GC Image Users' Guide

Analysis

The Detect Blobs operation may detect thousands of separate blobs in the image. There are a number of important tasks in analyzing the large volume of blob data.

A user may wish to identify and report on only a fraction of the chemicals in the sample, so one of the tasks of analysis is to designate those blobs that are to be included for reporting.

In a report, the blob data usually should be associated with the name of the chemical that produced the blob and/or the chemical group that produced the blob, so one task of analysis is to identify the blobs by associating chemical names and/or chemical group names with the blobs to be included for reporting.

Calibration of the system and accurate quantification of peaks may require the identification of internal standards (chemicals of known quantity injected into the sample mixture) and the association of sample chemicals with specific internal standards. So, analysis may require the identification of blobs produced by internal standards and the correct associations between sample blobs and internal standard blobs.

Ideally, blobs are well separated and correctly distinguished in the Detect Blobs operation. In practice, imperfections due to noise and small proximity between peaks can lead to detection errors that require editing. So, another analysis task may be to correct mistakes in the detection of blobs to be included for reporting.

Similar patterns of blob peaks are seen in runs of similar samples under similar conditions. Analyses can be performed quicker if blob peak chemical names, chemical groups, and internal standard associations in previously analyzed images are reused in analyzing subsequent images. Ideally, the computer would recognize with high accuracy the relevant blobs and automatically provide chemical names, chemical groups, and internal standard associations.

GC Image has rudimentary tools to interactively store and re-use blob metadata (user-defined data about the blob peaks such as chemical name, chemical group, and internal standard association). The improvement of these tools is an ongoing priority. Improved tools will reduce the interactive work necessary for GCxGC analysis.

Display Blobs

GC Image graphically highlights detected blobs in the Viewport of the Image Viewer with a variety of settings accessible via Configure->Configure Settings on the Image Viewer menu bar.

A configuration setting determines whether graphical highlights are displayed for all blobs, for only blobs included for reporting, or for no blobs. The default is to graphically highlight all blobs.
A configuration setting determines whether the graphical highlighting is a blob outline, a filled outline, or a bounding box. The default is to highlight the blob outline.
A configuration setting determines whether or not associations between sample chemicals and associated internal standards are highlighted with a line between the blob peaks. The default is to highlight the associations with a line.
Configuration settings determine the colors used for included blobs (default cyan), excluded blobs (default red), internal standard blobs (default orange), internal standard association lines (default green), and selection box (yellow).

Also, after blob detection, when the cursor lingers over a blob in the Image Viewer a tool tip appears with information about the blob.

An example of the graphical highlights is shown in Figure 1. Figure 1: Graphical highlights show the included blobs, internal standards, and associations between included blobs and internal standards.

The next section describes the process of including blobs for reporting and setting the metadata values, such as chemical name and group name.

Blob Metadata and Computed Attributes

GC Image maintains metadata about each blob, including:

chemical name,
chemical group name,
constellation name,
whether the blob is to be included for reporting, and
the internal standard associated with the blob,

None of the metadata values are set during blob detection. All are set with information provided during analysis.

To set the metadata for a blob, it must first be selected. Figure 2 shows the Blob Mode button on the Image Viewer palette. Figure 2: To select blobs for inclusion in the report, first set the cursor mode on the Image Viewer palette to Select Blobs.

The Image Viewer palette has four modes for selecting blobs and one mode from drawing a blob:

Point blob selection,
Line blob selection,
Rectangle blob selection,
Polygon blob selection, and
Draw blob.

The Blob Mode button on the Image Viewer palette shows only the current or most recent blob-selection mode. The Blob Mode can be changed from the pull-down menu that is adjacent to the Blob Mode button.

In pixel blob-selection mode, a blob is selected by moving the cursor over any pixel inside the border of the blob and clicking the left mouse-button. Once a blob is selected in pixel blob-selection mode, other blobs can be added to the selection set by holding the Control-Key during the click of the left mouse-button while the cursor is inside the next blob to be selected.

