Melanie 9.2.4 (2021.5.20.0)

This page describes the new features, changes and fixes that were introduced in the Melanie software since the release of Melanie 9.2.3 (2020.5.12.0).

You can learn about the installation requirements and instructions for Melanie 9.2.4 (2021.5.20.0) in its Readme file.

Changes

Projects

  • Name changes of items such as projects, images, DIGE/DIBE gels/blots and alignment groups are now validated immediately (rather than when changing step).

Quality control

  • Within a gel/blot, the Gray levels % and Dynamic range % are now calculated with respect to the highest Estimated bit depth of any images in the same gel/blot.
  • The Warning and Caution thresholds for the Dynamic range % have been adjusted to 10% and 25% respectively (from 5% and 10% respectively).
  • In Overall image consistency, a Caution message is now displayed when all images in the project do not have the same Estimated bit depth.
  • In Overall image quality, a Warning message is now displayed when any images (within a gel/blot) have low Estimated bit depth compared to others.
  • Caution messages now appear when original image sizes are smaller than 1000 x 1000 pixels.

Alignment

  • The Align process parameter was removed from the Workflow options of the Alignment step.

Results

  • The PCA calculations have been optimized to decrease the time needed to display the PCA results by 40%.
  • Spots detected in areas with background clipping or saturation can have abundance values of 0. Certain calculations using these values are impossible (e.g., one cannot divide by 0). Where appropriate/possible, problematic values are excluded from the calculations. Where this is not an option, the software now displays a dash “-” for invalid values.

Fixed bugs

Projects

  • Due to file path constraints on Windows OS systems (260 characters maximum), projects could get corrupted when renaming the project, images in the project or alignment groups (in Alignment setup).
  • After restoring an expression analysis project (that does not contain picking information) from a .pex file, the Opened date of the restored project in the Project list is modified at each display of the Project list, even if the project was not opened. This was true until a change was made to the project.
  • At each display of the Project list, the date in the Opened column was updated to the current date for all projects in the list. As a consequence, all projects were grouped in the section Opened: Last 24 hours.

Quality control

  • For some calibrated images, background clipping was not correctly calculated.
  • Estimated bit depth was calculated on the crop area and not based on the entire image, as it should.
  • No quality check information was displayed when only selecting the second or third image in a gel/blot.
  • Image names in DIGE/DIBE projects could overlap when they were too long.

Alignment setup

  • After editing the alignment setup of an existing, hierarchical setup, a “Fail to move [image]” message could appear when advancing to the Alignment step. This was accompanied by a project corruption, resulting – after closing and reopening the project – in a reading error mentioning that some gels could not be opened.

Results

  • Software crashed when returning to the Results step after factor levels were renamed while the Expression ratio table using those factor levels remained open.
  • Due to an issue introduced during code refactoring, PCA results for releases 9.2.0, 9.2.1, 9.2.2 and 9.2.3 were incorrect (input values were not normalized). This fix restores the results as they were obtained in 9.0.0, 9.1.0 and 9.1.1.
  • In PCA, the total variance of all the principal components could add up to much more than 100%.
  • For DIGE with internal standard projects, the Standard Deviation (SD) that appeared in the tooltip of the Expression profile didn’t take into account the Display ratio as option (Usual, Signed, Log10, Log2). The SD value displayed was always that for the Log10 option.

Coverage

  • When switching between different coverage pairs/tabs, the software always displayed a message about saving modifications, even if no changes were made.

Picking

  • After editing a previously saved selection of spots to pick and then cancelling the edits – with Reset modifications or Ignore modifications on leaving the Picking step – all alignments in the project were destroyed.
  • When the Experiment image used for picking, and then the project, were renamed, the project could become corrupted.
  • In the Spots to pick table, the Pixel X and Pixel Y coordinates were those of the spot on the Image to pick instead of the Experiment image.
  • While the IDs in the Spots to pick list were correct, the identifiers in the generated pick files were not.

Undo / redo

  • Matches were corrupted when, after deleting spots in the Spot edition step, changes were reset using Reset modifications or by selecting the Ignore modifications option on leaving the step.

Exports and reports

  • When a project name contained the special character #, the exported Project report (PDF) did not include any images.
  • In expression analysis workflows, when the Result step was not yet visited, the software crashed when generating a Project report with the option Save spot measurements in a separate appendix/file ticked.
  • For a TIFF export of a PCA plot, the colors in the exported file were different from those in the plot.

Image view

  • Adding a column in the Gel table in Image view could make the software crash.