Core API

Colors generic used to stored default color enumeration Colors Properties: R - red value in RGB Range value : 0 to 1 G - green value in RGB Range value : 0 to 1 B - blue value in RGB Range value : 0 to 1 Usage:

 %Enum the list of color: 
 enumeration Colors
 
 %get the number of Colors:
 mc = ?Colors;
 length(mc.EnumeratedValues);
 
 %Get first color:
 mc.EnumeratedValues{1}.Name
 
 %Get the rgb color value:
 redColor=Colors.Red;
 color=[redColor.R redColor.B redColor.G];

Marker class used to define a Marker Marker Properties: color - the color used to display the marker value : a Color value (e.g., 'Red'), see available value in class Colors. Usage:

 %Marker 1
 add_marker(subpop{1},'Actin','Green');

Marker_Operation_Queue class used to store operations affecting Marker. This class is used internally. Marker_Operation_Queue Properties: operations - the color used to display the marker value : a Color value (e.g., 'Red'), see available value in class Colors. Overlap_Specification Methods: AddOperation - Add a marker operation -operation: the operation which will be add to the object marker queue of operations DeleteOperation - remove a marker operation -operation: the operation which will be add to the object marker queue of operations CloneOperationQueue - clone the object marker operation queue Usage:

 %Define a new Marker operation
 op=Constant_Marker_Level();
 set(op,'mean_level',0.7);
 set(op,'sd_level',0.1);
 
 %Add this operation to your marker for the predefined shape cytoplasm
 subpop{1}.markers.Actin.cytoplasm.AddOperation(op);
 
 %Delete an operation
 subpop{1}.markers.Actin.cytoplasm.DeleteOperation(op);
 
 %Clone an operation
 operation_queue=subpop{1}.markers.Actin.cytoplasm.CloneOperationQueue();
 

Overlap_Specification class used to define how shape will overlap Overlap_Specification Properties: (Private) Overlap_Specification Methods: AddOverlap - Set the overlapp values between a list of objects -object_list: the list of object -overlap_value: the overlap value 0- no overlapp, 1 full overlap allowed (1 shape can 100% overlap the other one). Range Value: 0 to 1 construct_overlap_matrix - build the overlap matrix -subpopulations: subpopulations strcuture containing the full subpopulations information. Used internally by the engine. Usage:

 overlap=Overlap_Specification;
 overlap.AddOverlap({subpop{1}.objects.cytoplasm,...
   subpop{2}.objects.cytoplasm},0.05);
 simucell_data.overlap=overlap;

Parameter class used to define parameters passed from user to SimuCell plugins. The Parameter class is used by SimuCell as an interface to accept all information input from users. The Parameter class defines the name, type,allowed values, and a description of the input variable. Parameter properties: name - a string defining the name of the variable (this is the name seen in the GUI) value - default value of the variable (this is used if the value is not specified by the user). The type must match the variable 'type'. type - the class/type of the input variable. Allowed types are defined in SimuCell_Class_Type. allowed_values - allowed values for this input variable. The format depends on the variable 'type' description - a short string description of the variable. This will show up as a tooltip in the GUI Usage:

 overlap=Overlap_Specification;
 overlap.AddOverlap({subpop{1}.objects.cytoplasm,...
   subpop{2}.objects.cytoplasm},0.05);
 simucell_data.overlap=overlap;
 
 Parameter events:
   Parameter_Set      - This is triggered by the script when value 
     of a parameter is set.
 
    

SimuCell_CellArtifact_Operation The template class from which all plugins for adding artifacts to individual cells are derived. SimuCell_CellArtifact_Operation methods: Apply - A function that returns a a cell array(# cells(biological) ,# markers). Each element of the cell is a matrix (image_height,image_width). The value of each element of this matrix is the pixel intensity of one marker on one cell.

SimuCell_Class_Type The template class from which all plugins for adding artifacts to individual cells are derived. SimuCell_Class_Type enumeration: SimuCell type allowed for plugin's arguments. -number: A integer or double -simucell_shape_model: any SimuCell_Object_Model object that you can find in plugins/shape/ -simucell_marker_model: any Marker_Operation_Queue containing objects from plugins/marker. Defne a marker on a shape done by a series of operations. -list: any kind of list, usually string list. -file_name: a file path (used to load SLML MATLAB files).

