GC Image Users' Guide

New Features and Improvements in Release 1.5

GC Image Release 1.5 has many new features and improvements. The GC Image Users' Guide soon will be updated to fully document these enhancements.

Text elements and labels:
- Text elements - Users can add text elements to images and templates and set display parameters such as font, font style, and font size.
- Text labels for blobs and graphics elements - Users can set flags in blobs and graphics elements to display the name in a text label.
- Text configuration - Users can set the default font characteristics for text elements and labels.
Graphical elements for excluded blob sets:
- Exclusion flag for graphical elements - Users can set an exclusion flag for graphical elements so that the indicated blob sets are excluded from processing and reporting.
- Improved percent response computation - Percent response values exclude blobs in excluded graphical elements from the total response (the denominator in the computation).
Improved tools for blob information:
- Multiple blob display configurations - Users can set up multiple blob display configurations and toggle or cycle between modes with the 't' (or 'T') key.
- Configurable mouse-overs for blob metadata - Users can define the meta given in blob mouse-overs.
- Set blob metadata in the blob table tool - Users now can enter blob metadata (such as the chemical name, chemical group, and inclusion flag) directly in the blob table tool.
- Bubble plots for blob highlighting - Users can graphically highlight blobs with disks indicating both retention times (by image location) and volume (by disk size).
- Improved interactivity with the blob table - The blob table tool has other improvements for interactivity, including highlighting of blobs selected in the image and maintaining sort order.
Improved tools for GCxGC-MS:
- Improved baseline correction for GCxGC-MS - Each channel of the GCxGC-MS data is baseline corrected.
- ANDI compatibility - GCxGC-MS import and export of GCxGC-MS data maintains ANDI compatibility.
Enhanced I/O options and file information:
- Time offset - Users can set the start time of the data to a non-zero offset.
- Modulation cycle not evenly divisible by the sampling interval - Users can correct for modulation cycles that are not integer multiples of the sampling interval. The software leaves all data as it is acquired and pads the background as necessary to create a rectangular image.
- Import chromatography files in ANDI format - Users can import chromatography files in the ANDI format.
- Image attributes tool - Users can display a popup window that displays information about the image (acquisition conditions, operator name, etc.).
Improvements in GC Project:
- Group processing and review - Users can select sets of runs for automated processing or select sets of images for sequential review.
- External standard reports - Users can create reports using external standards.
- Response factors - Users can create fractional response reports that correct fractional responses by chemical response factors.
- Retention-time template report - Users can generate a template from consensus retention times.
- File copy tool - Users can copy files to project directories without leaving GC Project.
Improved 3D perspective view:
- Vertical scaling for 3D perspective view - Users can set relative or absolute scaling for 3D perspective view.

Additional short-cuts and hot-keys:

Menu Short-cuts - Use the <Alt>-key plus short-cuts to access any menu option from the keyboard.
Menu Hot-keys - Use <Ctl>-key combinations and other hot-keys to access common menu options from the keyboard.

Palette Mode Hot-keys - Use <Ctl>-key combinations to change the palette mode.

Keystroke(s)	Action
<Ctl>+O	Open Image
<Ctl>+S	Save Image
<Ctl>+I	Import Image
<Ctl>+A	Select All (depending on palette mode)
<Ctl>+X	Cut blob metadata
<Ctl>+C	Copy blob metadata
<Ctl>+P	Paste blob metadata
<F3>	Find blobs (in blob palette mode)
<Del>	Delete or exclude selected object(s) (depending on palette mode)
t or T	Toggle blob display configuration
<Arrows>	Pan or scroll the image
<PgUp> and <PgDn>	Scroll the image with large steps
<Ctl>+1	View palette mode
<Ctl>+2	Text palette mode
<Ctl>+3	Graphics palette mode
<Ctl>+4	Blob palette mode
<Ctl>+5	Multi-channel palette mode
<Ctl>+6	Template palette mode

General improvements:
- Automated intensity mapping - User's can specify automated value mapping so that the full color scale is used to highlight peaks.
- Dialog position and size - During a session, dialogs are opened with the previous position and size.
- Chemical properties - Additional properties were added to the chemical properties table.
- Virtual memory configuration - Users can set the virtual memory configuration for GC Image according to system resources. (The software must be restarted for the change to be effective.)

Improvements in Release 1.5b1

Fixed a bug that caused the start time of Agilent CH files to be interpreted in seconds rather than milliseconds.
Fixed a bug that caused a failure to import ANDI/netCDF-format files in which there are fewer MS points than samples.
Changed the test for a USB key to terminate the program only after two consecutive polls of the USB key have failed. Previously, the program was terminated after a single poll failed.
Compiled with an updated compiler. This recompilation may help with occasional out-of-memory errors in three-dimensional viewing. This error is caused by a memory management failure in the operating environment. In addition to recompiling the code with the new compiler, we also have added additional code intended to force the operating environment to increase available memory. We believe that these steps will prevent or reduce occurrences of this problem, but users who experience out-of-memory errors can take the following additional steps:
1. Make sure the "Virtual Memory" setting of the software is appropriate. In general, it should be as large as the computer's RAM. At least 1GB RAM is recommended. The "Virtual Memory" setting is available on the "System" pane of the "Configuration" tool, which is invoked from the "Configuration" menu. Any changes to the "Virtual Memory" setting are effective only after the software is restarted.
2. Close other memory intensive programs during execution.
3. Run only one three-dimensional view at a time.
4. After closing a three-dimensional view, wait at least 10 seconds before starting a subsequent three-dimensional view.
5. Occasionally, click the "Collect Garbage" button to request that the operating environment increase available memory. The "Collect Garbage" button is available on the "Memory Monitor" tool, which is invoked by the "Show Memory Usage" button on the toolbar.
6. After several invocations of three-dimensional viewing, save and close the software at a convenient time. Restarting the software provides the maximum memory available. So, for example, after finishing with one image, closing and restarting the software to process a subsequent image will provide the maximum memory available.
7. If an out-of-memory error does occur, either (a) wait a few seconds for more memory or (b) invoke garbage collection as described above before proceeding. Either may provide enough memory to proceed. Otherwise, save the image and then close and restart the software.

Contents Next: Introduction