selection defined by two Cell Selectors using well defined logical rules. The AND operator defines the intersection of two Cell Selectors i.e. only cells that are selected by both Cell Selectors the AND is defined on are selected. The OR operator on the other hand defines the union of two Cell Selectors i.e. it selects all cells that are selected by at least one of the two Cell Selectors it is defined on. Combination of Cell Selectors can be defined in the Cell Selectors Management Tab which provides access to the central Cell Selector management system. For more detailed information about Logical Operators and their meaning see 5.3 Logical Operators and Cell Selector Combinations.

5.2.2 What is the Current Cell Selector?

The Current Cell Selector can be of any type. This is the Cell Selector that can currently be edited in the system. When a Cell Selector should be edited in a view then the user first needs to define which Cell Selector should be edited. This Cell Selector is the so called Current Cell Selector. The Current Cell Selector is always displayed even if the user has not set it to be displayed in order to make it possible to edit the Cell Selector. The Current Cell Selector can be defined in many different ways in order to allow a fast and intuitive work flow. The Current Cell Selector can be defined:

  1. In the central Cell Selector management system (see the Cell Selector Management Tab)
  2. In the Scatterplots when selecting a "Cell Selector Scatterplot" in the tab bar with all scatterplots the Data Cell Selector by the selected scatterplot is automatically set to be Current Cell Selector in order to allow immediate editing of this Cell Selector.

5.2.3 Overview of Cell Selector Management:

PointCloudXplore provides a central and in parts also a distributed Cell Selector management where approbriate. In the then central Cell Selector management system all Cell Selectors defined in the system can be accessed. In the central Cell Selector management system basic properties of any kind of Cell Selector, i.e. color, name, display weight (brightness), display status, can be defined. Beside this the main function of the central Cell Selector management system is it to allow to combine Cell Selectors of any type using Logical Operators. The distributed Cell Selector management system refers to the fact that creation of new cell selectors is supported directly by the different views.  For Data Cell Selectors -- which can be edited and created in scatterplots-- a dedicated management system has been integrated directly into the main GUI of the scatterplots (see the Scatterplots). For each Data Cell Selector a new tab with a so called "Cell Selector Scatterplot" is shown. Here basic properties of the cell selector can be defined while editing of the cell selector is possible in the according scatterplots. When a Data Cell Selector is deleted then the according "Cell Selector Scatterplot" which was responsible for the management of that cell selector is also closed. The Current Cell Selector can be selected either in the central but also in the different parts of the distributed Cell Selector management. An overview of the Cell Selector management available in PointCloudXplore is shown in the figure below. 

5.2.4 Central Cell Selector Management:

The main component of the central Cell Selector Management system is Cell Selector Management Tab displayed in the left part of the main window. Here it is possible to access all Cell Selectors define in the system and to edit their basic properties,i.e.color, name, display weight (brightness), and whether a Cell Selector should be displayed or not. Beside this the main function of the central Cell Selector management system is it to allow to combine Cell Selectors of any type using Logical Operators. In addition to the Cell Selector Management Tab there is also the Cell Selector Editor which can be used e.g. to manually edit a Data Cell Selector.  

5.2.4.1 Cell Selector Management Tab:


 

Operation Name

Function
1 Delete Delete the current Cell Selector
2 Current Cell Selector Name of the current Cell Selector
3 Display Current If this option is checked then the current cell selector is always displayed even if the display option for that cell selector is not checked explicitly. This option is provided for convenience to ensure that the cell selector that can currently be edited is also displayed.
4 Show Advanced Management Controls Show the part of the window with the advanced management controls.
5 Select Cell Selector Define which Cell Selectors should be displayed.

CAUTION: The current Cell Selector is always displayed even if the according check box has not been selected. In this was the current Cell Selector needs not to be defined as displayed in order to edit it in the according view.

6 Cell Selector View This symbol illustrates in which view the according Cell Selector can be edited. For the phyiscal views the symbol of the Cell View is shown as representative symbol but Cell Selectors marked with this symbol can be edited in any phyiscal view. For logical operators the according graphical symbol is shown.
7 Cell Selector Name Define the name of the current Cell Selector.
8 Cell Selector Type Type of the according Cell Selector ( POS = Position Cell Selector ; DATA = Data Cell Selector ;  PATTERN=Pattern Cell Selector ; AND, OR, NOT = Logical Operator )
 9 Color Define the basic color of the Cell Selector either manually in the line edit or using a file chooser dialog. The file chooser dialog is shown after the "Hue Value" button has been clicked.
10 Brightness Brightness value of the Cell Selector ( 0 = black , 1.0 = full color brightness )
11 % of Cells Percentage of cells selected by the Cell Selector

 