SimuCell_Compositing_Model The template class from which all plugins for defining object models (shapes of cells, nuclei) are defined. SimuCell_Compositing_Model methods: calculate_compositing_matrix - A function that returns a matrix containing describing how object the marker level overlap between the different objects. USED BY THE ENGINE EXCLUSIVELY, DEFINED BY THE COMPOSITING PLUGINS

SimuCell_Engine_Notifier class used to notify when warning or error happend SimuCell_Engine_Notifier Properties: message - the message that would be display when the warning/error occur. USED IN THE ENGINE EXCLUSIVELY, RIGHT NOW TO CATH EVENT ON THE GUI

SimuCell_Marker_Operation The template class from which all plugins for markers are derived. Each plugin defines a single operation, and a series of operation is performed sequentially to set the final marker distribution. SimuCell_Marker_Operation methods: Apply - A function that returns the intensity of the marker at every pixel in the image after application of the marker operation. needed_shape_list - A function that returns a cell array containing all the other objects (nuclei, cells etc) that are required by the make_shape function. Each element is of type SimuCell_Object. This function is used internally by the engine to determine the order in which objects should be drawn. prerendered_marker_list - A function that returns a cell array containing all the other markers (defined on a specific shape) that are required by the Apply function. Each element of the cell is of type Marker_Operation_Queue. This function is used internally by the engine to determine the order in which markers should be rendered.

SimuCell_Model Template abstract class for all simucell models Template abstract class for all simucell models, so everything can be be derived from this class. property set and get interface. hgsetget is a subclass of handle, so any classes derived from hgsetget are handle classes. classdef MyClass < SimuCell_Model makes MyClass a subclass of SimuCell_Model. Classes that are derived from hgsetget inherit property description and do inherit methods SET that perform a check to see if the value is a PARAMETER . SimuCell_Model methods: set - Set MATLAB object property values performing a check to see if the value is a PARAMETER .

SimuCell_Object Template abstract class for all simucell models Template abstract class for all simucell object (like a nucleus, cytoplasm, nuclear body etc... ), so everything can be be derived from this class. property set and get interface. hgsetget is a subclass of handle, so any classes derived from hgsetget are handle classes. classdef MyClass < SimuCell_Object makes MyClass a subclass of SimuCell_Object. Classes that are derived from hgsetget inherit property description and do inherit methods SET that perform a check to see if the value is a PARAMETER. SIMUCELL_MODEL methods: SET - Set MATLAB object property values performing a check to see if the value is a PARAMETER .

SIMUCELL_object_model The template class from which all plugins for defining object models (shapes of cells, nuclei) are defined. SimuCell_Object_Model methods: make_shape - A function that returns a binary mask(image_height,image_width) of the shape of the object being drawn. prerendered_object_list - A function that returns a cell array containing all the other objects (nuclei, cells etc) that are required by the make_shape function. Each element is of type SimuCell_Object. This function is used internally by the engine to determine the order in which objects should be drawn.

SimuCell_Placement_Model The template class from which all plugins for object (cells, nucleus etc) placement are derived. SimuCell_Placement_Model methods: pick_positions - A function that returns the position where an object will be placed

SimuCell_imageArtifact_Operation template class from which all plugins for adding artifacts to an image are derived. SimuCell_imageArtifact_Operation methods: Apply - function that returns a a cell array(#colors,1). Each element of the cell is a matrix(image_height,image_width). The value of each element of this matrix is the pixel intensity of all the cells(biological) for one color channel.

Subpopulation Properties of cells in a specific sub-population (cell-types) are described by this class. It is the primary class that needs to be defined by the user. Subpopulation properties: objects - a class of type dynamicprops that defines the different objects (nucleus, cytoplams). markers - a class of type dynamicprops that defines thes the different markers. placement - the chosen placement model (plugin) to place the various objects. compositing - the chosen scheme to combine marker levels on overlapping objects. cell_artifacts - a cell containing a list of operations (plugins classes derived from SimuCell_CellArtifact_Operation), used to apply artifacts on a cell by cell basis e.g. Focal Plane Effects Subpopulation methods: Subpopulation - Create a new Subpopulation add_object - Add a new object (nucleus, cytoplasm) to the subpopulation add_marker - Add a new marker to the subpopulation add_cell_artifact - Add a new cell level artifact operation to the subpopulation

dependancy_resolution Based on a dependancy matrix return the optimal order to run. [OPTIMAL_ORDER] = dependancy_resolution(DEPENDANCY_MATRIX) displays a dialog box for the user to fill in and returns the filename and path strings and the index of the selected filter. A successful return occurs if a valid filename is specified. If an existing filename is specified or selected, a warning message is displayed. The user may select Yes to use the filename or No to return to the dialog to select another filename. The DEPENDANCY_MATRIX parameter .

MERGED_CELL_INTENSITIES function [MERGED_IMAGE] = MERGED_CELL_INTENSITIES(CELL_INTENSITY_LIST,NEW_WEIGHT) The CELL_INTENSITY_LIST parameter . The NEW_WEIGHT parameter .

overlap_check function [OVERLAP_ACCEPTABLE] = overlap_check(EXISTING_OBJECT_MASKS, CURRENT_MASK, OVERLAP_MATRIX, OBJ_NUM) The EXISTING_OBJECT_MASKS parameter . The CURRENT_MASK parameter . The OVERLAP_MATRIX parameter . The OBJ_NUM parameter .

simucell_engine function [simucell_result] = simucell_engine(simucell_params, number_of_images) The simucell_params parameter . The number_of_images parameter .