In line blob-selection mode, a series of blobs can be selected by moving the cursor to one side of the series of blobs, depressing the left mouse-button, moving the cursor to the other side of the series (defining a line through the series), and releasing the mouse button. All blobs crossed by the line will be selected.

In rectangle blob-selection mode, a group of blobs can be selected by moving the cursor to a point above (or below) and left (or right) of all blobs to be selected, depressing the left mouse-button, moving the cursor below (or above) and right (or left) of all the blob peaks to be selected (defining a bounding box), and releasing the mouse button. All blobs with the peak pixel in the rectangle will be selected.

In polygon blob-selection mode, a group of blobs can be selected by moving the cursor to a point near the blobs to be selected, clicking the left mouse-button, repeatedly moving the cursor around the blobs to be selected and clicking the left mouse-button (drawing a polygon), and double clicking the left mouse-button (to close the polygon). All blobs with the peak pixel in the polygon will be selected.

In blob draw mode, pixels are included by depressing the left mouse-button on the border of the new blob, moving the cursor along the desired outline of the blob (drawing an outline), and releasing the cursor at the end of the outline (causing the outline to be closed and all unassigned interior pixels to be assigned to the new blob).

The blob(s) that are selected are highlighted with a colored box. Figure 3 shows a selected blob with a mouse-over that shows information about the blob. Figure 3: Selected blobs are highlighted by a box.

After one or more blobs are selected, a click of the right mouse-button will invoke a popup dialog box for editing the metadata, such as illustrated in Figure 4. Figure 4: The Blob Metadata popup dialog displays and allows setting of metadata about the blob, including chemical name, group name, etc.

The Blob Metadata popup dialog for a single blob displays the blob's unique ID number and several computed attributes:

ID - a unique identification number assigned by GC Image,
Area - the number of pixels in the blob,
Volume - the sum of the values of the pixels in the blob,
Peak value - the largest value of the pixels in the blob,
Peak location - the coordinate of the peak value in each dimension,
Internal standard - the label of the internal standard (0 if not set),
Volume ratio - the ratio between the volume of the blob and the volume of the associated internal standard,

If a single blob is selected, the popup dialog will display the current values for the chemical name, chemical group name, and constellation name and allow those values to be changed. For a single blob, there are also checkboxes to indicate whether or not the blob is to be included and whether or not the blob is an internal standard. (A blob that is an internal standard must be included for reporting.)

If multiple blobs are selected, the popup dialog will not display the values specific to individual blobs. If multiple blobs are selected the popup, illustrated in Figure 5, allows setting only the chemical group name and constellation name (with the values applied to all selected blobs), a checkbox to indicate whether or not the selected blobs are to be included, and a checkbox to indicate whether or not the selected blobs are internal standards. Figure 5: The Blob Group Metadata popup dialog allows setting of metadata about the selected blobs.

The internal standard of a blob that is not itself an internal standard is, by default, set to the nearest blob that is an internal standard. The defaults are applied when blobs are included and when an internal standard is included or excluded. The internal standard of a blob can be changed by selecting the blob and cycling the association from one internal standard to the next until the correct association is made. Cycle the internal standard by first selecting an included blob (that is not an internal standard) and then clicking the Cycle Internal Standard from the tool bar or Edit menu of the Image Viewer.

GC Image provides a Find Blobs tool, pictured in Figure 6, for selecting blobs on the basis of blob ID, compound name, group name, and constellation name. For example, all blobs with a specific group name could be selected en masse.

Figure 6: The Find Blobs tool allows selection of blobs on based metadata.

GC Image provides a Filter Blobs tool, pictured in Figure 7, for selecting (or deselecting) blobs on the basis of area, volume, peak value, and volume ratio. For example, all blobs with a sufficient peak height could be selected en masse. Similarly, all blobs with insufficient area could be deselected.

Figure 7: The Filter Blobs tool allows selection or deselection of blobs on based on important computed features.

