In LC Image, graphical elements can be used for visual annotation and for analysis. LC Image supports drawing and editing of graphical elements, including points, polylines, rectangles, and polygons. The Image Viewer palette contains a button to set the cursor mode to graphics mode and there is a pull-down graphics mode selector. The selectable graphics cursor modes are:
There is also a palette button to delete one or more selected graphic objects, a menu item for selecting all graphic objects, and menu items for importing and exporting files that describe graphic objects. The Configure -> Configure Settings interface allows the user to set visibility options and set default colors for graphic objects.
As described below, graphics objects can be designated as Areas, which allows reporting of information for the designated region as if it were a blob (or detected peak), e.g., in an Areas Table. Area objects are quite useful where peak detection is unreliable.
Create a point graphic by first setting the graphics mode to Draw Point. In this mode, click the left mouse-button to set the location of the point. After the point graphic is drawn, the graphics mode reverts to Select Graphic mode and the newly created point graphic is selected. Selected points are outlined graphically, as illustrated in Figure 1.
|
| Figure 1: A selected point graphic. |
Create a polyline graphic by first setting the graphics mode to Draw Polyline. In this mode, move the cursor to the starting point of the polyline and click the left mouse-button. Then, similarly move to each successive point of the polyline and click the left mouse-button. At the ending point of the polyline, double-click the left mouse-button. After the polyline is drawn, the graphics cursor mode reverts to Select Graphic mode and the newly created polyline graphic is selected. The knots of selected polylines are highlighted graphically, as illustrated in Figure 2.
 |
| Figure 2: A selected polyline graphic. |
Create a rectangle graphic by first setting the graphics mode to Draw Rectangle. In this mode, click the left mouse-button to set one corner of the rectangular sub-region, drag the cursor to the opposite corner of the rectangular sub-region, and release the mouse button. After the rectangle is drawn, the graphics cursor mode reverts to Select Graphic mode and the newly created rectangle graphic is selected. The corners of selected rectangles are highlighted graphically, as illustrated in Figure 3.
 |
| Figure 3: A selected rectangle graphic. |
Create a polygon graphic by first setting the graphics mode to Draw Polygon. In this mode, click the left mouse-button to set one vertex of the polygon, repeatedly move the mouse to subsequent vertices and click the left mouse-button, and double-click the left mouse-button at the final vertex. After the polygon is drawn, the graphics cursor mode reverts to Select Graphic mode and the newly created polygon graphic is selected. The vertices of selected polygons are highlighted graphically, as illustrated in Figure 4.
 |
| Figure 4: A selected polygon graphic. |
In graphics cursor mode, the default mode is Select Graphic. In this mode, when the cursor is positioned over an existing graphic (a point, polyline, rectangle, or polygon) and the left mouse-button is clicked, the indicated graphic is selected. When selected, a graphic is highlighted with handles at the knots (e.g., vertices of polygons).
Multiple graphics can be selected with successive control-clicks with the left mouse-button. Control-click with the left mouse button on a selected graphic will remove it from the selection set. All graphics can be selected by choosing "Edit -> Select All" (or using the <Ctl>-A keys) in graphics mode.
In Select Graphic mode, one or more selected graphics can be moved (i.e., translated) by click-and-drag with the left mouse-button, beginning in the interior of a selected graphic. In Select Graphic mode, a vertex of a selected graphic can be moved (independent of other vertices) by click-and-drag with the left mouse-button, beginning on the knot around the vertex.
In Edit Vertices mode, a vertex can be added to or deleted from a selected polyline or polygon. In this mode, clicking on a knot around a vertex will delete it (unless it is one of only two vertices in the object) and clicking on a segment will add a vertex in the middle of the segment. To move a vertex in strictly a vertical or horizontal direction, hold down the Shift key while moving the cursor.
