GC Image Users' Guide

Project Management

Introduction

GC Project provides support for organizing and reporting on sets of data developed during GCxGC analyses.  GC Project is invoked from the desktop icon, from the Microsoft Windows Programs menu, or from the GC Image bin folder.

The GC Project graphical user-interface (GUI) is pictured in Figure 1.  At the top of the interface are the title bar, menu bar, and tool bar.  The lower-left pane contains the Project Tree that visualizes and provides access to the project components.  The lower-right pane presents Component Information page about the user-selected components and provides access to component operations.

Figure 1: The GC Project graphical user-interface (GUI).

The File menu supports creating a project, saving a project, opening a previously saved project (from the .gcp file), opening a project from the Recent Projects sub-menu (which lists recently opened projects, closing a project (without saving), and exiting.  The tool bar has corresponding buttons for creating, saving, opening, and closing projects.

The Project Tree presents subtrees for each of several components of a project:

Each of these components and the operations supported by GC Project are described here and in Reports.

Creating Projects

To create a new project, click the New Project button on the tool bar or select from the File menu of GC Project.  Then, specify the directory location and the project name.  GC Project creates a new folder with the project name in the user-specified directory.  In the project directory, GC Project creates a GC Projects file (.gcp extension) and several subdirectories (described below).

New projects also can be created with the GC Project Wizard.  To launch the wizard, select New Project Wizard from the File menu.  As described in GC Project Wizard, the wizard guides users through the steps necessary to create a complete project. 

Vials

The Vial structure encapsulates basic data and metadata about the mixtures analyzed by GCxGC. For example, the ASTM D2887 analysis may involve two mixtures:
  1. A calibration mixture comprised of a few known chemicals with known boiling points that is analyzed in order to calibrate the retention times to boiling points.
  2. A sample mixture that is analyzed in order to estimate the boiling point distribution.
Other standard methods involve different calibration mixtures. For example, internal standard calibration mixtures have known amounts of the chemical components.

Just as the physical vial contains the actual chemical mixture, so the Vial data structure contains data and information about the mixture that is analyzed. The vial metadata includes creator, date, notes, and Composition Table. The Composition Table lists the known chemical compounds in the Vial mixture and the (relative or absolute) amounts. As described below, runs are associated with Vials, allowing images that are created during analysis to reference the composition table of the associated vial.

GC Project currently supports several operations on vials:

The Project Tree pane (lower-left) of GC Project contains a Vials node, as pictured in Figure 2. If the node has a '+', then it can be expanded by clicking to list the vials as leafs in the tree. If the node has a '-', then it can be collapsed so that the list of vials is not shown. If there is neither a '+' nor '-', then there are no vials in the project.

Figure 2: The Vials node in the Project Tree.

A user views the list of all vials in the project by clicking on the Vials node in the Project Tree. Then, the list of all vials is presented in the Component Information pane (lower-right), as in Figure 2.

One can start modifying the table by clicking the "Edit" button.  Vials can be added while in editing mode, but vials are only created when the user clicks "Apply Changes".  These fields are shown in the vial table: Vial Name, Composition Table to import for each vial, Date, Author, Status, and Notes.  The "Status" of the Vial indicated whether or not it can be modified or deleted.  Currently, once a vial is created it cannot be deleted.  An "Active" status indicates that the vial already has been created, therefore, the name cannot be changed and the vial cannot be deleted.  A vial in "Editing" status does not exist until after the user applies changes and so can be deleted.

There are several ways to create a vial using the Vial Free Edit table:

New Vial - Creates a new vial with pre-filled Date, Author, and Status.
Delete Row - Deletes a selected vial row.
Next Vial - Creates an incremented Vial Name based on the selected vial row (i.e. if Cal01 in row 1 is selected, then clicking Next Vial will created a Cal02 in row 2 if it does not already exist).
Add Multiple Vials - adds more than one vial at a time by specifying the prefix part of the Vial Name, the starting count for the vial name, the count (number of vials to be created), and other information such as Date, Notes, and Author.

Figure 3 shows the dialog for creating multiple vials.

Figure 3: The Add Vial(s) popup dialog.

As Vials are created, if there is a CSV-format composition table file in the project's Vials folder with the same name as the vial to be created (e.g., a file named Cal01.csv and a vial to be created named Cal01), if the composition table is already present inside the project, the Import Composition Table column will be automatically filled with the matching composition table name. If the composition table is not present then the user can manually select from the combo box or select browse inside the combo box to select a composition table located outside of the project. A composition table imported from outside of the project will show up as a full path to where it is located.

 
Figure 4: The Vial Free Edit table

Once a new vial(s) is created, it is added to the Existing Vials list and also is also added as a leaf node in the Project Tree under the Vials node. A user views the information about a specific vial by clicking on the Project Tree leaf node corresponding to the desired vial. Then, data and metadata for the vial, including Composition Table, creator, date, notes, and status, are presented in the Component Information pane, as in Figure 5.