GC Image provides a Visualize Blobs tool, pictured in Figure 8, for graphing bi-variate relationships between blob statistics. For example, the tool can be set to show volume and peak value of each blob.

Figure 8: The Visualize Blobs graphs bi-variate relationships of statistics.

The Visualize Blobs tool is useful for identifying blobs with certain statistical characteristics (e.g., anomalies). The user can draw a polygon enclosing graphical points of interest, as illustrated in Figure 9, by clicking at each vertex and double-clicking at the final vertex.

Figure 9: The Visualize Blobs with designated blobs enclosed by a polygon.

Then, the user can click the Assign Properties button to bring up a popup, shown in Figure 10, for setting metadata of the corresponding blobs.

Figure 10: The Visualize Blobs popup for setting metadata of designated blobs.

Blob Table

GC Image can present metadata and computed attributes for all blobs in tabular form. Clicking the Show Blob Table button on the Image Viewer tool bar or selecting Show Blob Table from the Edit menu invokes a simple sortable spreadsheet with a row for each detected blob. On each row is that blob's unique label, metadata, and computed attributes. Figure 11 illustrates a portion of an example blob table.

Figure 11: The Blob Table displays information about each blob. The table can be sorted by clicking on a column header.

The blobs in the spreadsheet can be sorted in forward or reverse order by clicking on the label at the head of the column to be used as the sort key. (Consecutive clicks reverse the sort order.) Clicking to select a row (or using shift-click to select a range of rows or control-click to select multiple rows) causes the blob selected in the Blob Table to also become selected and highlighted graphically in the Image Viewer.

GC Image supports more than 80 of computed attributes and metadata for blobs. The white paper, GCxGC Blob Metadata and Statistics in GC Image, describes in detail each of the available metadata and computed attributes in GC Image.

The blob table columns can be configured via the Configure->Configure Blob Table on the Image Viewer menu. The Configure Blob Table tool, pictured in Figure 12, allows the user to add or remove columns from the blob table configuration. A column(s) can be reordered by removing and re-inserting in a new position. Figure 12: The Configure Blob Table allows the user to select the columns of the blob table.

The blob table can be exported as a text file from the File->Save Blob Table menu item on the Image Viewer. The exported blob table will contain only the columns specified by the blob table configuration. The blob table is saved as text in comma-separated-values (CSV) format, which can be imported directly in the Microsoft Excel and other data analysis software.

Edit Blobs

In cases where blob detection fails to properly delineate a blob that is required for reporting, GC Image provides the Edit Blobs tool available in the Edit menu in the Image Viewer. Figure 13 illustrates the Edit Blobs tool.

Figure 13: The Edit Blobs tool allows a variety of actions, including deleting and redrawing blobs.

The first step in using the Edit Blobs tool is to select a blob in the Image Viewer (as described above using one of the blob-selection modes from the palette) or to select a rectangular sub-region of the image (as described in chapter Graphics). After a single blob or a rectangular sub-region is selected, start the Edit Blobs tool from the Edit menu in the Image Viewer.

The Edit Blobs tool resembles the Multi-Projections tool in that it has a sub-image in the upper-left, graphs of slices of rows in the bottom-left, graphs of slices of columns in the upper-right, and a control pane in the lower-right. The sub-image can be shifted by click-and-drag in the sub-image. The Edit Blobs tool can be resized to show a larger or smaller sub-image, but the resolution is fixed.

The Edit Blobs tool also shows three row and three column slices. The cross-hairs indicate the three row and three column slices in the sub-image that are graphed. The cross-hairs can be relocated in the sub-image by holding the Shift-Key while clicking the left mouse-button on the desired location. The cross-hairs can be moved incrementally with the four arrow buttons on the Edit Blobs control pane.

Blobs along the sliced rows and columns can be edited in one dimension by moving the delimiters at the edge of the blob. The delimiters are moved by clicking with the left mouse-button and dragging to the desired location. The change in the blobs outline can be seen both in the slice and in the sub-image. If a shared delimiter is moved, both blobs are affected.

