GC Image Users' Guide

File Input and Output

GCxGC chromatograms have an intensity value (or total intensity value for MS data) for each chromatographic data-point pixel. GC Image supports full double-precision floating-point representation, which is higher precision than most digital image formats and many chromatographic and multi-spectral formats. For this reason and to support storage of ancillary data, GC Image employs special file formats for representing GCxGC chromatographic images and metadata. For each GCxGC image, there are two files:

• A GCI file with .gci extension stores ancillary data about the image (e.g., its size, color mapping, etc.) in plain text format tagged using an eXtensible Markup Language (XML) schema for GCxGC images.
• A binary file. For GCxGC, the file has a .bin extension and stores the binary image data in time order, each value stored as number, with support for representations up to IEEE double-precision, floating-point (with big-endian byte order). For multi-channel or multi-spectral data, GC Image uses a different binary format, described in GCxGC-MS Data.

File Menu Options

The File menu in the Image Viewer provides access to utilities for image input and output, including:

• opening and saving images in the GC Image file formats,
• importing and exporting images in other file formats,
• exporting and importing image models and,
• printing images.

In addition images (or images of 3D views) can be copied to the system clipboard (from where they can be pasted into other applications), by clicking on the image pane (or 3D view pane) and then pressing the <F2> key. The user is asked to choose either to copy the full image or to copy a selected region. (The full image is copied from 3D view.) A region is selected by click-and-drag of the left mouse-button.

As illustrated in Figure 1, there are several File menu options for input and output.

Figure 1: The File menu with the Import Image option selected.

Specifically, the image input and output options are:

• File->Open Image launches a file-system browser to open an image file in GC Image format. The user specifies the folder and GCI filename (with .gci extension). GC Image also expects a binary file (e.g., a file with .bin or .cdf extension) in the same folder and with the same root filename. If there is a currently open image, another GC Image process is initiated.
• File->Save Image saves the current open image to the GCI file (with .gci extension) and binary file (e.g., a file with a .bin or .cdf extension) from which it was opened or to which it was last saved (whichever is more recent). The image remains open. This menu option is not available if no image is open.
• File->Save As launches a file-system browser to save the current image to a file specified by the user. The user specifies the folder and GCI filename (with .gci extension) and GC Image also saves a binary file (e.g., a file with a .bin or .cdf extension) in the same folder and with the same root filename. The current open image remains open, but the associated file location and name is changed (e.g., for subsequent Save operations). This menu option is not available if no image is open.
• File->Close Image closes the image without saving. If the image has been altered since the last Save or Save As operation, the user is prompted whether or not to save the image before closing. It is best to save the image, if that is desired, before requesting the image be closed. This menu option is not available if no image is open.
• File->Recent Images provides a sub-menu list of the most recently opened images. An image file in the list can be opened by simply selecting the file name from the list. If there is a currently open image, another GC Image process is initiated.
• File->Import Image provides a file-system browser to specify the source location of the foreign-format file. The determination as to the source image file format is made on the basis of the file name extension, so files to be imported should be named with the proper extension. When imported, the image is converted from the foreign file format. GC Image also creates a binary file (with .bin extension or with a .cdf extension for MS files) in the same folder and with the same root filename. If there is a currently open image, another GC Image process is initiated for importing the image. A destination file name is automatically generated for the file from the source name (e.g., example.CVS_img02.gci).

  GC Image can import images in a variety of file formats. The import source file browser offers an "All Supported Files" format filter, as well as individual format filters. The import source file format filter defaults to the "All Supported Files" format.

