The detection algorithm for Extract Ion Peaks has been updated. The 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.
Compatibility: A Version setting is available for methods. This setting allows users to specify the Legacy version of the algorithm to be backward compatible with v2024 or older versions.
A new view, Difference, has been added to Compare Images. It computes and displays a pixel-by-pixel difference, highlighting what is present in the first operand image but absent or reduced in the second.
The computation supports alignment correction and includes options for normalization, relative difference filtering, SNR filtering, and fuzzy radius pixel correction.
A new table, Review - Matches & Differences, has been added to Compare Images. It allows for tracking specific reviewed compounds of interest, which may then be exported for further use.
Compare Images now features a new layout with the Selected pane on the side, allowing it to be viewed while interacting with the other tables.
When opening a reference image in Compare Images, the Only use included option can be enabled to limit the automatic initialization of alignment markers to included blobs.
The automatic initialization of alignment markers for Compare Images has been improved to reduce the amount of overfitting in the initial alignment transform.
The performance for the FEATUREATBLOB and IDOF CLIC functions have been significantly improved on files with many detected blobs.
The chromatogram images shown in the Images View of Investigator are now smoother and less pixelated.
Investigator has a new Compare Images action, accessible on the main toolbar in the upper-right. This action integrates the Compare Images interface and functionality directly within Investigator.
Investigator has a new Compare Classes action, accessible on the main toolbar in the upper-right. This action provides a quick way to generate a bubble plot of the mean pairwise class differences for a specified attribute.
Investigator has a new Run PCA action, accessible on the main toolbar in the upper-right. This action performs principal component analysis using the selected attribute for unsupervised clustering.
Investigator has a new Run F-Test action, accessible on the main toolbar in the upper-right. This action provides a quick way to generate bubble plots displaying F-values to evaluate compound significance for distinguishing classes.
In Investigator, the minimum size restriction for the main pane has been removed, allowing free positioning of the divider between the main pane and either sidebar.
In the 1D View, the hover effect for blob and area drawings was not cleared when the mouse exited the pane.
In some unexpected cases, the stored 3D View preference settings could get corrupted. If this happened, running 3D View with the corrupted settings caused an exception.
Workaround: Close software > Open "GCIRT.properties" file in a text editor (found in the bin/resources folder of the installation) > delete line with ThreeDViewLatTSB$Value > Launch software > use 3D view. This allows the correct settings to be regenerated.
Adding or removing axis labels or upper/right axes (Configure > Settings > Axis) or metadata/colorization legends (Configure > Settings > Legend) after running a method containing Save Summary Report would yield unexpected results for the displayed axes and legends.
Interactive Blob Detection did not clear the blob selection or template matching which could result in deleted blobs being selected or matched.
Workaround: Edit > Deselect All and Template > Clear Match and Transform before performing interactive blob detection
NIST auto locate (Configure > Settings > Search Library) would sometimes find and attempt to use previously uninstalled versions of NIST.
NIST Library Search failed if NIST was installed on a path containing spaces.
Affected Versions: This bug affects version v2022r3 or later.
Workaround: Reinstall NIST to a location without spaces in the path.
The NIST startup check was still being run on a second instance of the software even when the user specified to not perform the startup check on launch in the first instance of the software.
Workaround: After choosing no on the startup check dialog, close the first instance of the software before launching another instance.
Editing a method with a color map specified would cause the color map to be lost from the method.
Workaround: View > Colorize > Export the color map > edit the method > choose the exported color map from the list.
A method with a Detect Blob step would throw an exception when run in review mode.
Affected Versions: This bug affects version v2024 or later.
Workaround: Exit review mode prior to running a method containing a Detect Blob step.
Running a method from Method > Manage and Run Methods did not apply the Blob Set Table configuration stored with the method.
Running a method via Project, Command Line, and Import - Automated Actions with Method did not have this problem.
In Compare Images, applying a table filter on the Group Name column did not work.
In Compare Images, table selections cause the view to pan to the selected blobs. When zoomed, the panning would sometimes not include the apex of the blob in the view.
In Compare Images, sorting a table by the aCLIC column would cause an exception to be thrown.
In Compare Images, when hovering the mouse over one image, the cursor displayed on the opposite image was drawn at the target sample's lower left corner instead of the sample's center.
In Compare Images, when comparing images with a different number of samples in one or both dimensions (e.g. FID to MS), zooming on the image and swapping the displayed images via the Compare dropdown would sometimes cause an exception to be thrown.
Workaround: Reset the zoom before swapping the images.
After generating a Slice Report with the Show Distribution Plot on Chromatogram option enabled, resizing the main Image window would result in the image axes displaying wider.
When in Review mode, deleting the selected area (e.g. by undoing area creation or running Extract Ion Peaks as Areas) would cause an exception to be thrown.
The plots displayed in Investigator would throw an exception if the plot was resized such that it had a width of 0 pixels.
In some circumstances, closing Investigator with an open analysis file would throw an exception.
Closing an open analysis file did not terminate a running PCA thread which could prevent PCA from being run on a different newly opened analysis.
Workaround: Close the Investigator software.
Saving the Investigator Summary view to an XLSX file when only one stat column was present per attribute would throw an exception.
Workaround: Add another stat column via Analysis > Custom Settings....
The Find Compounds tool of Investigator would unexpectedly change the displayed plots or tab selection of the Compounds perspective.
The Find Compounds tool of Investigator would incorrectly open compound views based on the first table selection instead of the clicked row.
Saving Investigator results from panes with empty tables would yield unexpected results.
Running a method with a color map via Project > Run > Reprocess Images would apply the color map but not add it to the journal, preventing the step from being undone.
The legacy Export Graphics action has been removed from the File menu. Adding graphics to a template should be used instead.
Blob calculations have been switched to use the Apache Commons Math's FastMath library that relies only on IEEE-754 basic operations for better future compatibility.
This change may result in small variations to the following calculated attributes:
The XML header for .gci files, templates, and various other XML formats, which was outdated, has been updated.
The NIST startup check dialog has been removed. Instead, the check is silently performed on launch and when attempting to run library search.
The following default settings for Library Search (Configure > Settings > Search Library) have been changed:
The following default settings for Template Matching have been changed:
In Investigator, the "Class Label" column is now named "Class".
The Inspect Compounds right-click action in Investigator - Find Compounds is now limited to opening 10 tabs at a time.
Peak and Area compound views in Investigator now maintain independent persistence of various UI elements.
The PCA tab is no longer shown in the Attribute view. Instead, the PCA plot is available from the Run PCA toolbar button or the Run PCA button in the Attributes view.
The Auto Feature workflow previously ignored some of the current settings when Use Configuration was turned off. These settings now use the currently configured value. The affected settings included the following:
The following setting is still used regardless of the current configuration: