The most recent release of Melanie is Version 7.0.7 (5 Sep 2014).
Please register here
to download the currently available release.
Find out exactly what has changed since release 6.0.0 of Melanie:
September 5, 2014 (release 7.0.7)
- In the Class Analysis Table, in addition to the Center and Dispersion options in the drop down menu, the options "versus Class X" now enable to display, in each class’s column, the ratio of the spot value for the class versus the spot value of the selected reference class (X).
- Relative and Normalized options are removed in the Gel Analysis Table and Histograms of DIGE experiments when Volume Ratio is chosen as the quantification measure. These options are present for all other quantification measures.
- Gap, Ratio and Normalized options are removed in the Class Analysis Table and Histograms of DIGE experiments when Volume Ratio is chosen as the quantification measure. These options are present for all other quantification measures.
- Links to the Swiss-2D PAGE database, used by default for the Ac annotation category (http://world-2dpage.expasy.org/swiss-2dpage/), and to the list of federated 2-D PAGE databases (http://world-2dpage.expasy.org/list/) have been updated.
- When image names contain the text strings "Blue", "Green" or "Red", the default Staining proposed will correspondingly be Blue, Green or Red. However, the images are not grouped in a DIGE gel or treated as DIGE gels, as it is the case for images with the strings "Cy2", "Cy3" or "Cy5".
- Optimized memory management when processing images with the option "Keep image in memory" deactivated.
- Melanie, although still a 32-bit application, can now use more than the usual 2 GB of memory, thus enabling the analysis of larger data sets.
When run inside the WoW64 subsystem (Windows 32-bit on Windows 64-bit, a subsystem of the Windows operating system capable of running 32-bit applications and included on all 64-bit versions of Windows), Melanie can now access 4 GB of physical memory.
To make more memory available to your Melanie application on a 32 bit version of Windows XP, Vista, 7 or 8 operating systems, you need to enable the 3GB switch.
While the 3GB switch may be a useful tool that allows you to access more memory for your Melanie application, it should be mentioned that not all Windows updates or hardware and graphics drivers work well, or at all, with the 3GB switch enabled. If you experience any unexpected or abnormal behavior with the 3GB switch enabled, we recommend that you disable it.
To enable the 3GB switch on Windows Vista, 7 or 8:
- Right-click Command Prompt in the Accessories program group of the Start menu. Click Run as Administrator.
- At the command prompt, enter "bcdedit /set IncreaseUserVa 3072"
- Restart the computer.
To disable the 3GB switch:
To enable the 3GB switch on Windows XP:
- Right-click on Command Prompt in the Accessories program group of the Start menu. Click Run as Administrator.
- At the command prompt, enter "bcdedit /deletevalue IncreaseUserVa"
- Restart the computer.
- Right-click My Computer. Click Properties.
- In the System Properties dialog box, click the Advanced tab.
- On the Advanced tab, under Startup and Recovery, click Settings.
- In the Startup and Recovery dialog box, under System startup, click Edit. The Windows boot.ini file will be opened in Microsoft Notepad.
- Create a backup copy of the boot.ini file. Note: Boot.ini files may vary from computer to computer.
- Select the following line in the boot.ini file:
multi(0)disk(0)rdisk(0)partition(2)\WINDOWS="Microsoft Windows XP Professional" /fastdetect
- Press Ctrl+C to copy the line and then press Ctrl+V to paste it immediately below the original line.
Note: Your text string may be different from the text string in this solution, so be sure to copy the text string from your boot.ini file, and not the text string included here.
- Modify the copied line to include “ /3GB”, as shown in the following example:
multi(0)disk(0)rdisk(0)partition(2)\WINDOWS="Microsoft Windows XP Professional 3GB" /3GB /fastdetect
Note: Do not overwrite any existing lines.
- Save and close the boot.ini file.
- Click OK to close each dialog box.
- Restart your computer.
- During startup, select the 3GB option. If you do not select the 3GB option, the system will default to the 2GB total memory setting.
