This page describes the changes and fixes that were introduced in the Melanie software since the release of Melanie 9.2.6 (2024.5.28.0).

You can learn about the installation requirements and instructions for Melanie 9.3.0 (2025.1.23.0) in its Readme file. For the list of third-party materials included in or distributed with Melanie Melanie 9.3.0 (2025.1.23.0), and the notices and licenses applicable to those materials, you can read the Third-Party Material Disclosures.

New features

Image view

• The Multichannel view allows users to overlay multiple images (channels) in various complementary colors. Users can select the images to overlay, choose the color scheme, and assign a specific color to each channel. Each channel’s contrast can be adjusted individually. Multichannel color overlays can be displayed for any aligned images, not just images from the same gel or blot. The feature supports color overlays for 2 or 3 images. But it can also create a grayscale overlay for any number of selected images, creating a composite pattern representative of those images. The color overlay can be exported in .png, .jpg, .bmp or .tif format, printed, or copied to the clipboard.

Traceability, accountability and security

• The audit trail tracks all user actions carried out during the life of a project. Each action is logged in an audit file that is part of the project, and is timestamped and accompanied by the user ID. The action’s parameters, critical to reproduce the action, are stored as well. The history of actions can be displayed in a Project audit report and exported in .pdf, .xlsx, .txt, .html and .xml formats. Users have the option to include the audit trail directly in the PDF report or as a referenced appendix to the report.
• To ensure that users are aware of any alterations made outside the controlled environment of Melanie, the software now checks the data integrity and warns users if edits to a project were made manually or by third-party software.
• The software now efficiently manages concurrent access to projects. When one user opens a project, it is locked to prevent others from editing. Should another user attempt to access the same project, a warning message will appear, showing that the project is in use and displaying the Windows login name of the user currently editing it.

Projects

• In addition to the default Local folder (user’s Document folder), users can now define a Shared folder location where projects can be centralized for easy collaboration with colleagues.
• Users can choose to create a new project in either the Local folder or Shared folder.
• Users can move a selected project to the Local or Shared folder.
• Users can move a selection of local projects referenced in their Project list to the Shared folder (in one operation).
• Users can add multiple projects from a selected folder.
• Users can permanently delete projects that are not referenced in their Project list from their Local folder or the Shared folder, to free up space.

Quality control

• Users can assign Aliases – alternative, more descriptive names – to images in their analysis projects. Aliases are displayed in image labels, reports and plots and can be customized for internal use or anonymized for publication. In the Quality control table and a few other places, Aliases coexist with the original file names to maintain consistency across platforms. Aliases can be manually edited or imported from an Excel metadata file.
• Detailed metadata associated with images can now directly be imported into Melanie from an Excel file. This metadata includes information such as file names, aliases, acquisition dates, experimental parameters, and sample details. A metadata field can be imported as Alias, image Description, image Property (Coverage) or Factor (Expression).
• When Factors are imported, they automatically appear in the Experimental design step, bypassing the Experimental design wizard.
• The Column settings in the Quality control table options allow users to show or hide image metadata created or imported as Descriptions.
• In the Quality control table options, the Edit image description feature links to the Image view screen, to facilitate edition or deletion of Descriptions in the Gel table.
• The software now supports 16-bit float TIFF images, typically generated by LI-COR instruments.
• The software now supports SCN images generated by Bio-Rad instruments.
• Various image properties are now imported as individual gel descriptions. This is notably the case for properties from the Molecular Dynamics format (.gel) that were previously consolidated into a single Comment field, and for metadata fields from LI-COR instruments.

Coverage

• The Coverage donut chart is a new type of diagram available for intuitive visualization of coverage results. The chart visually represents the percentage of coverage and the number of spots, divided into various categories (Primary, Common and Secondary). The central space displays the total coverage percentage.
• The new Coverage by Volume metric enhances analysis by accounting for the volume of immunodetected protein spots, not just their count. This metric is useful for distinguishing between analysis options when traditional coverage percentages are similar.

Display area

• Spots can now be labeled in 3D view, similar to 2D view. You have the option to label all spots, adaptively label selected spots, or fix labels on currently selected spots, using values from a selected column. For example, labeling selected spots with their pI values in 3D view can enhance presentation of results from charge variant analysis.

Exports and reports

• In the Gel table, it is now possible to create, display, edit and export multiline Descriptions.

Performance and usability

• The software now alerts users when a new version of Melanie is available. While it doesn’t automatically update, it displays a message with the new version number and directs users to the website to download the latest installer.
• The software has been validated for compatibility with Windows 11.