  Extension	Format
  .7if	JEOL MassCenter Centroided MS Data Format.
  .asc	ASC - Thermo ASCII XY text format. Metadata values are read for "Sampling Rate" and "Y Axis Multiplier".
  .bin	Binary - big-endian, IEEE, single-precision, floating-point; optional byte-swapping supports little-endian format.
  .bmp	Bitmap - common Microsoft Windows format.
  .cdf	NetCDF - Analytical Data Interchange (ANDI) Protocol for Chromatographic and Mass Spectrometric Data, based on the Unidata/UCAR network Common Data Format.
  .ch	CH - Agilent ChemStation IQ Data File Format. Currently, all data values are imported, but not all metadata values are read.
  .csv	CSV - Comma-Separated-Values in text format; each line is "<time>, <value>" or each line has "<value>" only, without time or comma.
  .D	Agilent Mass Hunter .D Data Folder. (Note: the same extension also is used by Agilent ChemStation. GC Image automatically recognizes Mass Hunter .D data folders and displays them with a special icon. For a ChemStation .D data folder, GC Image can import .ch, .ms or .uv files under the folder directly.)
  .gcd	GCD - Shimadzu GCsolution Data File Format.
  .gctm	Text format - GC Image Text Multi-Spectrum Format.
  .gif	GIF - Graphics Interchange Format.
  .h5	HDF5 - Zoex FasTOF HDF5 File Format.
  .jpg	JPEG - Joint Photographic Experts Group format.
  .ms	MS - Agilent Mass Spectral Data File Format. Currently, all data values are imported, but not all metadata values are read.
  .mzData	mzData - Open data format for storage and exchange of mass spectroscopy data developed by the Human Proteome Organization (HUPO).
  .mzXML	mzXML - Open data format for storage and exchange of mass spectroscopy data developed at the SPC/Institute for Systems Biology.
  .peg	PEG - LECO file format for collected raw FID and MS data. (Note: the reader is unofficial and was tested only with files generated with ChromaToF 4.2. A known limitation is that the reader does not read the start time from FID data files and the modulation period.
  .png	PNG - Portable Network Graphics format.
  .qgd	QGD- Shimadzu GCMSsolution Data File Format.
  .sed	SED - SAI Experiment Description File Format for High-Precision Mass Spectral Data. (Data from recent versions may not be supported.)
  .tif	TIFF - Tagged Image File Format.
  .txt	Text format; each line ends with a value, possibly preceded by other text separated by a tab, colon, semi-colon, comma, or space.
  .uv	UV - Agilent ultraviolet liquid chromatography Data File Format.

  Most of these formats do not provide double-precision floating point numbers for scientific work. Color image formats may yield unexpected results when the values are extracted. Common import formats for GCxGC data are ASC, CH, CSV, and binary. Common import formats for GCxGC-MS data are CDF or MS. Contact GC Image, LLC to request support for additional binary and plain-text formats.

  After the source is specified, GC Image presents a dialog for import options, shown in Figure 2

  Figure 2: The Import Options dialog.

  There are three sets of import options to define what processing should occur when the raw data is imported. Most of these options are optional and do not need to be specified.

  1. General options:
     • LIMS Number
       The LIMS number is a number that indicates a set of runs from a vial related to a specific request. If a data file is an Agilent CH file and is inside a .D folder with a SAMPLE.MAC file, GC Image will try to read the LIMS number from the Sample Info field automatically.
     • Parameters
       For file formats that do not provide the modulation period, the user must enter the length of the modulation period in seconds. For file formats, such as CSV, that do not supply the dimensions of the image, the user must enter dimensional parameters (in pixels or time units) and the sampling rate in the pop-up dialog. If desired, the start time can be set to a non-zero offset. If the image metadata values are read from the source file, the value fields in the pop-up dialog will have values and be gray. Grayed values may be overridden by double-clicking in the text box and then entering a value.
     • Padding
       If the modulation period times the sampling rate is not an integer number of samples, the user may indicate whether or not padding should be performed and if so whether or not the padding details should be shown. If padding is performed, the number of pixels in each secondary chromatogram is rounded up to the next largest integer and one pixel in the background of some secondary chromatograms is duplicated to compensate for the extra, fractional sampling intervals in every secondary chromatogram. Padding typically is used to maintain timing synchronization between the data and modulation cycles across the chromatogram.
     • MS/MS Options
       The software supports extracting MRM data from a sequence of MS2/MRM spectra with a user-defined precursor ion list specified in a comma-separated format (e.g., "419,397,381,363") and integrating MS2/MRM spectra into MS1 spectra. The precursor must be listed in the exact same order as they appear in the raw data file in order to be correctly imported.
     • Multi-Spectral Filter
       The Multi-Spectral Filter is used to limit the intensity values that are imported. If No Filter is chosen then all multi-spectral data will be imported. Range Limit limits the data imported by importing only those spectral channels that are within the specified ranges (e.g., 91.1-104.8,115.25). Threshold Limit limits the data imported by importing only those spectral intensities that are greater than the specified threshold. Ordinal Limit limits each spectrum to the specified number of values that have the largest intensities. Any combination of limits can be used when importing. For example, if only the 10 largest intensities in each spectrum are required and intensities less than 10000 can be ignored, then use Threshold and Ordinal limits with values 10000 and 10 respectively.
  2. Advanced options:
     • Interpolation
       For some formats with time stamps for each data value, the import dialog has an optional flag to indicate that missing data values should be interpolated by nearest-neighbor or linear interpolation, or that the missing values should be filled by zeroes.
     • Cropping/Prepending/Appending
       The image can be altered by adding or removing data through the CPA (Cropping, Prepending, Appending) interface. GC Image will ignore CPA fields that are left blank. For example, if the first dimension is from time "blank", to five minutes, the regular start time will be used and the imported image will run until it reaches five minutes or end of file. The lower bounds for first and second dimensions are zero.
     • Transformation
       The image can be transposed so that its columns become rows. Visually the original image is rotated a 90 degree clockwise and then mirrored on a horizontal line. The software assumes the sampling rate is unchanged and recalculates the modulation period based on the new column size.
  3. Automated actions:
     If desired, the user may choose to apply a specified processing configuration file, as described in Configuration Files . If desired, designate optional phase shift, optional background removal, optional blob detection (if background removal is performed), optional template matching with a specified template file (if blob detection is performed) with a specified template, optional saving of the blob table to a specified file (if blob detection is performed), optional saving of summary report, optional saving of the image to a specified file, and optional exiting. These operations are described in subsequent chapters.

