GC IMAGE - GC Image LCxLC Edition - User Guide 2024R2

New Features and Improvements in Version 2.9

GC Image LCxLC Edition 2.9 has many new features and improvements. See the GC Image LCxLC Edition User Guide for full documentation.

What's New in Version 2.9 Release 3 (March 2020)

New and Improved Support for 2D-LC Data

Version 2.9R3 has new improvements for 2D-LC data, including:

The File > Import Agilent 2D-LC action now supports importing CDF data files with Agilent 2D-LC metadata, which provides support for customized coupling Agilent 2D-LC with third-party MS instruments.
The File > Import Agilent 2D-LC action now supports importing data up to the user-specified run time.
The Files of Type selection for the File > Import Agilent 2D-LC now defaults to list all supported Agilent data files (*.ch, *.ms, *.uv, *.d). Also, the recently used Files of Type selection is now remembered.

New and Improved I/O Support

Version 2.9R3 has new I/O improvements, including:

The file chooser for File > Import now remembers the most recently used Files of Type selection.
The file chooser for File > Import now includes vendor-specific file format categories, All Agilent Data Files and All Shimadzu Data Files, in the Files of Type selection.
The software now displays and logs more detailed error messages for troubleshooting if a VUV .db file fails to be imported.
The software now displays "wavelength" as the spectral axis label for VUV spectra imported from a VUV .db file.

New and Improved Split Tools for Editing Blobs

Version 2.9R3 has new tools and improvements for splitting blobs, including:

The Detect/Edit Blobs cursor mode now supports performing a horizontal or vertical split on a blob through the right-click menu. Un-excluded blobs that are not wrap-around can be split by selecting the menu option. Use left-click drag to set a split location and double-click the left mouse button to apply the split.
The Split Blob operation now shrinks the new blob bounds to fit tightly around both halves of the split blob.
The Filter Blob Outline action from the Detect/Edit Blobs mode can now edit the boundary with a 0 threshold value, which allows the unexpected large blob bounds to be manually shrunk without altering the blob area.
The Filter Blob Outline action from the Detect/Edit Blobs mode now displays a more accurate error message when given an invalid percentage parameter.

New Log-linear Regression for Retention Index Calibration

Version 2.9R3 has a new a new log-linear regression setting for Retention Index calibration. When enabled, the option allows fitting the selected function in the log-space of the output retention index, i.e., ln(RI) = f(x), which is useful for performing calibration from retention times to some chemical properties such as molecular weight.

New Spectral Constraints for Template Matching

Version 2.9R3 has a new set of configurable Spectral Constraints for Template Matching including Match Factor and Reverse Match Factor. They can be set as global matching constraints for all template peaks instead of editing Qualifier CLIC for individual template peaks. The constraints can be configured from Configure > Settings > Template Matching, and can be enabled individually.

In addition, Version 2.9R3 has other improvements for template matching and template display, including:

A new toggle button was added to the Interactive Match dialog for displaying only the peaks of a template.
A new Template Peak Display Size setting has been added to Configure > Settings > Template to control the display size of template peaks.
The Load Template dialog now defaults to Overwrite instead of Append. Once changed, the setting will be remembered.

New Peak Plot for Investigator

Version 2.9R3 has a new Peak Plot view in the Images Perspective of Investigator. The view provides an interactive bubble plot of the Blob Table or Area Table for the selected image.

In addition, Investigator now saves an existing analysis with many images much faster than before.

What's New in Version 2.9 Release 2 (November 2019)

New and Improved I/O Support

Version 2.9R2 has new and improved I/O facilities, including:

File > Import has a new Extract MS/MS from Alternating MS and MS/MS Data option for Agilent MassHunter targeted MS/MS data files. This new option allows separating MS and MS/MS data acquired with alternating MS and MS/MS modes to create a properly aligned chromatographic image.
The new File > Import Agilent MassHunter IMS Data menu allows importing drift spectra from Agilent MassHunter IMS data files. This feature is only available in HRMS Edition software.

New Improvements for Spectral Views

Version 2.9R2 has new and improved operations for displaying and exploring spectra data, including:

The software now recognizes common spectral types (including mass, UV, and drift spectrum) automatically based on the source data file, and displays the corresponding spectral axis label (i.e. m/z, wavelength, and drift time). The supported source data file formats include Agilent ChemStation, MassHunter, and Shimadzu LCD. Also, a user can configure the axis label by setting the MS Axis Label custom attribute in View > Image Attributes > Miscellaneous.
The new View > BPC View menu allows viewing the base peak chromatogram.
View > MS Cube UI has a new layout and default 2D View display settings for browsing and exploring SICs.

In addition, View > SIC View has a new option that allows generating selected ion chromatograms with adducts. A user can select adducts from a list of common observed adducts in positive and negative ion modes. In addition, the new option is available in MS Viewer that allows adding and overlaying mass ranges computed based on adduct selection to a spectrum for visual inspection.

