GC Image (LCxLC Edition) Users' Guide

Reports

The final product of an analysis is typically a report(s). Because many types of reports entail a set of multiple runs, i.e., a batch of runs, LC Project is the nexus for generating reports. Various types of reports are selectable from the LC Project Reports menu, as illustrated in Figure 1:

• Summary Reports
• Filter Reports
• Comparison Report
• Fractional Response Reports
• Corrected Fractional Response Reports
• Internal Standard Reports (including ASTM D5580)
• External Standard Reports
• Retention Time Reports

Figure 1: The Reports menu in LC Project.

The first two reports, Summary Reports and Filter Reports, also are available for single images from LC Image in the File menu. Tools for comparing chromatograms, including Comparison Report, which is available from the Reports menu, and the Image Investigator, which is available from the Actions menu, are described in Comparative Analysis and Visualization.

Each of the reports can be generated in various file formats:

• the eXtensible Markup Language (XML),
• the HyperText Markup Language (HTML),
• comma-separated values (CSV), and
• Microsoft Excel (XLS).

The XML file format is preferred, because LC Project can parse XML-format reports for summarizing archived reports. In the future, LC Project will support searching of XML-format reports. XML-format reports can be displayed in recent-generation web browsers, such as Microsoft Internet Explorer. The XSL stylesheets used for reports can be modified by users, for example to include a company name or logo on the report. Screen-shots of examples of the different reports are shown in sections below. The user selects the output file format on a popup dialog, as shown in Figure 2.

Figure 2: The Report format-selection popup.

LC Project allows the user to select a filename for a report, which then is stored in the Reports folder and listed in the Project Tree under the Reports node. Clicking on the Reports node in the Project Tree presents in the Component Information pane a table of saved reports, as shown in Figure 3. Reports from LC Image can be saved to any folder.

Figure 3: The Reports node in the Project Tree.

In LC Project, clicking on a report under listed under the Reports node in the Project Tree presents the report in the Component Information pane, as shown in Figure 4. Double-clicking on a report listed under the Reports node in the Project Tree opens the file with the default Windows program for the file type.

Figure 4: A Report node in the Project Tree.

Summary Reports

A Summary Report provides summary information about individual chromatograms. Summary Reports can be saved in LC Image from the File menu or from the automated actions for Import. In LC Project, Summary Reports can be saved from the Reports menu or from the automated actions for Auto Process and Process Runs.

Summary Reports offer offer nine sub-reports selectable by the user:

• Image Attributes,
• Image Viewer,
• Blob Table,
• Area Table,
• Blob Set Table,
• Excluded Blob Table
• Template Match Results
• Journal, and
• External Table

Summary Reports can be saved in XML (*.xml) or Microsoft Excel (*.xls) file format. By default Summary Reports are formatted in XML with a user-accessible stylesheet for browser viewing. An example summary report is shown in Figure 11.

Figure 11: An example Summary Report.

When an Excel formatted summary report is saved in LC Image, the report will have one sheet per sub-report. For example, if a summary report was saved with Image Attributes, Journal, and Blob Table. Then the excel file would have four sheets, one for the title/header, one for Image Attributes, one for Journal and one for Blob Table. If a subreport reports errors, an additional Messages tab will be added, stating the problem.

Figure 12. a: A Summary Report in Excel file format.

When an Excel formatted summary report is saved in LC Project, the layout is dependent on the type of summary report chosen, either “Generate Multiple Reports” is chosen or not. If it is chosen, then each image selected will be printed to a separate file with one sheet per sub-report. If multiple reports is not chosen, then one excel file will be printed with all selected images inside. In this case, each image will have its own tab, listing all sub-reports together.

Figure 12. b: Multiple Summary Reports in Excel file format.

Summary Report Configuration

LC Image allows users to save and reuse report configurations. The Summary Report Configuration stores which subreports are to be included and their order. Then, when generating a Summary Report, the user is able to indicate a saved configuration, which will be used to configure the Summary Report.

• Create a new Report Configuration
  1. Go to Menu: File -> Save Summary Report.
  2. In the Generate Summary Report Dialog, shown in Figure 13, select the “Generate Report from Existing Configuration” radio button.

  Figure 13: The Generate Summary Report dialog.

  3. Click “New” button to create a new report configuration
  4. Enter a name for the new configuration
  5. Complete the “Build Summary Report” dialog, shown in Figure 13, as described below, then click Save to save the Summary Report configuration and return to the “Generate Summary Report” dialog).

  Figure 13: The Build Summary Report dialog in LC Image.

  In "Report Components", add or remove subsections from the report(s), as desired. Other report settings are below the section selector. Selecting "Include CSV Tables" will include links to CSV-format tables for each image in the report.

