GC Image Users' Guide
New Features and Improvements in Release 1.7
GC Image Release 1.7 has many new features and improvements.
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New functions in the Computer Language for Identifying Chemicals
(CLIC).
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HitList("<name>") returns the ordinal position of the
named chemical in the hit list of the analyzed blob. If the chemical
specified by "<name>", (enclosed in double quotes),
is not in the hit list (or the analyzed blob does not have a hit list),
the maximum integer value is returned.
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HitMatch("<name>") returns the match factor with the
mass spectrum of the named chemical in the hit list of the analyzed
blob. If the named chemical is not in the hit list, -1 is returned.
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HitRMatch("<name>") returns the reverse match
factor with the mass spectrum of the named chemical in the hit list of
the analyzed blob. If the named chemical is not in the hit list, -1 is
returned.
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HitProbability("<name>") returns the match probability
with the mass spectrum of the named chemical in the hit list of the
analyzed blob. If the named chemical is not in the hit list, -1 is
returned.
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Match("<mass_spectrum>") returns the match factor
for the given mass spectrum and the mass spectrum of the analyzed
blob. The mass spectrum can be specified in a text string of
comma-separated-value pairs "<m/z>,
<intensity>", separated by semicolons, e.g., "41, 75;
43, 90; 57, 100". As described below, if the Match function
is used in a template peak, then the mass spectrum associated with the
template peak can be specified as the string "<ms>".
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RMatch("<mass_spectrum>") returns the
reverse match factor for the given mass spectrum and the mass spectrum
of the analyzed blob. The mass spectrum can be specified in a
text string of comma-separated-value pairs "<m/z>,
<intensity>", separated by semicolons. As described
below, if the RMatch function is used in a template peak, then
the mass spectrum associated with the template peak can be specified as
the string "<ms>".
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Use CLIC expressions with geometric objects and template peaks.
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The metadata for geometric objects (polygons, rectangles, polylines,
and points) now includes a user-specified CLIC expression. The
blob set defined by the geometric object is constrained to blobs that
satisfy the CLIC expression. For example, suppose four blobs are
within a polygon, three of which satisfy the CLIC expression and one
which does not. Then, the blob set for the geometric object
contains only the three blobs that are both within the polygon and
satisfy the CLIC expression.
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The metadata for geometric objects in templates now includes a
user-specified CLIC expression. When a matched template is
applied to a dataset, each geometric object is instantiated with its
CLIC expression. Then, the blob set defined by the geometric
object in the dataset is constrained by the CLIC expression, as
described above.
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The metadata for template peaks now includes a user-specified CLIC
expression. For template peaks, the CLIC expression is applied
during template matching. For a template peak to match a blob in
the analyzed image, it must satisfy the CLIC expression associated with
the template peak as well as be consistent with the retention time
pattern of the template. With this facility, a template can
identify peaks using both the retention time template and other peak
characteristics such as the mass spectrum.
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Mass spectra for template peaks.
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The metadata for template peaks now includes a user-defined mass
spectrum. When a selected blob is copied to the template, its
mass spectrum is copied into the template peak. The mass spectrum
is specified in a text string of "<m/z>,
<intensity>" pairs, separated by semicolons, e.g.,
"41, 75; 43, 90; 57, 100". CLIC functions (e.g.,
Match and RMatch) can be used to compare mass spectrum of an
analyzed blob to the mass spectrum that is associated with the template
peak. With this facility, blobs can be identified subject to a
match between their mass spectrum and a previously observed mass
spectrum. For example, the mass spectrum for a chemical observed
in a calibration can be recorded to a template peak. Then, in
subsequent analyses, a CLIC expression associated with the template
peak could require the match factor with the previously recorded mass
spectrum to be above a threshold, e.g., "Match(ms)>=900".
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Characteristic ion features.
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The metadata for blobs now includes a "Characteristic_Ions"
field, which can be set by the user, and a
"Characteristic_Ions_Response" field, which is computed for
the given characteristic ions. If the user sets the
Characteristic_Ions field, then the value of the
Characteristic_Ions_Response is computed as the intensity at the
indicated mass-to-charge ratio summed across the blob.
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Users can include the characteristic ions fields in the blob table
through the "Configure -> Configure Blob Table" dialog.
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Users can test the characteristic ions response in CLIC expressions,
e.g., "(Characteristic_Ions_Response > 100)".
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Chemical structure graphics.
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The GC Image palette now has a Chemical Structure cursor mode. In
this mode, users can instantiate chemical structure graphics by
providing a chemical name and specifying graphical attributes such as
scale and color. GC Image retrieves the chemical structure
description for the named chemical from the NIST library and renders a
graphical structure representation on the image. If the given
name is not found in the NIST library, the chemical structure graphic
is not added. (Note that users can create user-defined libraries
within the NIST MS Search software.)
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The "Configure -> Configure Settings" tool has a tabbed "Structure
Display" pane for specifying the modes in which chemical structure
graphics are displayed and for setting the default scale, color, and
other options.
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The metadata for blobs now includes a flag to add a chemical structure
graphic to the image visualization. If the flag is checked, GC
Image retrieves the chemical structure description from the NIST
library and renders a graphical representation on the image with a line
connecting the chemical structure graphic to the blob.
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Colorization options.
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GC Image now supports tailored colorization for individual blobs or
multiple blobs. The priority for colorization (from high to low)
is blob, group, constellation, blob set(s) defined by geometric
objects, and blob status. So, for example, if a blob has a
tailored color, it is displayed in that color. If a blob does not
have a tailored color, but the group to which the blob belongs has a
tailored color, the blob is colored with the color for the group.
The tailored color hierarchy works the same at the other priority
levels. If no other level has a tailored color, the blob is
colored according to is status: internal standard, included, excluded,
or unflagged. If a blob is colored according to its membership in
set(s) defined by geometric objects and if the blob is in more than one
such set, the blob is colored with the average of the colors of the
sets of which the blob is a member and which have a tailored color.
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The blob set table provides a button that shows the color of the set
(defined by group, constellation, or geometric object) and which can be
clicked to change the color.
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Improved 3D visualizations.
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GC Image V1.7 has improved 3D color rendering which reduces vertical
color artifacts on steep peaks.
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GC Image V1.7 has improved 3D surface rendering which provides greater
precision in detailed regions. The number of polygons used for
surface rendering now can be limited through the configuration pane to
better provide 3D rendering on computers with limited memory.
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Add and remove polygon and polyline vertices.
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The geometry graphic mode class on the GC Image palette now has an Edit
Graphic Knot mode for adding or deleting vertices from polygons and
polylines. In this mode, clicking on a vertex will delete the
vertex and clicking on a line segment will add a vertex on the
segment.
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GC Image Reader.
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A version of GC Image V1.7 with limited functionality, GC Image Reader,
is available at no charge. GC Image Reader has tools for reading
and viewing GCxGC and GCxGC-MS data, but many of the analytical tools
of the regular version are disabled. This versions allows users
to more easily share GCxGC data with non-analysts and users of other
systems.
Contents
Next: Introduction
GC Image™ Users' Guide © 2001–2005 by GC Image, LLC, and
the University of Nebraska.