Figure 5: A Vial node in the Project Tree.

Below the vial information in the Component Information pane are three buttons for manipulating the Composition Table:

Currently, GC Project can import composition files in comma-separated value (CSV) text format with each line formatted as "compound-name, amount". For example, GC Project could import a file with:

benzene, 0.09
2-hexanone, 9.99
Compound names containing commas should be enclosed in quote marks. As described above, if there is a CSV file with the vial name in the project's Vials folder when the vial is created, the user is queried with the option to import the composition table.

Clicking the Add Record button presents a popup dialog, pictured in Figure 6, in which the user enters the compound name and amount for the added Composition Table record.

Figure 6: The Add Record popup dialog to add a record to the composition table.

A typical process for creating a vial and importing its composition table follows. (The same process can be followed for creating multiple vials.)

  1. Create or copy a CSV file containing the composition table for the vial into the Vials subdirectory (under the project directory).
  2. Click on the Vials component in the Project Tree.
  3. Click the Add Vial button below the list of vials in the Component Information pane.
  4. In the popup, provide the root-name, sequence number, and metadata for the vial. Then, click OK.
At this point, if the CSV file has the same name as the vial, then the user confirms importation of the composition table and the process is complete. Once created, the new vial is listed in the Project Tree under Vials.

If the CSV file does not have the same name as the vial, two additional steps are necessary.

  1. Click on the vial listed in the Project Tree under Vials. The information for the vial is listed in the Component Information pane.
  2. Click on the Import Composition button. Select and open the file in the popup.

Sequence Tables

Chromatograph control software uses sequence tables to perform injections, chromatography, and data acquisition.  For GC Image, Sequence Tables provide information about runs, including source vials for runs, and are used in GC Project for Auto Processing.  Figure 7 shows the Sequences branch of the Project Tree and Sequences information pane.
Figure 7: Create/Import Sequence Table(s)

Three different sequence table formats can be imported by GC Project:

Two sequence table formats can be exported from GC Project:

To create a Sequence Table, click the "Create Table" button on the Sequence Table information pane. Then, provide the following metadata:

Prefix - name of the Sequence Table
Date - current date
Notes - notes about the table
Author - creating of the table

Figure 8: Create Sequence Table Tool dialog

Several editing operations can be performed on Sequence Tables:

Figure 9 shows an example of a finished Sequence Table with an auto-generated data file name from using "Next Vial".

Figure 9: Editing a Sequence Table in GC Project Wizard

Once finished, click the "Done" button.  The Sequence Table is created, as shown in Figure 10, and is selectable and editable by clicking the "Edit Table" button.

Figure 10: A Sequence Table created and ready for use or for editing

Runs

The Run structure encapsulates information about the raw chromatograms that are produced in a run (i.e., each run of the instrument creates a single chromatogram). The raw data for all of the chromatograms are stored in the Runs subdirectory and each chromatogram in the Runs subdirectory is listed in the Project Tree under the Runs component, as illustrated in Figure 11.

Figure 11: The Runs node in the Project Tree.

To fully incorporate a chromatogram into a project, the user must associate the run with a vial (created as described above). Each run is associated with a single vial, but a vial may have multiple runs from it. The color of the dot next to each chromatogram run in the Project Tree indicates whether or not an association has been made for that run. A red dot indicates that there is no vial association for the run and a green dot indicates there is a vial association.

Clicking on the Runs component of the Project Tree presents in the Component Information pane a table of runs that have been associated with a vial, as shown in Figure 11. Each associated run in the table has the data file of the chromatogram, the associated vial name, and a sequence number for the run. The sequence number is automatically assigned when the run is associated with the vial.

As pictured in Figure 11, the Component Information pane for Runs also contains a GUI for associating un-associated runs with specific vials. To make an association between a vial and one or more runs, select a vial from the list of vials, select a run(s) from list of runs, and then click the Associate button. Then, the run(s) are removed from the list of un-associated runs and added to the table of associated runs (with vial name and sequence number), and the color of the dot(s) in the Project Tree are changed from red to green. To un-associate a run from a vial, select the run from the list of associated runs, then click the Un-associate button. The run is removed from the list of associated runs and added to the list of un-associated runs, and the color of the dot in the Project Tree is changed from green to red. The un-associate operation is not allowed if the chromatogram has been processed into an image which may have been used in a report.

Once and run data files and the vials are associated, the user can double click on the (green) run data file node inorder to invoke the Process Runs dialog for processing the runs as shown in Figure 13.

Processing Files

GC Project analyzes data in runs to produce processed images. Analysis typically utilizes various files, including GC Image configuration files, templates, and other types of files. The Processing subdirectory for the project, shown in Figure 12 is provided as a convenient location for file used for analysis.
Figure 12: The Processing node in the Project Tree.