Note: If problems occur during startup, you may try to resolve the issue by updating some of your drivers. However, recall the notice at the beginning of this solution, noting that all Windows updates or hardware and graphics drivers do not necessarily work with the 3GB switch enabled.
For more information on the 3GB switch, refer to the following articles:
- Implementation of a new demo mode.
- When the size of a project increased following edition of the data set, and got close to the 2 GB application limit, there was an Out of Memory exception that was not properly handled. In very specific conditions, when the data in memory, incomplete, was subsequently saved upon closure of the software, some information (such as matches) was not saved, thus corrupting the data.
- Dots in match set names were not managed correctly. As a result, the concerned match sets could not be reopened. The software now checks that no dots and other special characters are used in match set names.
- When images were stacked and image names were too long to be displayed at the bottom of the pane (for navigation purposes), the images in the pane were flickering constantly.
- A calculation error for the calibration option "Force Through Origin" could give different weights to the points used to calculate the coefficients of the curve (low OD values could contribute more strongly than large OD values). For most scanned tablet images this has no influence, but on some images the calibration could be strongly influenced.
- Bad display of the calibration curve when the image contained a transformation table.
- After creating a new calibration, the last calibration points in the saved calibration file (*.cal) had a raw data value of -1 instead of a negative measured value (the minus sign indicates that the point was excluded from the calculation of the calibration curve, because considered unreliable).
- The installer has been modified to fix an issue ("DIGE module not found") with the registration of the Codetect.dll that could occur in certain circumstances.
- When the codetect.dll module was not found, no re-normalization was carried out after deleting spots on DIGE gels with a single image.
- Crash when deleting spots on a DIGE gel with a single image.
April 5, 2012 (release 7.0.6)
- New tutorials are provided with the software. The “Non-DIGE Tutorial” and “DIGE Tutorial” documents are available from the Help menu in the software, from the Windows Start menu, and from the folder Doc in the software installation directory. The corresponding images files can be found in the folder Tutorials/Images in the software installation directory.
- Refreshing of the Histogram Reports has been optimized.
- The use of memory to store displayed image data has been optimized.
- The possibility to unload image data from memory, to optimize the use of available RAM, is now accessible from Tools > Options > General > Raw Image. With 'Keep image in memory' selected, image data is continuously loaded. With 'Keep image in memory' deselected, image data is only loaded when specific operations (Detection, Adjust contrast, 3D view, Profile) require the use of raw image data. Some functionality (Pixel Intensity in the Cursor Information Window and Status Bar) will not be available in that case.
- DIGE images can now be imported (and automatically grouped) by opening .DS files.
- In the Create calibration option it is now possible to force the calibration to go through the origin.
- The Gel Calibration Plot was modified to display the calibration / transfer table of files coming from various image acquisition devices.
- For improved usability, a Fold column has been added in the Class Analysis Table. This value displays the fold-change between the class with the lowest Central value and the class with the highest Central value.
- For more simplicity, Relative and Normalized options were removed in the Gel Analysis Table and Histograms of DIGE experiments.
- For more simplicity, Gap, Ratio and Normalized options were removed in the Class Analysis Table and Histograms of DIGE experiments.
- Values for the DIGE Internal Standard images are excluded from the Gel Analysis Tables and Histograms in a MatchSet sheet, when Vol Ratio is the selected quantification value.
- 3D views are now normalized for DIGE data sets.
- The number of images that can simultaneously be viewed in 3D view is limited to 24, to ensure satisfactory performance and avoid getting out of memory. Images to be viewed in 3D can be selected both before opening the 3D view, and while being in the 3D view, from a list that contains information about the match sets or classes to which the images belong. The image selections are kept as long as the sheet remains open.
- New templates for printing tabular reports and the History have been created, compatible with both Microsoft Internet Explorer 6 and Mozilla Firefox 3 and higher versions.
- Image scaling is now proposed for images with resolutions starting from 226 dpi.
- A specific issue with DIGE co-detection resulted in some spots not being detected for datasets with many saturated regions. Regardless of the correction, it is recommended to avoid saturation as it will decrease the quality of spot co-detection, DIGE normalization and matching.