Operation Name

Function

1 Select Management Operation Select the management operation to be executed next. For more detailed information about the different management operations see the Management Operations.
2 Cell Selector Editor Show the Cell Selector Editor Window which can be used to edit properties of the current Cell Selector. For Postion Cell Selectors and Logical Operators only basic properties like e.g color can be edited here but for Data Cell Selectors also the selected ranges in gene expression can be defined as well as the minimum and maximum values to be displayed can be imported into the Cell Selector.
3 Auto Cell Selector Weight Automatically define a display weight for all Cell Selectors. This option is disabled by default.
4 Cell Selector Tree Viewer The Cell Selector Tree Viewer is the central place where all Cell Selectors defined in the system can be accessed and managed. For each Cell Selector one button is shown. If Cell Selectors are connected via logical operators then blue lines are drawn between the different Cell Selector button visualizing the so define Cell Selector tree. Cell Selector buttons can be selected using the mouse in order to execute a Cell Selector management operation e.g. to combine to Cell Selectors with AND. A Cell Selector button is defined as follows:
  1. Button Color: Basic color of the Cell Selector.
  2. Monitor Icon: The monitor icon means that this Cell Selector is displayed.
  3. T1 : POS  : The first part of the text (here T1) is the name of the Cell Selector. The second part refers to the type of the Cell Selector (here POS). If !!! are displayed behind the type then this Cell Selector is undefined for the current PointCloud. This can be the case when a Position Cell Selector has been defined for another PointCloud and not for the current one.
The current Cell Selector is always shown in gray color. The current Cell Selector is the Cell Selector that can currently be edited in the system. Therefore the current Cell Selector is always displayed even if the user has not set it to be displayed (in this case the Monitor Icon is not shown)

5.2.4.2 Management Operations:

 

Operation Name

Function
1 Select Current Cell Selector Select the current Cell Selector
2 Combine with AND Combine two Cell Selectors with an AND Cell Selector. To combine two Cell Selectors with AND select the two according Cell Selector buttons in the Cell Selector Tree Viewer after selecting this management operation in the Cell Selector Management Tab.
3 Combine with OR Combine two Cell Selectors with an OR Cell Selector. To combine two Cell Selectors with OR select the two according Cell Selector buttons in the Cell Selector Tree Viewer after selecting this management operation in the Cell Selector Management Tab.
4 Combine with NOT Combine a Cell Selectors with an NOT Cell Selector. To combine a Cell Selector with NOT select the according Cell Selector button in the Cell Selector Tree Viewer after selecting this management operation in the Cell Selector Management Tab.
5 Replace Subtree Replace a subtree in a Cell Selector tree with another Cell Selector or Cell Selector tree. This option is especially useful when a part of a Cell Selector tree should be replaced. In this way recursive deletion of parts of the tree can be avoided when a subtree should simply be replaced with another Cell Selector/Cell Selector tree. To replace a subtree select in the Cell Selector Tree Viewer first the according Cell Selector button which should be replaced and the Cell Selector button that should be inserted instead. The Cell Selector to be replaced must be inside a Cell Selector tree and the Cell Selector to be inserted must not have a parent Cell Selector ,i.e. the Cell Selector to be inserted must not be combined with other Cell Selectors.
 6 Change Cell Selector Change a AND to an OR and the other way arround. Select the according Cell Selector button in the Cell Selector Tree Viewer after selecting this management operation.
7 Insert NOT Insert a NOT inside a Cell Selector tree. Use this operation to invert a Cell Selector that is connected to other Cell Selectors via a Cell Selector tree. This management allows to invert subtrees of a Cell Selector tree without disconnecting the according Cell Selector to be inverted from the tree which would possibly cause recursive deletion of other Cell Selectors. To insert a NOT inside a Cell Selector tree select the according Cell Selector button in the Cell Selector Tree Viewer after selecting this management operation in the Cell Selector Management Tab.
8 Delete Cell Selector Delete a Cell Selector. To delete a Cell Selector select the according Cell Selector button in the Cell Selector Tree Viewer after selecting this management operation in the Cell Selector Management Tab.

CAUTION: If the Cell Selector to be deleted is connected to other Cell Selectors then deletion of the Cell Selector will cause other Cell Selectors to be undefined, i.e. logical operators like AND, OR, and NOT are only defined when connected to two (AND, OR) or one Cell Selector (NOT). Deletion of a child Cell Selector of a logical operator causes the logical operator to be undefined. Such undefined Cell Selectors are deleted automatically. Via recursive deletion of undefined Cell Selectors a Cell Selector tree is in this way automatically reduced to its actually meaning after a Cell Selector has been deleted.

ATTENTION: Recursive deletion applies only to logical operators and not to Cell Selectors defined by the user, e.g. Position Cell Selectors or Data Cell Selectors. These Cell Selectors are always defined and will not be automatically deleted.

9 Disconnect Cell Selector Disconnect a Cell Selector from a Cell Selector tree without deleting it.

5.2.4.3 Cell Selector Editor Window:

The Cell Selector Editor Window is actually only of interest for manual definition of properties of Data- and Pattern Cell Selectors. For Position Cell Selectors and Logical Operators only general properties like color and so on can be defined here which can also be directly defined in the Cell Selector Management Tab itself. The Cell Selector Editor Window allows editing the properties of the current Cell Selector. In the figure shown below a Data Cell Selector is chosen as current Cell Selector.