  The software allows the user to provide a logo image (e.g., a picture file) to be included in Summary Report. The logo will be placed at the top-left corner. A recommended size for the logo should be no bigger than 50 pixels in height. Any image that is bigger will be resized to fit this height. The software also allows the user to include textual comments in Summary Report.

  The software allows the principal summary tables (blob table, area objects table, and blob sets table) to be exported in CSV format. Check "Export Combined CSV Tables". The Combined Table are saved in the report file folder with a naming convention: "<image name>_Combined_Tables.csv". The XML report also contains a link to the Combined Table at the end of the report.

  There are additional settings for specific report components including:

  • Image region selection, size, and orientation
    The software allows users to control image region selection, size, and orientation of the Image Viewer sub-report.

    Figure 14: Configure the Image Viewer component.

    The controls include three range types:
    1. Entire Image: the full chromatogram
    2. Current View: the display region in the current viewport
    3. Ranges: a user-specified range by retention times provided by the user
    Additional controls include:
    1. The orientation for the printed image (portrait or landscape)
    2. The printed size of the image in inches or pixels.
  • Metadata reporting
    The software allows control over the inclusion and order of metadata for the Image Attributes subreport.In Build Summary Report dialog,
    1. Choose the Image Attributes tab.
    2. To include attributes for display in the Summary Report, choose from the “Invisible Attributes” list, then click on the right arrow to move to the “Visible Attributes” list.
    3. The order seen in the “Visible Attributes” list will be the order displayed in the Summary Report. To reorder this, choose the item in the list, then click the up/down arrow to move.
    All Miscellaneous attributes are treated as one block because users manually add them in Image Attributes and have the full control over the names and order.
• Edit an existing Report Configuration
  1. Go to Menu: File -> Save Summary Report.
  2. Choose “Generate Report from Existing Configuration” radio button.
  3. Select a report configuration from the list of stored configurations.
  4. Click “Edit” button to change configuration through the “Build Summary Report” dialog.
  5. Click Save (this will save the Summary Report configuration).
• Delete an existing Report Configuration
  1. Go to Menu: File -> Save Summary Report
  2. Choose “Generate Report from Existing Configuration” radio button
  3. Select a report configuration from the list of stored configurations
  4. Click “Delete” button to remove the selected configuration
• Import a Report Configuration
  1. Go to Menu: File -> Save Summary Report
  2. Choose “Generate Report from Existing Configuration” radio button
  3. Click “Import” button to summon file chooser to locate a saved report configuration in the file system
  4. Click “Open” to import the chosen report configuration
• Export an existing Report Configuration
  1. Go to Menu: File -> Save Summary Report
  2. Choose “Generate Report from Existing Configuration” radio button
  3. Select a report configuration from the list of stored configurations
  4. Click “Export” to save the report configuration anywhere in the file system

Creating Summary Reports in LC Image

1. Go to menu: File -> Save Summary Report.
2. Choose “Generate New Report” or an existing configuration and then click OK
3. If “Generate New Report” is chosen, a configuration dialog is presented. The user can set report configuration, then click "Save". This configuration is remembered by the software.
4. A file browser shown below is presented, which allows specification of the path and file name for the report. Check the View after saving option to view the saved report in a web browser.

   

Summary Reports also can be generated automatically during Import in LC Image and during Process Runs and Auto Process in LC Project. Figure 15 shows the Import dialog in LC Image, with a checkbox to "Save Summary Report". To specify the path and filename, click the "Browse" button. To configure the summary report, click the "Configure" button.

Figure 15: Save Summary Report when Import Image in LC Image.

Creating Summary Reports in LC Project

1. Go to Menu: Reports -> Summary Report.
2. Then, in the images selection dialog shown below, select the images for reporting. By default, the image reports will be concatenated in a single report. To create separate reports for each image, select "Generate Multiple Reports".

   

3. Choose “Generate New Report” or an existing configuration and then click OK
4. A configuration dialog, the same as in LC Image (shown in Figure 13), is presented. In Report Components, add or remove subsections from the report(s), as desired. Other report settings are below the section selector. Selecting "Include CSV Tables" will include links to CSV-format tables for each image in the report.
5. Click Save and a dialog will pop up for specifying the filename for the report.
6. Click OK when done. The report will be saved to the project's Reports folder.

Include External CSV Files in Report

The software allows users to include an external CSV file in a Summary Report. The software assumes that the CSV file always contains a header line. This feature provides users with complete freedom in reporting, e.g., to represent in any fashion the tabular data generated by the software.

1. Go to Menu: File -> Save Summary Report
2. Choose “Generate New Report” radio button, click OK
3. Add “External Table” to the list of included reports
4. Click “Save”
5. Choose a path for the external table associated with each image and Click “OK”.