In graphics mode, when one graphic is selected, clicking the right mouse-button brings up a graphic metadata popup, in which metadata, including the name of the graphic, a description, area flag, inclusion flag, text object flag, and color, can be assigned. Figure 5 illustrates the Graphic Metadata dialog.
 |
| Figure 5: The Graphic Metadata dialog. |
The Group Name field makes this graphic a part of a graphic group. All graphics that share the same group name will be reported in the Blob Set Table as a single row. This is explained further in the Graphic Group section.
The Area flag indicates that this graphic is marked as an area and values are generated for this graphic. The data for the indicated region will be reported under the Area section of the blob table. It also allows the user to view this data by selecting the Area Properties tab. The values are calculated from all pixels contained by the graphic. Figure 6 illustrates the Area Properties dialog.
 |
| Figure 6: The Area Properties dialog. |
The Include flag for a graphic is used in generating reports, indicating that the blob peaks defined by the graphic are reported as a set. As described in Blob Analysis, a polygon or rectangle graphic can be used to indicate a set of blobs whose peaks are intersected or contained in the graphic and which satisfy the CLIC expression of the graphic. (CLIC expressions, described in Chemical Identification , impose rule-based constraints on set inclusion.)
The Exclude flag for a graphic is used in generating reports, indicating that blobs with peaks contained in a polygon or rectangle or blobs intersected by a point or polyline are excluded from reporting (e.g., in the total response of all blobs). Use of the include and exclude flags for graphics is described more fully in Blob Analysis and Reports .
The Add Text Object flag indicates that a text label with the name of the graphic is shown. See Text and Chemical Structure Annotations for a description of text objects in LC Image.
The Set Color setting can be used to override the default color of the graphic. (The default color is set according to the inclusion class: included, excluded, or unflagged.) First, check the Set Color flag and then click the Color button to invoke the color chooser. As described in Blob Analysis, the color also can be applied to the blob set defined by the graphic, using the Color Blobs setting.
In graphics mode, when multiple graphics are selected, clicking the right mouse-button brings up a popup for shared metadata. Figure 7 illustrates the Graphics Metadata dialog for multiple graphics.
 |
| Figure 7: The Graphics Metadata dialog for multiple graphics. |
To delete a graphic(s), first enter graphic mode, then select the graphic(s) to be deleted, and then click the Delete Object button on the palette. If multiple graphics are selected, all selected graphics are deleted. The delete key may also be used.
To export all graphic objects, text annotations, and chemical structure annotations from the current image, select File -> Export Graphics Table from the menu, then indicate the folder and filename in the popup dialog.
To import a set of graphic objects and annotations previously exported to a file, select File -> Import Graphics Table from the menu. Then, in the popup dialog, indicate whether the imported graphics are to be appended to or replace any existing graphics and the file from which the graphics are to be imported.
To configure the default settings for graphics, select Configure -> Configure Settings from the menu and open the Graphics Display tab, as illustrated in Figure 8, which allows the following settings to be changed:
 |
| Figure 8: Graphics Display configuration. |
A group name can be assigned to a graphic object. For each graphic group, two possible entries will be reported in Blob Set Table. For a group of included polygons (i.e., with the same group name), LC Image reports the union of the blob sets defined by individual included graphics. For a group of area objects, LC Image reports the information as if the areas are included blobs.
 |
| Figure 9: Blob Set Table showing graphic groups. |
The software provides a “Close” flag for included graphics and areas that can be used to prevent double counting for polygons inside other polygons. If an included graphic is closed, it will prevent any of its blob/peaks from being included by any other graphic as shown in Figure 10. If a blob/peak is claimed by two or more closed graphics, the disputed blob/peak is assigned to graphic with the largest ID (which is the one most recently created). Similarly if an area is closed, it will prevent any of its pixels/data points from being included by any other area. If a pixel is claimed by two or more closed areas, the disputed pixel is assigned to graphic with the largest ID (which is the one most recently created).
 |
| Figure 10: A closed graphic inside another graphic. |
To set a graphic as closed,
GC Image (LCxLC Edition)™ Users' Guide © 2001–2011 by GC Image, LLC, and the University of Nebraska.