GC Image (LCxLC Edition) represents LCxLC images in two files:
- A 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 LCxLC images.
- A file with .bin extension stores the binary image data in time order with each value stored as a number, with support for representations up to IEEE double-precision, floating-point (with big-endian byte order).
GC Image (LCxLC Edition) can import images in a variety of file formats.
Extension Format .asc ASC - Thermo ASCII XY text format. Currently, 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 Mass Spectrometric Data, based on the Unidata/UCAR network Common Data Format. Currently, not all ANDI metadata values are read. .ch CH - Agilent Chemstation IQ Data File Format. Currently, 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. .gif GIF - Graphics Interchange Format. .jpg JPEG - Joint Photographic Experts Group format. .ms MS - Agilent Mass Spectral Data File Format. Currently, not all metadata values are read. .png PNG - Portable Network Graphics format. .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.
Step 1: Select Import Image from the File menu
of the Image Viewer (or the Import Image button from
the Image Viewer tool bar).
Step 2:
LC Image presents a pop-up dialog box for specifying the source and
destination folders and filenames.
Specify the source and destination folders and filenames,
either by typing in the text boxes or by using the file-system browsers.
The determination as to the input image file type is made on the basis of the file name extension, so files to be imported should be named with the proper extension. For more information on importing images, see chapter File Input and Output.
Step 3: For file formats, such as CSV, that do not supply the
acquisition parameters of the data, enter size parameters (in either
pixel or time units) in the pop-up dialog box. For file formats, such
as CDF, CH, and MS, that may supply the acquisition parameters, values
from the file are presented in gray boxes. If it is necessary to
override a value read from the file, double-click on the dialog box.
Step 4: If desired, choose to apply a specified processing configuration file and indicate the file.
Step 5: 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 the image to a specified file, and optional exiting.
Step 1: Select Open Image from the File menu
of the Image Viewer (or the Open Image button from the
Image Viewer tool bar).
LC Image launches a file-system browser to locate the folder and
.gci file.
Step 2: Specify the folder and filename in the file-system browser.
Step 1: Select an image from the sub-menu list for the Recent
Images item on the File menu of the Image Viewer.
Step 1: Select Save Image from the File menu of the
Image Viewer (or the Save Image button from the Image Viewer
tool bar).
Step 1: Select Save As from the File menu of the
Image Viewer.
LC Image launches a file-system browser to specify the folder and
GCI .gci filename.
Step 2: Specify the folder and filename in the file-system browser.
Step 1: Select Export Image from the File menu
of the Image Viewer.
LC Image launches a file-system browser to specify the folder and
GCI .gci filename.
Step 2: Specify the folder and filename in the file-system browser. Also, choose to attach or not to attach axes to the exported image.
Step 1: Click on the image in the Image Viewer.
Step 2: Type the <F2> key.
Step 3: On the popup dialog, choose to copy the visible pane or to copy only a region.
Step 4: If capturing only a region, click-and-drag with the left mouse-button to indicate a the rectangular region.
Step 1: Select Print Image from the File menu of the Image Viewer.
LC Image launches a print preview popup to specify the printing layout.
Step 2: Specify the printing layout and click the Print button.
Step 1: Select Close Image from the File menu of the
Image Viewer (or the Close Image button from the Image
Viewer tool bar).
When Close Image is selected, the current image is discarded. If the current image has been altered since the Save Image or Save As operation for that image, LC Image prompts the user whether or not the image is to be saved before closing. It is best to save all 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 image be closed. This menu option is not available if no image is open.
The Image Model is an XML-based format that distills essential information from the LCxLC data in a form that is smaller and easier to communicate than full LCxLC datasets. The model represents peaks by horizontal and vertical profiles computed by directional integration. Multi-channel (e.g., MS) models contain spectral profiles with channel-intensity values for each peak.
Step 1: Select Export Image Model from the File menu of the Image Viewer. LC Image launches a file-system browser to specify the folder and Image Model file name with extension .gcm.
Step 2: Specify the folder and filename in the file-system browser; then save.
Step 1: Select Import Image Model from the File menu of the Image Viewer. LC Image launches a file-system browser to specify the folder and Image Model file name with extension .gcm.
Step 2: Specify the folder and filename in the file-system browser; then open.
If the modulation period is not an integer multiple of the sampling rate, then there are a fractional number of samples per modulation cycle. For example, if the modulation period is 8 seconds and the sampling rate is 24.6Hz, then there are 196.8 samples per modulation cycle. In that case, the first 8/10ths of the 197th pixel are in the initial modulation cycle and the last 2/10ths of the 197th pixel are in the subsequent modulation cycle. This presents an issue for displaying the data so that the samples for each modulation are used to form one column of pixels in the image.
Padding is a method of dealing with fractional samples that are split between modulation cycles. If an imported image is padded, the number of pixels per column is set to the smallest integer that is greater than the number of pixels per modulation period. In the example above, the image size is set to 197 pixels (the smallest integer greater than 196.8). Then, the first 197 samples are included in the first column and the next 197 samples are included in the second column. However, if 197 samples are included in each column, the pixels drift 0.2 pixels per modulation cycle from the actual samples in the modulation cycle. In the example, as illustrated in the "No Padding" column of the table below, the image with 197 samples per image column drifts a full sample every 5 columns.
| Column | Actual | No padding | Padding |
|---|---|---|---|
| 0 | 0.0-196.8 | 0.0-197.0 | 0.0-197.0 |
| 1 | 196.8-393.6 | 197.0-394.0 | 197.0-394.0 |
| 2 | 393.6-590.4 | 394.0-591.0 | 394.0-590.0 |
| 3 | 590.4-787.2 | 591.0-788.0 | 590.0-787.0 |
| 4 | 787.2-984.0 | 788.0-985.0 | 787.0-984.0 |