Images

After associating a run with a vial, the user can initiate processing of the chromatogram. GC Image allows the user to designate a group of runs to be processed in an identical fashion. Choosing the Process Runs option on the Actions menu presents the dialog pictured in Figure 13. The dialog is similar to the import dialog described in Configuration Files, but the user can choose multiple runs to be processed. In the Process Runs dialog, the user may indicate that timing parameters available in the data file are to be used, but must supply information about the GCxGC data that is not available in the data file (e.g., modulation cycle time). The user may specify other import settings (such as interpolation or a limit on the number of MS intensities), a configuration file as described in Configuration Files, and processing actions (such as background removal, blob detection, and template matching) as described in File Input and Output. Each processed image is set automatically to reference the associated vial's composition/amount table and the user can specify that each image references a calibration file (as described in Reports). The user also can indicate that a Summary Report be generated automatically for each image. With Process Runs, as the specified runs are processed, the progress is reported in a Group Processing Log, which can be saved as a report and left open or closed after the last run of the group is processed.
Figure 13: The Process Runs dialog.

To initiate processing of a single chromatogram, the user can simply double-click on the chromatogram in the Project Tree under Runs. The user is presented with the run selected in the Process Runs dialog for importing the chromatogram.

The Auto Process option on the Actions menu allows the user to process new runs as they are created in or added to the Runs folder. The menu option "Actions -> Auto Process" instantiates the Auto Process dialog, shown in Figure 14, which resembles the Process Runs dialog. The user indicates the settings that will be used for processing all runs — for example, if the vial is specified, then all new runs will be associated with the specified vial. The Start button initiates Auto Process, beginning with any un-associated runs in the Runs folder and then any new runs discovered by periodic polling of the Runs folder. If the runs are not associated with vials automatically, they must be associated manually before they are fully integrated into the project. Auto Process generates a report for all processed runs.

Figure 14: The Auto Process dialog.

When a run is processed in GC Project, the resulting image is stored in the Images subdirectory. GC Project maintains an association between the image and the run. Multiple processed images may be created for a single chromatogram run (e.g., to test different processing parameters), but each processed image is associated with a single chromatogram run. The processed images are named with an image sequence number for the run. For example, Cal01_Run03_Img02 is the name for the second image created for the third run from the vial named Cal01. All of the images in the project are listed under the Images node in the Project Tree, as illustrated in Figure 15. Clicking on the Images node in the Project Tree presents in the Component Information pane a table of images in the project with the status of each.

Figure 15: The Images node in the Project Tree.

Clicking on an image listed under the Images node in the Project Tree presents in the Component Information pane information about the specific image, such as its dimensions and an overview of the processing information, as shown in Figure 16. The Component Information pane for an image also provides buttons for viewing the image blob table and blob set table. Double-clicking on an image listed under the Images node in the Project Tree opens the image in GC Image.
Figure 16: An Image node in the Project Tree.

The Review Group option on the Actions menu allows the user to select a group of images for review. GC Image is started to open each image sequentially. The user is left to process and save each image interactively, if desired, and then exit the instance of GC Image, at which point the next image is opened for review. Figure 17 illustrates the Review Group dialog.

Figure 17: The Review Group dialog.

Existing images (i.e., image files that have been processed and analyzed with GC Image) can be imported into a project and renamed based on the Run-Vial association.  To import previously processed images, select the Images branch of the Project Tree, then select "Actions -> Import Files" or click the Import Files button. In the dialog, select the files to be imported and their Vial-Run association. When the list is complete, click the "Import & Rename" button.  Then, the project tree is updated with images that have been imported and renamed according to the Run-Vial association. Imported and renamed images do not replace existing images; instead, the image count in the file name is incremented.  For example, if Cal01_Run01_Img01.gci exists, the imported image is renamed Cal01_Run01_Img02.gci.

Overview

The Overview in the Project Tree presents the hierarchy of vials, runs, and images, as pictured in Figure 20. A project may have one or more vials, each of which may have one or more runs, each of which may have one or more images. Clicking on the Overview node in the Project Tree presents in the Component Information pane a table of the vials in the project.

Figure 20: The Overview in the Project Tree.

Clicking on a vial listed under the Overview node in the Project Tree presents in the Component Information pane information about the specific vial, such as its composition table, and a table of the runs from the vial.

Clicking on a run listed under an Overview->Vial node in the Project Tree presents in the Component Information pane information about the specific run, including a table of images for the run.

Clicking on an image listed under an Overview->Vial->Run node in the Project Tree presents in the Component Information pane information about the specific image.

Double-clicking on an image listed under an Overview->Vial->Run node in the Project Tree opens the image in GC Image.

Batches and Reports

The end product of an analysis is typically a report on the processing of a set or batch of runs. GC Project provides tools for creating and managing batches and reports. These batch and reporting tools of GC Project are described in Reports.

Contents       Previous: Operations Journals and Scripting      Next: GC Project Wizard

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