GC Image Users' Guide
New Features and Improvements in Release 1.6
GC Image Release 1.6 has many new features and improvements.
- Image Comparisons.
GC Image has a new image comparison tool which provides 2D, 3D, and
tabular comparative visualizations.
Users select a reference image to be compared to the current analyzed
The reference image is registered and scaled to the analyzed image.
Then, users can view 2D images of the grayscale difference, colorized
difference, fuzzy difference (grayscale or colorized), ratio (grayscale
or colorized, direct or fuzzy), color addition, or flicker.
The 3D view is based on an elevation map of the difference, value of
either image, or maximum at each pixel with a color overlay of one
of the 2D images.
The interactive tabular view provides a sortable table of quantitative
data and comparisons and interactive control of graphical highlights
in the image view.
- Deconvolution and unmixing co-eluting peaks.
GC Image has a new deconvolution and unmixing tool that supports
optional separation of co-eluting peaks.
Users select one or more blobs containing two or more chemical peaks.
The peaks are extracted from the blobs based on a separable model with
shift-variant peaks for single-channel (e.g., FID) data and or on a
tri-linear model for multi-channel (e.g., MS) data.
The tool displays the resulting separation for the user to accept
The Configure->Blob Detection pane has parametric settings
for deconvolution and unmixing.
New features in other tools support overlapping peaks created by
deconvolution and unmixing.
In blob palette mode of the image viewer, a left-button click selects
the peak with the smallest ID at the current location.
Other peaks overlapping at that location can be selected with the
<TAB> key (which deselects the current peak and selects the peak
with the next smallest ID at that location) or the <CTL>+<TAB>
keys (which maintains selection of the current peak and cycles to the
peak with the next smallest ID at that location without selecting it).
In text view, there is a toggle switch to show (or not show) peak
If the toggle is off, only the pixel values are shown. If the toggle
is on, the text view also shows, at each pixel, the ID and percentage
value for each peak overlapping the pixel.
The blob edit tool, described below, also has new facilities for
handling overlapping peaks.
- Blob edit tool improvements.
The blob edit tool has several new features.
Most notably, the blob edit tool allows interactive rescaling and
A rectangular region of interest can be selected for rescaling and
resizing by click-and-drag of the mouse right-button.
The blob edit tool also supports overlapping peaks (generated by
deconvolution or unmixing).
The <TAB> key and <CTL>+<TAB> keys are used to select
from multiple overlapping peaks, as described above.
The one-dimensional horizontal and vertical profiles show total
value and individual peak values at each pixel.
The merge blobs utility requires a click of the merge blobs button
to complete the operation (so that the overlapping peaks can be selected).
- Image view improvements for 2D and 3D.
The 2D and 3D image views have several new facilities.
The pull-down scale menu now includes a "Fit View" option to resize
and rescale the image to the view window.
The resize dialog (accessible from "View->Resize"), has fields to
set the position of the image in the viewport as well as the image
GC Image now maintains a view stack and provides arrow buttons on the
toolbar to move backward (previous) and forward (next) between different
Users can now select different image interpolation modes: nearest
neighbor, bilinear, and bicubic.
Bilinear interpolation, used in previous versions, is still recommended
for general use.
Users can copy the 2D and 3D image views to the clipboard (from
which they can be pasted into other applications).
Just click on the image and type the F2 key.
In 2D copy, users can select the entire image or a portion of the
Users can quickly export 3D images to a file using a button
on the 3D view panel.
Users have more flexibility in the 3D view, including toggles for
including the axes and region box, a toggle for opening and closing
the 3D control pane, and cursor keys for navigation.
- Blob table improvements.
The blob table includes several additional fields.
Separability and Largest Border Value are useful indicators for
blobs that may be co-eluted or otherwise misshapen.
Separability measures the fit to the data by the separable product
of the integrated horizontal and vertical profiles.
(Fidelity is one minus the ratio of the pixelwise sum-of-square-differences
to the sum-of-square-intensity.)