 

 Name

Function
1 Cell Selector Name Define the name of the current Cell Selector.
2 Display Weight Define the display weight/brightness of the current Cell Selector.
3 Display Cell Selector Define if the Cell Selector should be displayed or not.
4 Color Define the basic color of the Cell Selector either manually in the line edit or using a file chooser dialog. The file chooser dialog is shown after the "Hue Value" button has been clicked.
5 Import Min/Max Disp Values Import the minimum and maximum displayed values into the Cell Selector. The minimum and maximum displayed value are used in the color mapping of the Physical Views and can be defined in the Gene Selection Tab. By importing the values into a Data Cell Selector it is possible to also the minimum and maximum displayed values for cell selection.
 6 Define Cell Selector values Manually define the expression ranges for the three different genes used by the Data Cell Selector. If the current cell selector is a Pattern Cell Selector then a table with all genes used bu the cell selector is one. Here one can define the according min/max values for each gene as well as remove genes from the selection by unchecking the checkbox shown in the first column of the table.
7 Confirm/Cancel Confirm the made changes by clicking the "Ok" button or abort the change of the Cell Selector by clicking the "Cancel" button. All changes made here are copied into the Cell Selector after the "Ok" button has been pressed and are inactive before.

5.2.5 Distributed Cell Selector Management:

Beside the central Cell Selector management system basic functionality for the management of Cell Selectors is also available in the different views itself. All abstract views support creation and editing of cell selctors. For Data Cell Selectors, -- which can be edited and created in scatterplots-- a dedicated management system has been integrated into the main GUI of the scatterplots (see the Scatterplots). For each Data Cell Selector a new tab with a so called "Cell Selector Scatterplot" is shown. Here basic properties of the cell selector can be defined while editing of the cell selector is possible in the according scatterplots. When a Data Cell Selector is deleted then the according "Cell Selector Scatterplot" which was responsible for the management of that cell selector is also closed. For more details see the Cell Selectors Tab of the Gene Selection Window and the Scatterplots Main User Interface.

5.2.6 Create Cell Selector Window:

The Create Cell Selector Window is used to define a color and name of a cell selector before it is created. This window is used in all views that allow creation of a new cell selector. The new cell selector is created after the user has confirmed the entered name and color by clicking the "Create Cell Selector" button. By clicking the "Cancel" button the user can cancel the creation of a new cell selector.

 

 Name

Function
1 Cell Selector Name Define the name of the Cell Selector to be created.
2 Hue Define the basic color of the Cell Selector to be created.
3 Create Cell Selector Confirm the name and color of the Cell Selector to be created and intiate creation of the new Cell Selector.
4 Cancel Cancel the creation of a new Cell Selector
5 Help Here a brief desctiption of how the new Cell Selector can be edited is usually displayed. Depending on which type of Cell Selector is created and depending on which view is used for creation of a new Cell Selector a different help text may be displayed.

5.2.5 Distributed Cell Selector Management:

Beside the central Cell Selector management system basic functionality for the management of Cell Selectors is also available in the different views itself. All abstract views support creation and editing of cell selctors. For Data Cell Selectors, -- which can be edited and created in scatterplots-- a dedicated management system has been integrated into the main GUI of the scatterplots (see the Scatterplots). For each Data Cell Selector a new tab with a so called "Cell Selector Scatterplot" is shown. Here basic properties of the cell selector can be defined while editing of the cell selector is possible in the according scatterplots. When a Data Cell Selector is deleted then the according "Cell Selector Scatterplot" which was responsible for the management of that cell selector is also closed. For more details see the Cell Selectors Tab of the Gene Selection Window and the Scatterplots Main Use

5.2.7 Logical Operators and Cell Selector Combinations:

Combination

Effective Result

NOT( A )

Invert selection of Cell Selector A. A NOT Cell Selector selects all cells not selected by A.

AND( A , B )

Intersection of Cell Selector A and B. A AND Cell Selector selects all and only cells that are selected by both, Cell Selector A and B.

OR( A , B )

Union of Cell Selector A and B. A OR Cell Selector selects all cells that are either selected by Cell Selector A or B.

AND( A , NOT(B) )

Invert Cell Selector B first and build then the intersection with Cell Selector A. This operation is equal to subtraction. All cells selected by Cell Selector B are subtracted from the selection defined by A.

NOT( OR( A , B) )

Invert the union of Cell Selector A and B. Select all cells that are neither selected by A nor B.

NOT( AND( A , B) )

Invert the intersection of Cell Selector A and B. Select all and only cells that are not selected by both Cell Selectors A and B.

AND( A , OR(B,C) )

Following the distributive law of boolean logic this is equal to OR(AND(A,B) , AND(A,C)). This is important because in PointCloudXplore a Cell Selector can only have one parent Cell Selector and is not allowed to occur in several combinations at the same time.

OR( A , AND(B,C) )

Following the distributive law of boolean logic this is equal to AND(OR(A,B) , OR(A,C)). This is important because in the PointCloudXplore a Cell Selector can only have one parent Cell Selector and is not allowed to occur in several combinations.