New and Improved Tools for Editing Peaks

Version 2.9R2 extends the previous Detect Blob cursor mode to be Detect and Edit Blob mode with new blob editing tools, including:

The cursor mode now supports merging the selected blobs through the right-click menu.
The cursor mode now supports editing the boundary of a blob using the peak height based threshold. The Interactive Blob Outline Filter UI can be invoked through the right-click menu item Filter Blob Outline. It allows adjusting the threshold and examining the result interactively.
Edit Blobs UI can now be invoked directly from the right-click menu. When invoked, the UI is set to focus on the currently selected blob.
Exclude Blobs is now enabled for multiple blobs. Left mouse click while holding Ctrl key can be used to select multiple blobs in the cursor mode.

In addition, Edit > Edit Blobs now copies all blob properties from the active blob to the new blob when merging two blobs.

Other New Improvements

Version 2.9R2 has other new and improved operations, including:

New Search Library for Blobs and Search Library for Areas commands can now be added to a Method.
Investigator now uses less memory on average for large analysis files with many samples.
Investigator now opens large analysis files faster than before.

What's New in Version 2.9 Release 1 (July 2019)

Improved Smoothing for Baseline Correction

Version 2.9R1 has a new default filter type, Median-Mean, for the Default Baseline Correction algorithm and automated noise estimation. This new filter can handle a rapid changing baseline along Column I dimension better than the filter in older versions.

New and Improved Support for Manual Noise Estimation

Version 2.9R1 has a new feature, Recalculate Signal Noise, that allows users to recalculate noise after baseline correction. It supports estimating noises from individual strides and/or specified regions, and allows users to specify background regions manually if automated noise estimation was affected by some background artifacts. Also, the new operation provides three different ways to estimate noise, IID, Standard Deviation, and Peak-to-Peak, and can be added to a method for batch processing.

In addition,

Blob Table now can be configured to show Peak-to-Peak noise and SNR columns.
Tools > Visualize Data now computes and displays both population and sample standard deviations of data point values in the selected region.

New and Improved Features for Peak Detection

Version 2.9R1 has a new Detect Blob cursor mode for Local Blob Detection. The mode supports detecting a blob at the location indicated by the mouse double click or drag selection. If the location is not contained by existing blobs, the program will detect a blob at the location automatically. If the location is contained by some existing blob, the program will select the blob, and invoke Local Blob Detection to allow users to re-detect blobs within the blob area.

In addition,

Local Blob Detection now remembers the recently used settings.
Blob Table now can be configured to show the following new pixel-based peak width properties:
- Size I (pixel) and Size II (pixel): Size of column I and column II bounding box in pixels.
- Size I(50.0) (pixel) and Size II(50) (pixel): Size of column I and column II bounding box for values 50% of peak in pixels.
- Size I(w) (pixel) and Size II(w) (pixel): Size of column I and column II bounding box for values w% of peak in pixels.
, in addition to axis-unit-based properties, which can be used to filter noisy artifacts detected as blobs.
Interactive Blob Detection now presents a list of suggested properties including Retention I, Retention II, Size II (pixel), Area (pixel), Peak Value, Volume, and SNR, when adding a new constraint as a filter. Also, all blob properties are organized into easy-to-find categories.

New Improvements for Importing Compound List

GC Image LCxLC Edition 2.9R1 has new improvements for Template > Import Compound List, including:

A new option for including all unspecified columns as custom attributes. When this option is selected, all unspecified columns will be imported into the Description field of corresponding template peaks as custom attributes.
A new import setting, Apply Phase shift that allows applying a shift to the imported compound peaks. The user can choose to apply the same phase shift as the image or specify a shift amount. The imported compound peaks will wrap around the image if required.
Compounds that are out of the lower retention bounds of the chromatogram are now highlighted in red. An error message will be shown if no valid compounds can be imported.

New Improvements for Investigator

Version 2.9R1 has new improvements for Investigator, including:

Investigator now supports filtering entries in Images and Compounds perspectives, in addition to Summary perspective. In Images Perspective, images can be filtered by name or class label. Blob Table, Area Table, and Blob Set Table of an image can be filtered by the selected column. In Compounds Perspective, compounds can be filtered by name.
In Attributes Perspective, Investigator now runs Principal Component Analysis (PCA) in the background, which allows users to switch between tabs and continue working while it is being processed. Only one PCA can be processed at a time. The process can be canceled using the Cancel PCA button at any time.
Investigator now has targeted views in Compounds perspectives
- Trend: Line charts show trends of the selected attributes based on the sorting order of the current table.
- Distribution: Bar charts show how values of the selected attributes are distributed across sample images.
- Spectra: Spectral views show the spectra of the selected compound across sample images if Spectrum attribute is available.

Other New Improvements

Version 2.9R1 has other new and improved operations, including:

Edit > CLIC Expression now lists all blob properties in easy-to-find categories next to the Functions list.
Configure > RI table now presents a list of suggested compound properties including Library BP, Library Molecular Weight, and Library RI, when populating the table. In addition, the Populate UI organizes all blob properties into easy-to-find categories.
All figures and chromatogram images in Reports are now saved as PNG instead of JPEG to provide the best quality for presentation. In addition, File > Export Image as Picture now can save a chromatogram image in a GIF format.

Contents Next: Introduction