Changes

Projects

• In the Projects list, the field ‘Staining’ has been renamed to ‘Reference stain’ to clarify that it represents the reference stain/dye for the project (Internal standard for DIGE projects, Primary reference for Coverage DIGE/DIBE projects).
• The software now supports virtual folders for project storage.

Quality control

• When selecting an option to edit pI markers – whether it’s user markers, a predefined strip, or a new strip – the pI tool activates automatically.
• The software now shows the type and calculated length of the selected IPG strip in 2D view, assisting in adjusting its length to match its known physical dimension.
• Strip templates can now be repositioned using a simple drag-and-drop action.
• In addition to editing the positions of individual pI or MW markers, you can now also reposition and adjust the extremities of IPG strips in 3D view.
• The placement of pI and MW labels in 3D view has been enhanced to better support charge variant analysis.
• The cursor symbol now updates to reflect the selected tool and permissible actions when editing pI/MW values.
• Management of the PhotometricInterpretation tag has been improved for cases where the value of this tag is 1.

Experimental design

• Tooltips have been added to the Experimental design wizard to provide more detailed information about each available design.

Review

• For Expression analysis projects, the Spot filter and Spot edition tools have been directly integrated into the Review screen, for increased usability.

Coverage

• Several improvements have been made to the display of coverage and coverage range in diagrams, tooltips, quadrants, and plots.
• The options under ‘Show spots that are’ have been completed and renamed for enhanced clarity.
• Users can now navigate directly from a Coverage tab to the Presence Summary screen by clicking on the Presence Summary icon.

Exports and reports

• The PDF report generation process has been enhanced to reduce the file size by approximately 10% while maintaining equivalent image quality. It now also better handles interruptions, partial analyses, and progress status.
• The pI calibration plot is now included in the PDF report.
• After a change in detection, the content of filter-based spot sets is cleared, and their column headers change to red. To refresh the spot set with the newly calculated values using the previously defined filter criteria, right-click on the column header and select ‘Update’.
• The print format of the Data export has been improved.
• Sorting behavior now aligns more consistently with Windows Explorer, using natural alphanumeric sorting.

Performance and usability

• The General options have been reviewed to improve clarity.
• The settings for displaying validation columns as color in reports and on the images have been enhanced.

Fixed bugs

Quality control

• In the 3D view, pI and MW labels could display horizontal stripes over them.
• The software didn’t correctly handle IPG strips that share the same pH value across different % length points.
• The pI values of strip templates could be individually edited.
• When switching from a strip definition to the ‘Pi user markers’ option, choosing ‘Keep markers’ incorrectly unlinked the pI markers and allowed their individual editing, instead of maintaining the strip definition.

Detection

• For Expression analysis projects, when adding images to an already analyzed project, the existing spot pattern was lost instead of being applied to all images, including both the previously analyzed and newly added ones.
• Input validation for the advanced Workflow options in the Alignment and Detection steps was not performed properly.
• Changing ‘Vol. Percent Height’ in the advanced Workflow options of the Detection step altered the selections in the Detection input.
• Changing ‘Vol. Percent Height’ in the advanced Workflow options of the Detection step was not undone when using the ‘Reset modifications’ option.
• The ‘Reset modifications’ option could be deactivated even though there were still actions in the Undo list.

Spot edition

• Spot pairs could become corrupted following the undo/redo of edits made to multiple spots.
• Moving a spot on an image other than the alignment reference did not flag the spot as edited.
• Moving a spot did not change its user state to uncertain.
• For Coverage analysis projects, excluded spots were incorrectly managed when adding images to a project that had already been analyzed.
• Undoing the definition of product spots didn’t work.

Coverage

• Spot states could be lost or altered after undoing edits to spots.
• Sorting by the Status column(s) in the Spot presence table failed if the status of some spots had been edited by the user.

Picking

• When the last spot selected for picking was cleared, its color on the Experiment image did not revert to the default active spot color.

Display area

• A change of units sometimes didn’t correctly recalculate the grid.

Spot sets

• Spots could be removed from spot sets after undoing edits to spots.

Exports and reports

• The software didn’t properly handle cases where users entered Annotation or Spot set names that were identical to predefined fields.
• Plot background color was not applied to Expression profile and Interaction plots.
• The software crashed when printing the Quality control table and selecting the option to split for reports containing more than 10 columns.
• In the Alignment section of the PDF report, the images didn’t always display in warped mode.
• When exporting the Normalization factor table in Excel format, numerical values were exported as text.

Performance and usability

• The software window froze at launch when using a high contrast theme in Windows. Please note that high contrast themes are still not supported.