The largest border value is the largest value among pixels on the
border (edge) of the blob.
The blob table contains fields for values returned by the NIST MS library
search software, including CAS#, Formula, Match Factor, Molecular Weight,
Name, Probability, and Reverse Match.
The blob table has a new mode for viewing excluded blobs.
GC Image now maintains metadata for excluded blobs.
- Blob set table improvements.
The blob set table now includes sets of peaks that share the same
group name (in addition to sets of peaks indicated by a graphical
This provides a comprehensive view of blob sets defined by both peak
metadata and graphical selectors.
- Image model export and import.
GC Image now supports export and import of image models.
These models allow users to extract information in a model that
is smaller and easier to communicate than large GCxGC datasets.
The models consist of horizontal and vertical profiles computed by
Multi-channel (e.g., MS) images contain profiles for each channel.
Other models will be developed and supported in future versions.
- CLIC tool improvements.
The calculator tool for the Computer Language for Identifying Chemicals
(CLIC) has several improvements.
Functions are available to access blob features, such as volume, peak
The CLIC tool can be used with single-channel (e.g., FID) images as
well as multi-channel images (e.g., MS).
Multiplication and division are implemented.
The interface for managing user-defined expressions is improved, e.g.,
for deleting unwanted expressions.
The interface for typing in the expression field is improved.
- Import data files in Agilent MS format.
GC Image now imports data stored in the Agilent MS file format.
- 2005 NIST/EPA/NIH Mass Spectral Library and Search Software.
GC Image is compatible with NIST05, the latest version of this popular
mass spectral library and search software.
NIST05 contains major enhancements:
For competitive pricing and information about purchasing NIST05,
190,825 EI mass spectra of 163,198 different chemical compounds --- approximately 20,000 additional EI spectra. Two CDROMs, with all ASCII and binary formats distributed by NIST, are included.
Improved quality, e.g., consistency of naming and structure representation, resolution of chemical structure ambiguities arising from different forms of the same compound, linking of closely related compounds with similar spectra (stereoisomers), and hundreds of spectra measured on ion trap instruments.
Gas phase retention index data and estimates. The data includes gas-phase retention indices on non-polar columns, with the Kovacs retention indices of 25,893 compounds. The estimated retention indices are provided for most compounds in the library, with recommended uncertainties, will allow removal of many false hits.
5,191 MS/MS spectra for of 1,943 different ions, most measured on ion trap and triple quadrupole instruments.
Search Program v.2.0d and Amdis 2.62.
- Other improvements.
Users can now set the threshold for rounding m/z values to integers.
Floating point m/z values must be converted to integers for searching
the mass spectral library.
Previously, 0.5 was the threshold for rounding up to the next largest
Now, the value can be configured to any non-negative value less than 1.0.
GC Image now supports arithmetic division by a scalar or another image.
The metadata dialog for multiple blobs provides additional functionality,
e.g., clearing the name, group, or constellation of all selected blobs.
There is a new button to clear all blob metadata, graphics, and text
in a single operation.
Previously, this operation could be performed only by separately
selecting and deleting all objects of each type.
This operation must be confirmed by the user.
There is now an option on the Edit menu to undo all operations.
This operation must be confirmed by the user.
Text objects and labels now are exported and imported with other
The configuration tool has a tabbed dialog for setting characteristics
for text objects.
The configuration tool has a tabbed dialog for setting the data shown
in blob mouse-overs.
Various attributes of the current image are available through the
"View->Image Attributes" menu option.
GC Image provides an option to fill temporal gaps in GCxGC and GCxGC-MS
data in order to produce images that maintain synchronization of the
modulation cycle with image columns.
GC Image now supports execution of scripts. A sequence of operations
can be recorded in an XML-format script and then used to specify
the same operation sequence on subsequent datasets. This feature is
GC Image™ Users' Guide © 2001–2005 by GC Image, LLC, and
the University of Nebraska.