GC Image Users' Guide

Introduction

GC Image is a software system for visualizing, processing, analyzing, and reporting on images produced in two-dimensional gas chromatography (GCxGC). GC Image has two main interfaces:

This introduction provides a brief overview of GCxGC data and a quick tour of some of the image processing facilities of GC Image. Chapter 2 contains installation instructions for the software. Chapters 3-14 describe the GC Image interface and Chapters 15-16 describe GC Project. Chapter 17 introduces the Help Resources for the software. Appendix A provides Answers to Frequently Asked Questions and Appendix B is a white paper on GCxGC Blob Metadata and Statistics in GC Image.

GCxGC separates chemicals according to the time each chemical requires to pass through two capillary columns. GCxGC data can be displayed as an image with pixels arranged so that the abscissa (X-axis) is the retention time for chemicals to pass through the first column and the ordinate (Y-axis) is the retention time for chemicals to pass through the second column. Each pixel value indicates the rate at which molecules are detected at a specific time.

The elution of chemical substance(s) in the sample produces a small blob or cluster of pixels with values that are larger than background values. The magnitudes of the pixel values indicate the quantity of the chemical(s) present. Figure 1 illustrates a greatly magnified view of a small region of a GCxGC image containing three blobs of pixels indicating (at least) three separated chemicals. The smaller values of the background are colorized light-blue and the larger values of the blobs are colorized dark-blue and magenta.

Figure 1: A region of a GCxGC image containing three blobs of pixels indicating three separated chemicals.

The position (i.e., the retention times in each dimension) of each blob is related to the physical properties the chemical(s) that produced the blob, so the position of a blob is useful in identifying each chemical in a sample. The sum of the pixel values in each blob is related to the quantity of the chemical that produced it, so the sum of pixel values of a blob is useful in quantifying the amount of each chemical in a sample. For a more extensive primer on GCxGC, visit www.zoex.com.

Quick Tour

GC Image has many tools that support various operations. This quick tour illustrates some of the steps in a typical processing sequence to analyze raw data produced by GCxGC, identifying and quantifying chemicals in a sample:
  1. Import a raw data file to create an image.
  2. Remove the background or baseline level from the image pixels.
  3. Detect the blob peaks in the image.
  4. Identify and characterize the chemical compounds for the blob peaks.
  5. Save the processed image.

The following figures illustrate each of these steps. Later sections of the GC Image Users' Guide describe these and other operations in greater detail.

Step 1a: Click the Import Image button on the tool bar (a tool tip is shown) or select File -> Import Image from the menu.

Step 1b: For the Import Image operation, GC Image presents a file chooser to locate the source file.

Locate the desired source file and click the OK button. For example, a source file containing the raw data can be a text file in comma-separated-value (CSV) format. The destination file name is automatically generated by GC Image, but can be changed by the user during the save operation.

Step 1c: After GC Image accepts the filenames, it presents a popup dialog box for additional information about the image dimensions and processing.

Specify the dimensions and optionally specify other processing options. The dimensions of the data are required and will be read from the source file if provided by the file format or may be specified by the user in pixel or time units. For example, the dimensions of data acquired at 200 Hz with a modulation period of 2 seconds and a run time of 20 minutes could be sized equivalently as 600 pixels for the first dimension (20 minutes / 2 seconds/modulation) and 400 pixels for the second dimension (200 samples/second * 2 seconds).

Specification of a configuration file and processing operations are optional in this pop-up. These optional specifications are a convenient mechanism for quickly directing processing at the time data is imported. Chapter Configuration Files describes these capabilities. The rest of this quick tour demonstrates how the processing operations are performed interactively.

Step 1d: After the data is imported to form an image it is displayed in the Image Viewer. A magnified region-of-interest (ROI) is shown below. Here and in other figures, the GC Image interface is resized to a small window for tutorial presentation.

Step 2: This image has a background level of over 12 pico-amps per pixel. (See the status bar below the image with the location of the cursor and the data value at that pixel.) Before quantifying the blobs, the baseline must be corrected.

Click the Correct Baseline button on the tool bar (a tool tip is shown) or select Filter -> Correct Baseline from menu.

Step 3: After the baseline is corrected, note the change in background value (indicated by the color change and by the value on the status bar). Now, the blobs associated with the separated chemicals can be detected and quantified. Press the Detect Blobs button on the tool bar or select Filter -> Detect Blobs from menu.

Step 4a: The blobs are detected and graphically highlighted by a thin outline. An image may have thousands of blobs, but an analysis may require only a few of them. Later sections of the GC Image Users' Guide explain how to use template pattern matching to automatically identify and characterize peaks of interest. Here, the quick tour shows interactive identification and characterization.

To select blobs for inclusion, first set the cursor mode on the Image Viewer palette to Blob Mode -> Select Blobs .

Step 4b: Select a blob by positioning the cursor on the blob and clicking the left mouse-button. The selected blob is graphically highlighted with a colored box.

Step 4c: Once a blob is selected, click the right mouse-button to access a popup to view blob attributes and set blob metadata, including chemical name, group name, etc.

Step 4d: Graphical highlights show the included blobs, internal standards, and associations between included blobs and internal standards.

Step 4e: To view the Blob Table, click the Show Blob Table button on the tool bar or select View -> Blob Table the menu. The Blob Table displays information about each blob. The table can be sorted by clicking on a column header.

Step 5: To save the image click the Save Image button or select File -> Save on the menu. Then, exit by selecting File -> Exit from the menu.

Subsequent chapters of the GC Image Users' Guide describe installation and details on using the software.

Contents       Next: Installation and Start-Up

GC Image™ Users' Guide © 2001–2007 by GC Image, LLC, and the University of Nebraska.