The Edit Blobs control pane has five additional buttons for editing blobs. There are buttons for splitting the blob at the center of the cross-hairs either horizontally or vertically along the cross-hair. Pressing these buttons will split the blob in the specified direction. There is a button for deleting the blob at the center of the cross-hairs. Pressing this button will delete the target blob. There is a button for merging two blobs. After pressing the button to merge blobs, the blob at the center of the cross-hairs is merged with the blob indicated subsequently by pointing the cursor and then simultaneously depressing the Shift-Key and the left mouse-button. There is a button for drawing a new blob anywhere in the sub-image. After pressing this button, locate the cursor on the desired border of the new blob, depress the left mouse-button, move the cursor along the desired outline of the blob (drawing an outline), and release the cursor at the end of the outline.

Blobs also can be deleted and drawn in the Image Viewer interface.

To delete a blob, first select it and then click the Delete Object on the palette. Multiple blobs can be selected and deleted. Confirmation for deletion is required.
To draw a blob, select the Draw Blob cursor mode. Then, click down on the mouse left-button, draw the cursor around the border of the blob (without crossing the line drawn or other blobs), and release the button to close the shape.

Note, currently there is not mechanism for journaling or undoing blob edits. These important features are in development.

Blob Templates

GC Image has rudimentary support for saving templates of blob patterns observed in one image so that matching patterns of blobs in subsequent images can be recognized. Once recognized, the metadata for the blobs (including chemical name, group name, and internal standard association) can be set from the template.

A template contains much of the metadata of the included blobs. To save a blob template, select the Save Template option from the File menu. The template is stored as a text file tagged using an eXtensible Markup Language (XML) schema. A template will contain all of the included blobs, but only a subset of the information from the blob table is retained in the template. Specifically, each peak in the template has a label, peak location, chemical name, group name, constellation name, and internal standard reference.

GC Image can match blob template(s) to the observed blobs in an image. Match Template is initiated from the Filter menu on the Image Viewer or with the button on the tool bar. The matching process has four steps, each step under user control:

The template is selected from the list of template files and the location of each peak in the template is displayed on the screen.
The template is matched by a search process that attempts to match peaks in the template to blobs in the image.
The template match is confirmed and the metadata values for chemical name, group name, and internal standard reference are modified in the matched blobs.
The metadata applied in the matching can be edited. For example, if one of the matches is with the wrong blob, then the metadata can be cut from the incorrect blob and pasted to the correct blob.

Figure 14 illustrates the template popup that is used to perform each of these steps.

Figure 14: The Match Template popup.

Figure 15.A illustrates the template peak locations overlayed on an image. As can be seen, the peak locations differ in the template and the image. Figure 15.B illustrates the result of matching the template peaks to the image peaks. Matched template elements are shifted to the matched location and color-filled. Unmatched template elements remain unfilled. Figure 15.C illustrates the result of applying the template metadata to the matched image blobs. A popup reports the number of the total template elements applied to the image and the names of the template elements that were not applied. Figure 15.A: In this example of template matching, the template peak locations, drawn with open circles, differ slightly from the image peak locations.

Figure 15.B: The matching algorithm matches the template peaks to the image peaks and graphically highlights the matched locations with filled circles.

Figure 15.C: After the template is applied to the image, the metadata of the matched peaks is set with the template metadata.

The template matching algorithm searches for a translation (i.e., horizontal and vertical shift) of the template that aligns it with target peaks. Then, only target peaks within a set distance of each template peak are matched. The algorithm can be parameterized via Configure->Configure Settings on the Image Viewer menu bar. The parameters are the half-width and half-height of the rectangular search window for translation of the template and the distance threshold for matching a template peak and target peak (after translation of the template).

GC Image has several tools for editing blob metadata. The Image Viewer menu and tool bar provide access to Cut Metadata, Copy Metadata, and Paste Metadata. The blob(s) must be selected with a blob selection tool before the blob metadata can be cut, copied, or pasted. Also, metadata values can be set directly in the Blob Metadata popup as described above.

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