- In some conditions, when the software crashed, part or all analysis data could be lost.
- Data could be lost when renaming DIGE images that were already detected and matched in the workspace.
- Crash related to Class Analysis Histograms for DIGE data sets.
- Dots in image file names were not correctly handled. Files containing dots were truncated.
- Accented characters in project names were not properly managed.
- In the Gel Analysis Table, the content of the Max column was not updated when changing the option in the Displayed Value drop down.
- Incorrect initialization of the Central Tendency in the Gel Analysis Table when selected statistic is Reference (value from reference gel).
- When a spot was absent from a class (when having more than 2 classes), a central value of 1 was displayed in the Class Analysis Histograms and in the Max column of the Class Analysis Table.
- .GEL files from the FLA-7000 and FLA-9000 images were not correctly supported (cut-off effect on high intensity values).
- Combine Spot Sets did not work for a single image or for non-matched images.
- Reports crash when clicking rapidly on a column header while the report is being constructed.
- Crash when closing a sheet after having created/applied a calibration.
- For floating license users, when the network connection to the license server was lost, the software crashed without saving (after a certain delay).
- At first opening of the Adjust Contrast window, it was not the histogram of the selected image that was displayed, but the histogram of the first image, at the top left of the sheet.
- After saving, closing and starting the software again, pI_MW labels were removed from the original annotation (if it had more than one label) and saved in a separate annotation on the same spot.
- Only the labels from the first annotation on each spot were included in the Spot Table (and exports of this table). In this new release, all labels from all annotations on a given spot appear in the Spot Table, except when the annotations bear labels of the same category. In this case, only the first label from each category will be included in the Spot Table.
- Manual selection of multiple annotations with Ctrl or Shift did not work properly on matched spots/annotations.
- It was not possible to import TIFF images with an alpha mask.
- There was an error on import of old ImageMaster/Melanie data containing a Master Gel.
- Import MatchSet failed.
- When printing tabular reports, all columns were displayed for printing, including the hidden columns.
- When validating existing landmarks on gels newly added to a match set (containing images that were already detected, land-marked and matched), the landmark numbers on the new gel(s) were wrong.
- For DIGE data sets, the selection of a region was automatically applied to the entire class (in a Class sheet).
- Some commands in the 3D View were not supposed to be accessible in particular display modes (e.g. Stack, Transparent Mode, Reference, Forward, Back, Animation).
- When canceling a free rotation action, the original image was not properly restored.
- Incorrect management of user response when asking for confirmation to edit selected spots with a Hidden status (in case the newly edited spot overlaps with a hidden spot).
November 30, 2009 (release 7.0.5)
- Improved speed performance in 3D View.
- After re-detection of matched DIGE gels, inconsistent matches are created.
- After detection of DIGE gels, the "Open File" and "Browse Folder" dialogs do not function correctly (on Windows XP).
- Rename of project failed in certain conditions.
- Errors in export to Genetix GelPix.
- Crash on Gel Analysis Report for match set with DIGE images that only contain a single image.
- When landmarks are removed and gels re-matched, matching still uses the deleted landmarks.
- Non-confirmed landmarks (projections) are taken into account for the matching.
- Wrong landmark numbering and consequently inconsistent matching after Undo Delete Annotations (when the delete concerned suppression of Landmark annotations).
- pI and MW values were not propagated to matched gels.
- pI_MW annotations were unlinked from spots after closing and reopening images.
- For images with a transfer table the inversion of the gray levels fails (images were unchanged).
- When inverting gray levels, the Adjust Contrast Histogram and the Gel Table are not updated.
July 24, 2009 (release 7.0.4)
- The software installation now includes tutorial images that can be found in the folder C:\Program Files\GeneBio\Melanie 7\Tutorials\Images. In addition, when the software is started for the first time, two tutorial projects are restored. These projects can be completed with the tutorial images described above (please consult the Melanie 7.0 Quick Start Manual for more information about the Tutorial experiments).
