GC Image (LCxLC Edition) Users' Guide

Meshes

LC Image supports mesh objects for comprehensive group analysis. A mesh object is a collection of polygonal panels that supports shared edges and vertices. Chemically similar compounds often form a cluster of peaks. A panel of a mesh can be drawn to include the peaks of desired compounds and exclude the peaks of other compounds. The mesh allows a set of panes that can be used for comprehensive analysis, i.e., covering all of the relevant regions of the chromatogram. Mesh panels are similar to graphical polygons, with one main difference: the panels of a mesh can share vertices. This sharing allows for more accurate analysis as it eliminates overlaps and gaps between two polygons. Also, unlike polygons, which are treated as individuals, panels of a mesh are treated as part of the whole. So if a shared vertex is moved, it affects multiple panels. Similarly if one panel is moved, the whole mesh moves.

Figure 1: An example image with a mesh.

Each polygon in a mesh is called a panel. A point is considered to be inside a panel, if and only if:

it lies completely inside the edges surrounding the panel, or
it lies exactly on an edge surrounding the panel and the space immediately adjacent to the point in the increasing second-dimension direction is completely inside the panel, or
it lies exactly on a vertical edge (along the second dimension) and the space immediately adjacent to the point in the increasing first-dimension direction is completely inside the panel.

In a well-defined mesh, every point within the mesh is in one and only one panel.

LC Image allows a user to draw a polyline to delineate panels in an existing polygon (thereby creating a new mesh object from a polygon) or in an existing mesh (thereby subdividing panels in the mesh). A new panel is created wherever the delineating polyline crosses from outside a polygon or panel into the interior and then back outside. Figure 2 illustrates the creation of a mesh by dividing a polygon into two panels, then the division of that mesh into four panels. Polyline segments that do not delineate panels are ignored, e.g., polyline segments that begin outside any polygon or panel, never cross any polygon or panel, and end outside any polygon and panel are ignored as are the initial and terminal segments of polylines that begin inside a polygon or panel, never cross any edge, and end inside the same polygon or panel.

Figure 2: Creation of mesh and delineation of mesh panels.

LC Image provides a suite of tools that can be used to quickly create complex mesh objects:

Create Mesh
Edit Mesh Metadata
Move Mesh
Edit Mesh Vertex
Split Mesh Panel
Merge Mesh Panel
Delete (Panel and Mesh)

Create Mesh

A mesh can be created in two ways. The first is by grouping two or more polygons or rectangles. The second is by delineating a polygon or rectangle with a polyline as described above.

Create Mesh by Grouping:
1. Select Graphic Mode:
2. If the image does not have any polygon, select the Draw Polygon tool from the Graphic Mode drop-down menu and create polygons.
3. Select two or more polygons or rectangles.
4. Right click on the selected polygon and choose Create Mesh:
5. Enter a unique mesh name and optional description in the Create Mesh dialog and then click OK.
Figure 3: New Mesh Properties Dialog.
Create Mesh by Delineation of Panel:
1. Select Graphic Mode:
2. If the image does not have any polygon, select the Draw Polygon tool from the Graphic Mode drop-down menu and create a polygon.
3. Select a single polygon or rectangle.
4. Select Split Graphics Mode:
5. Draw a polyline that crosses the selected polygon or rectangle by a sequence of Mouse Clicks and double click to finish drawing.
6. Enter a unique mesh name and optional description.
Figure 4: Split Polygon to Mesh.

Edit Mesh Metadata

The metadata for a mesh includes name and description. The metadata can be changed from the Mesh Properties pane.

Edit Mesh Metadata from one panel:
1. Select Graphic Mode:
2. Select a panel of a mesh.
3. Right click to show the Graphics Properties dialog.
4. Click Mesh Tab.
5. Edit the name and description as desired.
Edit Mesh Metadata from two or more panels:
1. Select Graphic Mode:
2. Select two or more panels of a mesh.
3. Right click and choose Edit Mesh Properties:
4. Edit the name and description as desired.

Move Mesh

When you drag any panel of a mesh all the mesh panels will be moved.

Select Graphic Mode:
Left click inside a panel of a mesh and drag to desired location.

Edit Mesh Vertex

A vertex that is shared between two panels can be added, moved, and deleted. A change affects all panels that share that the vertex.

Add Vertex

Adding a vertex to a mesh panel is the same as adding a vertex to a regular polygon, except that when added to an edge shared by two panels, the vertex is added to both panels.

