Processing > Correct Baseline has a new Median-Mean filter type for Default 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.
Compatibility: Median-Mean is the new default filter. The old filter in v2.8r3 or older versions is available as the Legacy option in Configure > Settings > Baseline Correction > Filter Type.
Processing > Recalculate Signal Noise can recalculate estimated noises from individual strides and/or specified regions after baseline correction. This new operation allows user to specify background regions manually if automated noise estimation was affected by some background artifacts. In addition, 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.
Processing > 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. In addition, the New Constraint UI organizes all blob properties into categories for easy searching.
Tools > Visualize Data now computes and displays both population and sample standard deviations of data point values in the targeted region.
Blob > Detect Blob 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.
Edit > Local Blob Detection now remembers the recently used settings. Reset button allows resetting its settings back to the current blob detection settings.
View > Blob Table now can be configured to show Peak-to-Peak noise and SNR columns.
View > Blob Table now can be configured to show pixel-based Size columns:
, in addition to axis-unit-based size columns.
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.
Compatibility: Summary Report, Filter Report, and other reports are now saving chromatograms as PNG instead of JPG. Any external usage other than viewing and printing needs to be updated too. PNM format is no longer supported by File > Export Image as Picture and Summary Report > Logo.
Template > Import Compound List now highlights rows in red that are out of the lower retention bounds of the chromatogram. An error message will be shown if no valid compounds can be imported.
Template > Import Compound List has 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.
Template > Import Compound List now 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.
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 categories for easy locating.
Edit > CLIC Expression now lists all blob properties in easy-to-find categories next to the Functions list.
Investigator > Attributes > PCA now runs 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 supports filtering entries in Images and Compounds perspectives, in addition to Summary perspective. In the 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 the Compounds perspective, compounds can be filtered by name.
Investigator now has targeted views in Compounds perspectives.
Also, all charts display an instructional message if chart axes are not completely specified.
Processing > Correct Baseline failed on an image that has 4 or fewer second-dimension chromatograms, and resulted in random errors, invalid data, or invalid noise estimates.
Workaround: Use Arithmetic Operations to subtract a constant baseline or a background image, and then Skip Correct Baseline.
After Configure > Settings > Baseline Correction, set to Filter Window Size to 0, and then Processing > Skip Baseline Correction, blob detection returned no blob due to invalid noise estimates.
Method > Run a script with the Baseline Correction command, and then View > Journal. The journal showed current configuration settings instead of the parameters in the script.
When baseline correction or undo is performed on MS data, Cancel button was enabled on the progress dialog although the operation cannot be cancelled.
Configure > Settings > Baseline Correction, and choose Rolling Ball as Algorithm. The Strides per Modulation Cycle was not visible although this setting is used for automated noise estimation.
Edit > Local Blob Detection within a tiny selected rectangle might fail with uncaught exception if the smoothing factors are set too big.
Processing > Interactive Blob Detection > Detect did not show detected blobs if Configure > Settings > Blob Display is set not to show Unflagged.
Processing > Register Image with Re-Detect Blobs > re-detect blobs with "Have detection match pre-registration blobs" option unchecked. Perform the same operation again, but the option was still checked.
Blob Table and Blob Set Table might report incorrect Size I property values in minutes for blobs of a chromatographic image acquired with variable modulation (i.e. multiple modulation periods applied in a single run).
Method > New Method from Current Image added the Correct Baseline step regardless if the baseline correction was skipped or not.
Method > Run Script with a saved Local Blob Detection command might detect blobs at a wrong location if some graphic object was drawn before the script is run.
Template > Import Compound List > Default Encoding was not remembered after restarting the program.
If a project had a run date file that has "&" in its file name and is associated with a vial, the project was not saved correctly. Trying opening the saved project will cause errors and missing vials.
Workaround: Manually remove "&" from a run data file name before it is imported into a project.
Processing runs associated with a vial that has ".csv" or ".xml" at the end of its name would fail with errors.
Workaround: Avoid naming vials with either of the problem extensions.
Loading additional images to an open analysis without a specified feature template might use a recently used template previously applied to another analysis by mistake.
Analysis > Multi-class Statistics > Summary perspective, set some Scatter Chart for Compound Sets , then switching between charts and views might cause an exception.