- Integration with the latest co-detection module (codetect.dll) from DeCyder 2D v7.0 to ensure compatibility with the most recent version of DeCyder. Please note that due to this change, v7.04 and later cannot co-exist on the same computer with older versions of ImageMaster 2D Platinum (<v7.0), DeCyder 2D (< v7.0) or Melanie (<v7.0).
- Spot Volume Ratio normalization is automatically carried out after deletion of spots.
- The software now provides the possibility to import images from the Bruker Proteineer SP, to send spots to the Proteineer SP for picking, and send images and spots to Bruker's ProteinScape, if these devices are installed. To have access to these functionalities, users with a version prior to v7.04 installed should reset their Menus (Tools > Customize, then click "Reset..." in the Toolbars tab).
- To optimize the use of available RAM, the user now has the option not to load the raw pixel values into memory, by editing the <Keep_image_in_memory> parameter at the end of the User Preference file (C:\Documents and Settings\UID\Application Data\Melanie\UserMelanie70.xml). When this parameter is set to "1", image data is continuously loaded. When the parameter is set to "0", image data is only loaded when specific operations (Detection, Adjust contrast, 3D view, Profile) require the use of raw image data. Certain functionalities (Pixel Intensity in the Cursor Information Window and Status Bar) will not be available.
- Possibility to display the SpotID for selected spots on the gel images.
- Expand/collapse state of each project is kept for next work session.
- When only one row is selected in a table, the green arrow icons in the Table toolbar ("Next Selection" and "Previous Selection") now select the next/previous row in the Table.
- Only visible columns are exported when saving a report.
- When saving a report while having rows selected, the software provides the possibility to save only selected or all lines.
- The license path is available in the license information.
- Possibility to access the FLEXible License Finder at all times to import a new license.
- Improved memory management.
- Landmarks are not longer imported from saved Annotation Tables (because not handled in the software).
- Improper reading of 24 bit colour images (horizontal lines).
- Some .img files (from Fuji LAS-3000 scans) could not be imported because of an error while reading the corresponding .inf file.
- Calibration from .gsc/.1sc files was not properly read.
- Crash when importing two images with same name but different extension.
- Import of annotations of type Set was not properly handled.
- Flip horizontally and vertically in the Image Pool had inverted functionality.
- Matches were lost when restoring a project using the original file paths.
- Custom shortcut settings were lost as soon as the application was closed.
- Internal error when changing the quantification value while having Scatter Plot and Scatter Table displayed.
- Deleted spots were not restored after undoing "Delete spot" when all spots were hidden (in mode View > Spots > None).
- Crash when attempting to propagate spot on DIGE images (not permitted).
- Crash when dragging (or copy/paste) a match set into another match set in the workspace.
- Colour palette in the 3D View was not automatically applied when selecting a new spot.
- Undo "Import Annotations" did not work.
- Histogram distribution in Adjust Contrast could change under certain conditions.
- Issue in creation of classes when converting projects from v6.0 to v7.0 of the software.
- Internal error when matching a DIGE-detected pick gel (single image) with other DIGE gels.
- Keyboard shortcuts were not available for sub-menu entries.
July 31, 2008 (release 7.0.3)
- "Combine spot set" feature modified.
- Improved license management.
- Calibration window can now be resized.
- Resolution in TIFF images sometimes presented negative values.
- Support of TWAIN module for scanning.
- Import and addition of projects and export files (.exp) in the workspace.
- Propagated spots were not saved.
June 20, 2008 (release 7.0.2)
- Optimisation of memory management in the alignment process.
- Possibility to apply a calibration to images is now only possible while working in the Image Pool. No calibration can be applied once images have been added to a match set.
- Crash when modifying a match set (e.g. adding a sub match set) while it was open in a sheet (and subsequently clicking in a menu).
- Class column in the Gel Table was always empty.
- Position of spots was shifted in the new image when the user cropped a detected image in a match set.
- When importing images with a calibration of type transformation table, the calibration was lost when the image was added to a match set.
- "Select > All Enabled Spots" failed when spots where hidden.
- Crash on closing a sheet when some annotations and spots were selected.
- Spot quantification was not initialized when the user propagated spots between images.