File->Print Image launches a print dialog to print an image, shown in Figure 3. The user can preview the printed page at varying magnifications; can control margins, orientation, and alignment; can stretch the image to a full page (changing aspect ratio); and can choose to attach or not to attach axes. Also, regions can be copied to the clipboard from the image view or 3D view, with the <F2> key, as described above and individual windows can be copied to the clipboard with the <ALT>-<PrtSc> keys, and then pasted into other applications (e.g., presentation software).

Figure 3: The Print dialog.

The File menu also provides options for reading and writing image-related data:

• Save Blob Table - save blob peak table as text in comma-separated-file (.csv) format.
• Save Blob Set Table - save blob set table as text in comma-separated-file (.csv) format.
• Save Summary Report - Save Summary Report.
• Save Template - save blob peak template as text in XML format.
• Import Graphics - import a graphics table.
• Export Graphics - export a graphics table.
• Save Journal - Save viewable journal of actions.
• Save Script - Save runnable script of actions.

and an option to exit:

• Exit - terminate the program.

The options for saving blob peak tables and templates are described in Blob Analysis and Chemical Identification. The options for importing and exporting graphics tables are described in Graphics and Areas. When the exit action is selected, the currently open image is discarded. If an image is open and has been altered since the last Save or Save As operation, GC Image prompts the user whether or not the image is to be saved before exiting. It is best to save changed images that are to be retained when they are changed to prevent the loss of unsaved work (e.g., in the event of a system crash or power failure) and before requesting the program to exit.

Image Attributes

The software provides basic information about the chromatogram (acquisition conditions, operator name, etc.) in Image Attributes. It can import and display additional readable metadata such as instrument model, method file and sample name, from data files generated by Agilent ChemStation. It also allows users to add and edit custom metadata fields. The Image Attribute dialog has two tabs as shown in Figure 4. The “General” tab shows the general image information. The “Miscellaneous” tab shows the metadata imported from raw data files. These imported metadata information are marked as “Instrument” and cannot be edited or deleted.

a. General Attributes.	b. Miscellaneous Attributes.
Figure 4 The Image Attributes Dialog.

To add or edit custom metadata in Image Attributes:

1. Go to Menu: View > Image Attributes
2. To add a custom metadata to the table click the Add Row button and enter Name and Value.
3. To delete a custom metadata select a row and click the Delete Row button.

LIMS Number

GC Image supports assigning a LIMS number that indicates a set of runs from a vial related to a specific request. If a data file is an Agilent CH file and is inside a .D folder with a SAMPLE.MAC file, GC Image will try to read the LIMS number from the Sample Info field automatically. Once assigned the LIMS number will be reported as part of Image Attributes sub-report in Summary Report.

• Assign LIMS Number When Import Image
  GC Image allows setting a LIMS number when importing an image.
  1. Go to Menu: File > Import Image.
  2. Select a file and OK.
  3. In the Import dialog, specify the LIMS number.

  If a LIMS number already exists in the file, it will preload to the field and the field will be grayed. To edit the number, double click on the field to enable editing.

• View/Edit LIMS Number in Image Attributes
  GC Image allows viewing and editing the LIMS number in an open image.
  1. Go to Menu: View > Image Attributes.
  2. To edit the LIMS number, double click on the field to enable editing.
  3. Click OK to apply the new LIMS number to the image.
• Assign LIMS Number in Sequence Table
  GC Project allows setting the LIMS number for a run in a Sequence Table in GC Project. The sequence table then can be used in Auto Process and the specified LIMS number will be assigned to each processed image.
• Assign LIMS Number in Run-Vial Association
  GC Project allows setting of the LIMS number for a run when associating it with a vial. If a LIMS number is not specified, GC Project will try to read it from the .D folder if the run file is an Agilent CH file. Otherwise, the specified LIMS number will be used. After the association is established, the specified LIMS number will applied to the images in Process Run.

Contents Previous: Image Viewer Next: Visualizing Image Data

GC Image™ Users' Guide © 2001–2010 by GC Image, LLC, and the University of Nebraska.