Select Graphic Mode:
Select a panel of a mesh.
Select Edit Vertices tool from the Graphic Mode drop-down menu:
Click on an edge of the selected panel and a vertex will be added to the edge.

Move Vertex

Moving a vertex of a mesh panel is the same as moving a vertex of a regular polygon, except that moving a shared vertex affects both panels.

Select Graphic Mode:
Drag a shared vertex to new location.

The software allows simultaneous movement of vertices on a vertical (or horizontal) line. This function is activated by holding down Ctrl + Shift.

Select Graphic Mode, select a mesh.
Hold down Ctrl + Shift, select a vertex and drag.
Dragging horizontally/vertically will move all the vertices that are horizontally/vertically in line with the selected vertex.

Delete Vertex

Deleting a vertex will delete the vertex from all panels sharing the vertex.

Select Graphic Mode:
Select a panel of a mesh.
Select Edit Vertices tool from the Graphic Mode drop-down menu.
Click on a vertex of the selected panel and the vertex will be deleted from the panel.

Edit Multiple Mesh Vertices

Users are able to drag multiple vertices of a graphic object in unison in the Edit Vertices mode. The supported object types include polygon, polyline, and mesh.

Select multiple vertices
1. Select Graphic -> Edit Vertices mode.
2. Select the graphic to be edited, if not already selected.
3. Hold down Ctrl and click on the desired vertex. The vertex will be added to the selection and highlighted with a yellow solid square box.
4. To deselect one of the selected vertices, click on it again while holding down Ctrl key.
5. Right click to deselect all.
The selected vertices now can be moved in unison by dragging one of the selected vertices.

Figure 5: Multiple Selected Vertices in a Mesh
Select multiple vertices with a polygon
1. Select Graphic -> Edit Vertices mode.
2. Select the graphic to be edited, if not already selected.
3. Right click inside the object. A menu will pop up.
4. Choose “Select Multiple Vertices”.
5. Draw a polygon around the desired vertices to select them.
The selected vertices now can be moved in unison by dragging one of the selected vertices.

Split Mesh

The Split tool divides mesh panels into multiple smaller panels. Only one mesh can be split at a time. Splitting can be applied to a single panel or the entire mesh, depending on the split type. LC Image provides limited selection operations through Ctrl-Left Click and Right Click in Split Graphics mode. They behave similarly as in the Graphic selection mode. Panels of a mesh can be split in multiple ways:

Polyline Split
Horizontal or Vertical Split
Snap Split line to Blob
Grid Split

Polyline Split

The polyline split tool is the default tool when in Split Graphics mode. The graphic(s) that are to be split can be selected before or while in Split Graphics mode. As described in the Create Mesh section, if split is preformed on a graphic that isn't part of a mesh, it splits the graphic and creates a new mesh. An example of a polyline split can be seen in Figure 4.

Select Graphic Mode:
Select a panel of a mesh.
Select Split Graphics tool from the Graphic Mode drop-down menu.
Draw a polyline that crosses the selected panel by a sequence of Mouse Clicks and double click to finish drawing.

Horizontal or Vertical Split

LC Image supports dividing a polygon, a mesh, or panels that belong to a single mesh with a horizontal or vertical split line.

Select Graphic Mode:
Select a Single polygon or rectangle or a Single mesh.
Select Split Graphics Mode.
Right click inside the selected graphic and a menu will popup:
Select “Split Panel Horizontally” or “Split Panel Vertically” to split only the selected graphic(s), or select “Split Mesh Horizontally” or “Split Mesh Vertically” to split the entire mesh to which the selected panel(s) belongs.
Left Click at a desired location to start a horizontal or vertical split line.
To change the location of the split line, hold down the left mouse key and drag the split line to a new location.
Double click to split the graphic(s).

Snap Split line to Blob

LC Image supports snapping a horizontal or vertical split line to the apex location of a blob. Blob Detection must be performed to enable this function.

When in Split Graphics mode with Horizontal or Vertical Split selected as described above:

Left click at a desired location to start a split line.
Hold down Shift key.
Hold down the left mouse key and drag the cursor onto a desired blob, then the split line will be snap to the apex location of the blob.
When done, double click to split the graphic(s).

To split with snapping at a faster pace,

Hold down Shift key.
Double click on a desired blob, then the graphic(s) will be split at the apex location of the blob.

Grid Split

LC Image supports dividing a polygon, a mesh, or panels that belong to a single mesh with a uniform grid.

