GC IMAGE - GC Image GCxGC Edition - User Guide 2025R3

New Features and Improvements in Release 1.7

GC Image Release 1.7 has many new features and improvements.

New functions in the Computer Language for Identifying Chemicals (CLIC).

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.
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.
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.
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.
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>".
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>".

Use CLIC expressions with geometric objects and template peaks.

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.
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.
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.

Mass spectra for template peaks.

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".

Characteristic ion features.

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.
Users can include the characteristic ions fields in the blob table through the "Configure -> Configure Blob Table" dialog.
Users can test the characteristic ions response in CLIC expressions, e.g., "(Characteristic_Ions_Response > 100)".

Chemical structure graphics.

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.)
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.
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.

Colorization options.

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.
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.

Improved 3D visualizations.

GC Image V1.7 has improved 3D color rendering which reduces vertical color artifacts on steep peaks.
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.

Add and remove polygon and polyline vertices.

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.

GC Image Reader.

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.

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