   

6. Choose location to save report

Figure 16: A Summary Report with an external CSV table.

Filter Reports

A Filter Report provides summary information about a single dataset. Summary Reports can be saved in LC Image from the File menu or from the automated actions for Import. In LC Project, Summary Reports can be saved from the Reports menu or from the automated actions for Auto Process and Process Runs.

A Filter Report reports compounds that satisfy the conditions given in a Rule Set. A Rule Set contains a number of rules (or conditions) that can be used for filtering compounds. Each rule has the following specifications:

1. Type. The method by which compounds are specified, by:
   • Compound
   • Group
2. Name. The name specifying the compounds to be tested:
   • If Type is Compound:
     1. A named compound, i.e., the user provides the name of a compound
     2. All named compounds
     3. All compounds
   • If Type is Group:
     1. A named group, i.e., the user provides the name of a compound group
3. Expression. The expression for the rule can be a single Blob Feature or a CLIC Expression
4. Constraint. The constraint operator used with the expression (True, False, =, !=, <, <=, >, >=, Between, Not Between)
5. Values. The value(s) used with the constraint. There can be up to two values specified, depending on the constraint.

The Rule Matching Policy has two steps:

1. If a blob peak matches the Type/Name specification, the rule is applicable to it.
2. For each rule applicable to a peak, if the result of the Expression for the peak satisfies the Constraint/Values, the compound passes the rule; otherwise the peak fails the rule.

The Rule Set Configuration specifies other information:

1. Report Title. A user-specified report title.
2. Match Type. The method by which rules are combined:
   • All Pass – report the compounds that pass all applicable rules.
   • All Fail – report the compounds that fail all applicable rules.
   • Any Pass – report the compounds that pass at least one of the applicable rules.
   • Any Fail – report the compounds that fail at least one of the applicable rules.
3. Included Only. Consider only the included compounds; otherwise, consider all compounds.

The Filter Report has several components:

• The Report Title specified by the user
• A Parameters Table that contains the information about the image being reported.
• A Rule Set Table that lists the rules used for the report.
  The table header indicates the Match Type and whether or not it is for Included Only. Each rule is labeled with an ID for reference purpose.
• A Filtered Blob Table that lists the compounds satisfying the rule set.
  Each row is for one compound. The first column gives the Compound Name (or ID if there is no name). Subsequent columns give each rule's Result and a Pass/Fail (P/F) indicator for each result. After that is a list of features for the compound.

Filter reports can be saved in both LC Image and LC Project. In LC Image, select Menu: File -> Filter Report. In LC Project select Menu: Reports -> Filter Report.

There are 4 steps to create a report:

1. Create a new Rule Set or Open an existing Rule Set.

   To create a new rule set, select the “New Rule Set” option as shown in Figure 17.

   To open an existing rule set, choose the “Open Existing Rule Set” and select a rule set from the list. A user also can select an existing rule set at other locations by browsing.

   Figure 17: Create or select a Rule Set.

   Click “Next” when done.

2. Modify the Rule Set and configurations for the report (optional for existing Rule Sets).

   The rule set can be modified by adding a new rule, editing an existing rule, or deleting an existing rule as shown in Figure 18.

   Figure 18: Edit a Rule Set.

   Edit a rule by selecting a row on the table, then click “Edit”. An editing window will popup for entering the fields for the rule as shown in Figure 19.

   Figure 19: Edit a Rule.

   Click “Next” when done. If the Rule Set is new or modified, the user will be prompted to save.

3. Select images for the report.

   In LC Image, the currently open image will be used to generate the report. In LC Project, a user can select one or more images to which the Rule Set will be applied as shown in Figure 20.

   Figure 20: Select image(s) for filtering.

   Click “Finish” when done.

4. Specify a file name for the report, then click “OK” to save the report.

Fractional Response Reports

The Fractional Response report provides the response (i.e., volume) of each included blob, group, constellation, and blob set as a percent of the sum of the responses (i.e., volumes) of all detected blobs which have not been excluded. The Fractional Response report expands on the percent response statistic in the blob table.

First, the user selects Fractional Response from the Reports menu of LC Project. Then, LC Project presents a chooser listing all of the batches and all of the processed images in the project, as illustrated in Figure 21. The user selects a batch or processed image by clicking on it in the Available list and then clicking the '>' button to select the choice. A selected batch or processed image can be deselected by clicking on it in the Selected list and then clicking the '<' button to deselect the choice. After selection is finished, the user clicks OK and is prompted for the output file format and name.

Figure 21: The Fractional Response report tool.

