GC IMAGE - User Guide 2025R3

New Features and Improvements in Version 2025

GC Image 2025 has many new features and improvements. See the GC Image User Guide for full documentation.

What's New in Version 2025 Release 3 (January 2026)

Expanded File Compatibility with Shimadzu LabSolutions GCMS

Version 2025R3 adds support for importing the latest Shimadzu LabSolutions GCMS (.gcd) files. This enhancement extends our existing Shimadzu import support, which already includes GCsolution (.gcd), GCMSsolution (.qgd), and LCMSsolution (.lcd) files.

Improved Import Match and Update Template Workflow for 2D RT Calibration

Version 2025R3 now provides improved support for the Import Match and Update Template workflow for 2D RT calibration, including:

• New Update Template Options: The Template > Update Template action now includes new options for creating the transform used to perform the update. Users can select the current template transform, create a new transform based on matched locations, or generate a transform from a match file.
• New Import Match Menu: A new Import Match... action has been added to the Template menu. This can be used to import a match file and apply its match assignments to the current template.
• Apply Match Constraints When Import Match: The Import Match... action now applies peak-specific and spectral match constraints by default when importing a match file. A new Enforce Match Constraints option allows users to disable this behavior for backward-compatibility purposes.

These enhancements enable users to use a reference standard to establish a match between previous and current conditions. Then, exported matches can be used to update sample templates directly. This workflow allows users to correct retention-time drift, adapt templates to new columns or method changes, and apply other automatic adjustments.

Enhanced Method Creation with Customizable Step Settings

Version 2025R3 now has enhanced method creation capabilities, with a focus on automatically capturing specific settings from already processed images and improving step-level customization. These updates streamline method setup and ensure greater consistency between image processing and method configuration.

• Customizable Step Settings: The Correct Baseline and Detect Blobs method commands now support a Use Step Specific Settings option, allowing users to override global configuration values and define custom parameters for individual steps.
• Automatic Capture of Image Settings: When creating a new method via Method > New Method from Current Image, the software now automatically enables step-specific settings and populates them with the baseline correction and blob detection parameters last used on the current image. This ensures that new methods accurately reflect the processing conditions applied during method development.
• User Color Map Support: Method Settings now allow browsing for an external color map file. Additionally, when selecting a configuration that was exported with a color map, the color map field is automatically populated.

Improved Data Refresh and Comparison Tools for Multi-Sample Analysis

The Investigator application includes new features for data synchronization and image comparison.

• A new Reload button has been added to the Images View toolbar of Investigator. This allows users to refresh data for all selected images from the source, ensuring the analysis table reflects the latest updates.
• The Compare Images action now offers two comparison methods:
  • Compare: Loads image data as it would appear in the analysis and perform any analysis-defined processing (such as applying the feature template or configuration).
  • Compare Original: Loads data as it was originally in the image without additional processing.

Refined Project Views for Easier Image and Report Management

Version 2025R3 introduces usability improvements to the Project interface, making it easier to manage large datasets and track file changes.

• The Run > Review Images dialog now supports selecting image batches, streamlining the review process and making it easier to work with large sets of images in complex projects.
• The Images details pane now supports filtering and includes a new Date Modified column, improving management and review of image files within a project. The Status column has also been refined to indicate active status only for images that are currently associated, providing a clearer and more accurate view of image usage.
• The Reports detail pane now includes filtering capabilities and a Date Modified column, enabling more efficient navigation and organization of report files within a project.

New Editing Capabilities in Adducts Library HRMS/Adv-MS Only

With Version 2025R3, the Configure > Adducts Library dialog now includes options to add, remove, and edit individual adducts, allowing for easier library maintenance.

What's New in Version 2025 Release 2 (November 2025)

Enhanced Data Import and Format Support

Version 2025R2 includes new and improved I/O support for LECO, Bruker, and JEOL data formats:

• Expanded LECO ChromaTOF .PEG and .SMP Support:
  • The software now supports reading modulation information (single and variable modulation) when importing .PEG files.
  • The software now supports importing additional versions of .PEG files, including those acquired with dual FID/SCD detectors.
  • The software now supports importing .SMP files generated from .PEG source files.
  • The software now supports importing certain newer versions of .SMP files that contain non-spectral signals.
• The software now supports importing Bruker timsTOF .TSF data files.
• The software now includes JEOL's msAxelDataReader version 1.4, adding support for data files acquired with JEOL AccuTOF GC-Alpha (JMS-T2000GC).

Customizable Adduct Library with Expanded Defaults HRMS/Adv-MS Only

Version 2025R2 now includes an enhanced adduct library that allows users to import their own adduct definitions, making it easier to tailor analyses to specific experimental needs.

• Support for importing user-defined adducts
  The new Configure > Adducts Library provides a centralized interface for managing the complete list of available adducts, with options to view, search, import, and restore entries. It supports importing custom adducts from CSV or Excel files, enabling laboratories to extend the library with specialized adducts.
  
  
• Updated default adduct list
  The default adduct list has been expanded to include additional positive ion species (M+, M+2, M+3, M+H-2H₂O, M+H-H₂O) and negative ion species (M-, M-2, M-3, M+HCOO, M+CH₃COO).

Streamlined Operation Journal with New Search and Undo Capabilities

Version 2025R2 includes a newly designed UI for the operation journal, which makes it easier to verify audit trails and quickly find previously used processing settings.

• Improved List Operations and Journal UI
  Edit > List Operations and View > Journal now present a redesigned dialog with:
  • A table layout for clearer visibility of operations,
  • A Find bar for quick searching,
  • A detail pane that displays parameter details of the selected operation.
• Undo Multiple Operations at Once
  A new Undo Multiple button has been added to Edit > List Operations. Users can now select and revert a sequence of operations up to and including the chosen row.