Select Graphic Mode:
Select a Single polygon or rectangle or a Single mesh.
Select Split Graphics Mode.
Right click inside the selected graphic and a menu will pop up.
Select “Grid Split” and a Grid Configuration dialog will pop up:
Select Entire Mesh check box to split the entire mesh to which the selected panel(s) belongs, or unselect Entire Mesh to split only the selected graphic(s).
Enter the desired number of horizontal and vertical grid lines.
Click OK to split the graphic(s).

Merge Mesh Panels

The Merge tool removes a shared edge between two panels of the same mesh. When the merge tool is active, the mouse cursor will change to a cross when it is over any shared edge that can be merged. When merging two panels, the metadata of the resulting panel is transferred from the selected panel as shown in Figure 6.

Select Graphic Mode:
Select a panel of a mesh.
Select Merge Mesh Panels tool from the Graphic Mode drop-down menu:
Move mouse over a shared edge of the selected panel
Click to remove edge

Figure 6: Merge tool used on blue panels right shared edge.

Delete Mesh

Panels can be deleted in two ways. The first is to delete mesh, which destroys all panels belonging to that mesh. The second is to select a mesh panel(s) and delete them from the mesh. A third option removes the mesh metadata and leaves all panels as regular polygons.

Delete Mesh

Select Graphic Mode:
Select one or more panels from same mesh.
Press Delete key and choose Delete Mesh.

Remove Panel(s)

Select Graphic Mode:
Select one or more panels from same mesh.
Press Delete key and choose Remove Panel.

Break Mesh

Select Graphic Mode:
Select two or more panels from same mesh.
Right click in selected panels to trigger menu.
Choose Break Mesh from menu:

Auto Mesh Construction

The Auto Mesh tool provides the ability to perform mesh panel divisions on the entire chromatogram (a) uniformly, (b) based on linear retention-time indices, or (c) based on selected blobs or blob sets. Auto mesh construction create mesh panels from marker-peak bounding box and create mesh division at the void time.

Create Uniform Mesh Grid
1. Select Menu: Edit -> Auto Mesh.
2. Select the Auto Grid tab.
3. Input the desired number of horizontal and vertical grid lines.
4. Specify the mesh name and description.
5. Click OK to create the mesh.
Create Mesh Grid Based on Linear Retention Index
1. Select Menu: Edit -> Auto Mesh.
2. Select the Auto Grid tab.
3. Choose “Linear Retention Index Grid”.
4. Check the “Use Linear Retention Index” check boxes.
5. Specify the mesh name and description.
6. Click OK to create the mesh.
LRI tables must already be configured in order to create a mesh based on retention index markers.
Create Mesh Grid Based on Marker Blobs
1. Select marker blobs (optional if using predefined blob set).
2. Select Menu: Edit -> Auto Mesh.
3. Select the Custom Grid tab.
4. Select “Use Selected Blobs” to use the manually selected blob or choose “Use Selected Blob Set." Then select a blob set from the list.
5. Choose “Create Marker Panels” to create the bounding-box panels for the markers.
6. Choose “Create Horizontal Grid Line” to split the mesh horizontally along the markers.
7. Specify the mesh name and description.
8. Click OK to create the mesh.
In creating custom-grid mesh panels, there are two types of bounding boxes used to create panels that enclose marker peaks:
1. Bounding Box – the rectangular bounding box (seen when selecting blobs).
2. Contour Bounding Box – the bounding box that is defined for the samples with values that are at least w% of the apex of a blob where w is the contour intensity as a percentage of the peak apex intensity.

Automated Mesh Gap Divisions

LC Image provides a tool, Polyline Auto Split, to draw mesh divisions along gaps in the second-column chromatograms. Because this operation is ill-defined (i.e., what makes one division better than another), this feature is exploratory and interactive.

The Polyline Auto Split tool considers flow paths with minimal intensities to find a gap division to split. The user can specify the number of neighbors used in the algorithm. Setting the number of neighbors to a larger number allows the mesh gap line to trend upward or downward more sharply. The parameters for the Polyline Auto Split algorithm can be accessed through the “Auto Split Settings” menu.

Auto Split Mesh with Different Number of Neighbors

Figure 7: A mesh with divisions that are automatically determined with different settings.

To auto split a graphical region,

Select a polygon or rectangle.
Select Split Graphics Mode.
Right click inside the graphic.
Select Polyline Auto Split
Left click on a desired point in a gap. A division line will be computed from the point to the left and right of the image.
Drag or Shift Click to the right or left of the original point to redirect the division line to a more desirable location. The division line will be recomputed in the original direction starting at the new point.
Double click to apply the division.

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