As shown in Figure 22, the Fractional Response Report for a processed image has:

• a title and subtitles;
• a parameter table with the vial, run, and image names;
• a blob fractional-response table with a row for each included blob in the image and a row for the residual (total for all of the blobs that are neither included nor excluded);
• a group fractional-response table with a row for all of the blobs in each named group and a row for the residual (total for all of the blobs that are neither reported in a group nor excluded);
• a constellation fractional-response table with a row for all of the blobs in each named constellation and a row for the residual (total for all of the blobs that are neither reported in a constellation nor excluded); and
• a blob-set fractional-response table with a row for each included blob-set.

The fractional responses in the blob, group, constellation, and blob-set tables are given as percentages of the total of all blobs (not including blobs that are excluded or in an excluded blob set).

If a batch with multiple processed images is selected for the report, all of the images in the batch are reported in sequence. Then, at the end of the report, there are consensus blob, group, constellation, and blob-set tables with mean, standard deviation, and count for each row in each table.

Figure 22: A Fractional Response report formatted in XML.

Corrected Response Reports

The Corrected Response Report uses response factors to adjust or correct the system's differing responses to different compounds. For each compound, the corrected response is computed as the response for the blob multiplied by the response factor for the compound. The response factor is determined by:

1. If the blob is named and the compound name is found in the Chemical Properties Table, then the response factor for that compound is taken from the Chemical Properties Table.
2. If the blob is not named or if the compound name is not found in the Chemical Properties Table, then the response factor is either the response factor of a nearest neighbor or a constant value (depending on the configuration of the report. To find a nearest neighbor with a response factor, the blobs are prioritized by group, then constellation, and then all others.

The Corrected Response Report has two selectable sub-reports: a response factor table and a sample report. Figure 23 shows the Corrected Response Report dialog. Figure 24 shows an example Corrected Response Report.

Figure 23: The Corrected Response Report dialog.

Figure 24: A Corrected Response Report.

Internal Standard Reports

Internal Standard reports, such as ASTM D5580, report the amounts of compounds in a sample relative to internal standards. This report requires calibration runs, with known ratios of target compounds and internal standards, and a sample run, which includes a known amount of internal standards and a known amount of sample. (An entry with the name "Sample" and the amount or relative amount of the sample should be present in the constituent amount table of each sample vial.)

First, the user selects ASTM D5580 or Internal Standard from the Reports menu of LC Project. Then, LC Project presents a configuration dialog with chooser, shown in Figure 25. The chooser for Internal Standard reports requires selection of a calibration batch and sample pair. The user selects the calibration batch in the Calibration list and a sample in the Sample list, then clicking the '>' button to select the pair. A selected pair can be deselected by selecting it in the Selected list and then clicking the '<' button to deselect the choice.

Figure 25: The Internal Standard Report Dialog.

The user also selects from the various sub-reports available, e.g., calibration report, sample report, etc. After all selections are made, the user clicks OK and is prompted for the output file format and name.

The Internal Standard report for a processed image has:

• a title and subtitles;
• a parameter table with the vial, run, and image names; and
• subreports with tables and graphs.

An example calibration graph for one of the target compounds is pictured in Figure 26 and a table of compounds and groups is pictured in Figure 27.

Figure 26: Calibration Graph.

Figure 27: A table of compounds and groups.

External Standard Reports

To generate an external standard report, select External Standard from the Reports menu of LC Project. Then, LC Project presents a configuration dialog with chooser. The user selects an image in the Available list, then clicks the'>' button to select the sample. A selected sample can be deselected by selecting it in the Selected list and then clicking the '<' button to deselect the choice.

The user also can select from the various sub-reports available, e.g., calibration report, least square fit, sample report, an linearity test. For linearity test, the user also must input a pass/fail threshold. Finally, the user must enter the location of the calibration file. After all selections are made, the user clicks OK and is prompted for the output file format and name.

Retention Time Reports

The Retention Time report provides a formal report format for the peak retention times. The Retention Time report is a more formal formatting of the peak retention-time statistics in the blob table.

First, the user selects Retention Time from the Reports menu of LC Project . Then, LC Project presents a chooser listing all of the batches and all of the processed images in the project. The user selects a batch or processed image by clicking on it in the Available list and then clicking the '>' button to select the choice. A selected batch or processed image can be deselected by clicking on it in the Selected list and then clicking the '<' button to deselect the choice. After selection is finished, the user clicks OK and is prompted for the output file format and name.

As shown in Figure 28, the Retention Time Report for a processed image has:

• a title and subtitles;
• a parameter table with the vial, run, and image names; and
• a retention time table with the compound name, the count of images in which the named compound occurs, and the mean and standard deviation of retention time in each dimension for the compound.

Figure 28: A Retention Time Report formatted in XML.

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GC Image (LCxLC Edition)™ Users' Guide © 2001–2011 by GC Image, LLC, and the University of Nebraska.