Enhanced Method Editor and Operations

Version 2025R2 includes an updated Method Editor and expanded set of operations that provide a more complete and customizable workflow. These improvements enhance usability, streamline template handling, and simplify saving key analysis tables.

• The Method Editor now has a more polished interface, including a new Find bar that enables searching and filtering across available operations.
• Template method operations can now be more flexible and allow users to combine multiple templates and apply templates after other alignment or match operations.
  • Apply Template operation includes two new options From Runtime Image (to use the template already in the image) and None for Match Type (to apply the template as-is without matching).
  • Load Template operation allows specifying a template at runtime or copying from the currently open image, with a Load Type parameter to overwrite or append to the existing template.
• New operations allow saving the Blob Table, Area Table, and Blob Set Table to Excel or CSV files. This makes it easier to export compound analysis results for reporting or further processing.
• New Run Custom Operation steps can be incorporated directly into a method to invoke executable plugin commands, enabling integration of external tools and extending method workflows with custom functionality.

New Interactive Notebook-Style Method

Version 2025R2 now supports interactive methods that enable standardizing workflows that require human input, with step-by-step execution and custom instructions at each stage. This approach helps retain and share expert know-how, while providing greater control and flexibility during method runs.

• Support for customizable titles and descriptions in method steps
  The Method Editor now supports adding descriptive text to the entire method and to individual steps. These descriptions accept basic HTML formatting, enabling headings, styled text, and lists, and are displayed before and during interactive runs.
  
  
• Support for step-by-step interactive execution
  Methods can now be executed in Interactive Mode as an alternative to running them all at once. This mode provides greater control by allowing execution step-by-step, with opportunities for manual verification and adjustments between steps.
  
  
• Support for pause and menu actions via Run Custom Operation
  The new Run Custom Operation steps can be incorporated directly into a method to pause execution or invoke any menu command by specifying its path, enabling more flexible and guided workflows.

Other Improvements in Reporting and Tools

Version 2025R2 introduces several enhancements across reporting and tool management, improving flexibility, compatibility, and user experience.

• Tools > Slice Report for Boiling Range Distribution now supports the use of an external calibration table stored in a CSV or Excel file.
• Both Summary Report and Filter Report can now be saved directly as HTML files, with HTML set as the default file type.
• The Save Summary Report method operation now includes a Preferred Report File Type parameter, allowing selection of HTML or Excel in addition to XML file type.
• The Plugin Manager now has an improved interface with a redesigned plugin table that highlights key columns, a Filter bar for quick searching by name, and an enhanced import process that prompts whether to remove an existing plugin before updating.

What's New in Version 2025 Release 1 (June 2025)

Improved Ion Peak Detection Algorithm with Better Reliability

Version 2025R1 includes a significant update to the ion peak detection algorithm with improving reliability and precision. This updated algorithm enhances ion peak merging and noisy peak filtering, delivering more accurate peak detection and deconvolved spectra. It replaces the previous version and is now the default.

Faster Performance for CLIC Columns in Blob Table

In Version 2025R1, calculations using CLIC functions, FEATUREATBLOB() and IDOF(), especially when referencing a specific identified blob like an ISTD, now run faster than ever. This enhanced speed allows for more complex and flexible normalization and calculations, for example, Volume/FEATUREATBLOB(IDOF("Biphenyl-d10", "Blob"), "Volume"), to be executed smoothly in Blob Table.

Enhanced Alignment Marker Selection for Compare Images Tool

Version 2025R1 introduces a smarter alignment marker selection process in the Compare Images Tool, enhancing accuracy and reliability. The updated algorithm refines initial matching by pairing identically named blobs across images while prioritizing consistency with the predicted transform. This ensures the most stable and globally reliable transformation.

Additionally, a new Only Use Included option allows users to exclusively utilize included blobs when initializing alignment markers, providing greater control over the selection process.

New Difference View for Side-by-Side Chromatogram Comparison

Version 2025R1 introduces Difference View, a powerful tool designed to quickly identify and analyze differences between two chromatograms. This directional comparison computes a pixel-by-pixel difference, highlighting what is present in the first operand image but absent or reduced in the second.

This new Difference View leverages precise alignment using alignment markers and transforms, and offers advanced options including:

• Normalization: Adjusts how the second image is normalized to the first.
• Fuzzy Radius: Optimizes pixel matching and counters local variations for improved accuracy.
• Relative Difference and SNR Filtering: Select None, % Recovery, or Fold Change, to refine results while accounting for baseline fluctuations.

In addition, a dedicated Review table displays differentiating compounds, either matched or unmatched, that have been reviewed and added for further analysis.

Enhanced Tools and Streamlined Interface for Multi-Sample Analysis

Version 2025R1 introduces new analysis tools in the Investigator interface including:

• Integrated Compare Images Support within Analysis: Now seamlessly integrate the Compare Images tool directly within the Analysis Actions. This integration enables a more comprehensive comparison of two samples by combining analytical insights with direct visual inspection of chromatograms and peaks, ensuring thorough evaluations.
• New Pre-Configured Analysis Tools:
  • Compare Classes: Generate a bubble plot of the mean pairwise class differences for a specified attribute.
  • Run PCA: Perform principal component analysis using the selected attribute for unsupervised clustering.
  • Run F-Test: Create bubble plots displaying F-values to evaluate compound significance for distinguishing classes.

In addition, Version 2025R1 introduces a refreshed interface for Investigator to optimize usability and visualization:

• Better Chromatogram View displays a sharper and more visually appealing chromatogram snapshot at any viewing size.
• Redesigned Analysis Navigation uses the new side-bar system, replacing the old tab-based interface for a more organized and intuitive experience.

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