This page describes the changes and fixes that were introduced in the Melanie software since the release of Melanie 9.3.0 (2025.1.23.0).

You can learn about the installation requirements and instructions for Melanie 9.3.1 (2025.12.11.0) in its Readme file. For the list of third-party materials included in or distributed with Melanie Melanie 9.3.1 (2025.12.11.0), and the notices and licenses applicable to those materials, you can read the Third-Party Material Disclosures.

Changes

Projects

• When restoring a project from a .pex file, the restored project is now automatically selected in the project list.
• When no Shared folder is defined, the option Move to Shared folder is no longer available.

Quality control

• When selecting or deselecting multiple images in Quality Control, the focus now remains on the image that was just selected or deselected, instead of the list scrolling back to the topmost selected image, based on its position in the list.

Alignment

• It is now possible to create an alignment hierarchy with more than two levels.
• The messages, options and behaviors that are triggered by changes to the Workflow options in the Alignment step have been clarified and improved.

Presence filter

• Instead of automatically categorizing edited spots as uncertain, the software now classifies them based on the Presence filter thresholds. It is still recommended to review the coverage or spot presence state of edited spots, indicated by ticks in the Edited column of the Coverage or Spot presence table. The visibility of these columns can be adjusted in the column settings.

Coverage

• The Presence plot has been enhanced to more clearly show where each spot’s abundance falls within the overall abundance range and relative to the presence threshold(s) of the image on which it was detected.
• The number of Absent and Product spots can now be displayed in the Targeted coverage table and the Coverage summary table. The visibility of these columns can be adjusted in the column settings.

Exports and reports

• When exporting spot presence states in coverage projects, users can now choose between two options: export as text only (faster), or include the corresponding spot presence state images (more time-consuming). Only the final, user-edited states are exported in the text format.

Fixed bugs

Projects

• After duplicating a project, renaming the original, and editing the duplicate, the original project disappeared from the Project list and could not be added from disk.
• Restoring the backup (.pex) of a project currently in use by another person, in the same location, was allowed and could potentially lead to data loss or corruption.

Quality control

• Reset modifications and Undo/Redo did not revert changes made to the extremities or position of a pI strip.
•  After a switch of IPG strip, using Reset modifications correctly reverted to the original strip, but this change wasn’t properly recorded. As a result, the software did not correctly handle the Apply modifications and Ignore modifications options when exiting the Edit pI/MW step.
•  Performing successive Reset Modification actions could corrupt a previously saved pI/MW calibration.
•  When removing gels from a Coverage or Coverage DIGE/DIBE project, the Primary reference information of remaining gels could be deleted. Since this field is not editable in Coverage DIGE/DIBE projects, it then became impossible to continue working with the project.
•  Canceling the import of the Image type during Import Metadata removed the Primary reference information. Since this field is not editable in Coverage DIGE/DIBE projects, it then became impossible to continue working with the project.
•  Import metadata failed when the Excel file contained more images than were in the project.

Alignment

• In Coverage DIGE/DIBE projects with a multi-level hierarchy, the Alignment setup window could incorrectly display a Multiplex pane. In combination with certain edits – notably the exclusion of gels in Quality control – this could lead to a software crash.
• When adding (and including) an image to a previously analyzed Coverage project, the image was not added to the Alignment setup screen and therefore could not be analyzed. Similarly, when removing (or excluding) an image from a previously analyzed Coverage project, it was not removed from the alignment hierarchy.
• When (re)aligning images after completing the Detection step, the software used the final spot detection pattern instead of performing a new preliminary detection. This increased the likelihood of triggering a message about exceeding the maximum number of spots recommended for alignment. A preliminary spot pattern is now recalculated when (re)aligning. If it exceeds the recommended spot limit, the user is prompted to adjust the detection parameters but cannot change the Intra align option during this process.
• In the Workflow options for Alignment, the Intra align option was not properly saved in certain cases, which could cause edited intra-gel alignments to become uneditable (after using Image view, for instance).

Spot edition / Review

• When adding images to a previously analyzed project and keeping the original spot pattern, the software could crash during operations in the Groups report (e.g., column sorting) if some groups contained missing spots because they fell outside the image area of the newly added images.

Presence filter

• Undo and Reset modifications for edits to the Presence filter thresholds were not always handled correctly.

Coverage

• When calculating coverage by volume, the ‘Secondary vs total number of spots’ formula was always applied, regardless of the formula selected in the settings.
•  Coverage by Volume was incorrect due to an error in calculating the volume of Common spots.
•  When calculating similarity with the ‘Intersection vs total number of spots’ coverage formula, the Counter diagram displayed a circle with a missing segment instead of a closed circle.
•  In the New coverage pairs list, certain Primary–Secondary combinations were displayed in reverse order, requiring a ‘Swap images for coverage calculation’ to obtain the correct coverage percentage.
•  When reordering images in the Presence summary, the image order in the Presence plot and Spot presence table was not updated accordingly.
• Creation, editing, and deletion of quadrants were not properly handled by Undo or Redo.

Annotations, Spot sets, Validation columns

• For newly created analyses in expression analysis projects, the corresponding Analysis-X column, useful for validation, was not always displayed by default.

Exports and reports

• When generating a Project report for Expression analysis projects, the number of spots for which statistics, plots and views are included could be inconsistent (when using the All spots option) or missing.
•  In the PDF generated with Project report, the spot sorting in the analysis tables of the Results section did not match the user’s sorting options from the current session.
•  When exporting tables with spot presence states in .txt, .xlsx or .xml format, the textual values for those states showed random characters instead of readable text.