May 27, 2008 (release 7.0.1)
- Export of annotations (save, copy to clipboard) in Table Report.
- Management of project and workspace backup of previous version.
- Creation of new images and DIGE gel when user crops DIGE gel in Image Pool.
- Synchronization of Gel Table and 3D View on image opening and closing.
- Add "Copy..." option in the workspace, allowing to create a copy of a project.
- Add MatchID, spotID ref in "Scatter Table" of "Scatter Plot" report.
- Add "Detect And Match Spots" toolbar.
- Area Value correctly initialized upon opening (this value could be initially expressed in pixel and then changed to mm2 on certain operations).
- Problems in opening and closing of hierarchical classes.
- Contrast was modified on cropped images.
- Bad image alignment when modifying landmarks with "Align Images" enabled.
- Conversion from old format: Images in the old workspace/project format that were detected, but not yet inserted in a match set are now added to a match set in order not to lose the detection.
- Management of the accessibility of customized menus.
- Management of the selection of annotations and spots (when linked).
- Category Set not editable in Annotation table.
- Common Labels not functional.
- "Fitting Table" and "Calibration Table" from "Create Calibration Window" were always empty.
- Initialization of the reference in the contrast mapping.
- Edit>Spots>Propagate failed when propagated spot positions were out of image destination.
February 8, 2008 (release 7.0.0)
Some of the new features in Melanie 7.0 include:
- Simplified import and visualization of images
- Simplified project management with easier population set up
- Synchronized data view for easier navigation: Content and selection of tables, histograms, plots and 3-D views are continuously updated to stay synchronized with the displayed sheet that contains the gel images
- Group selection: When selecting a spot belonging to a group, any matched spots of the group are automatically selected as well
- Improved matching efficiency with hierarchical match designs
- Management of multiple matches and composite spots
- Possibility to enable/disable spots from the analysis and save spot sets for later retrieval, filtering and combination
- Dedicated landmark tool
- New 3D View
- Adaptive display of histograms
- Student t-test replaced with ANOVA, expressed as probabilities
- Customized report templates
- Reviewed contrast adjustment feature
- Custom and context-related toolbars
- Reorganized menu structure with icons to allow the user to create custom toolbars
- One-click to choose desired layout of sheets and panes
- Option to surround spot selections by boxes, for easier localisation and identification
- Single tool to select/edit spots and annotations
- Measure tool to compute pixel, pI, MW, or linear (centimeter or inch) distances between spots
For more information, please see the Product Brochure.
May 14, 2007 (release 6.0.2)
- The match data of a project is now saved with the project file (in a "Matches" folder at the same level as the .prj file) for easier file sharing.
- The Melanie6.xml file is only written upon installation. This means that normal users no longer require write permission on this file.
- The software licensing system now supports Windows Vista.
- In LAU calibration (Fuji), a computational error could lead to completely white images.
November 15, 2005 (release 6.0.1)
- Graphical reports can now be docked alongside textual reports.
- When importing annotations, new annotations are only created when a label already exists.
- Import of pairs from Melanie 2 (in certain cases).
- Import Annotation from .txt files didn't work properly when certain labels were empty.
- For the option "File > Export > Gel Data to XML", pairs were not exported in particular cases in Class worksheets or when the pairs were not saved on disk.
- When a gel was renamed, the file extension was removed (Ex: Ecoli.mel -> Ecoli).
- When gels were stacked, the Cursor Information window was displayed, and the Next or Previous keyboard keys were pressed, the information in the Cursor Information window was not refreshed.
- Re-dimensioning of a column in a report causes the sorting of the adjacent column.
- Non-DIGE spot detection didn't give the same results (in terms of spot outlines) as in Melanie 5.0. The number and shape of spot outlines should now be identical as in version 5.0, but the quantification results will be slightly different.
July 15, 2005 (release 6.0.0)
The most important new features in Melanie 6.0 (compared to version 5.0) are:
- Support of DIGE technology (co-detection, internal standard, ...)
- Population matching
- Workspace with management of gels, match sets and classes
- Intelligent multi-worksheet display
- Dockable report windows
- Scrollbars for moving and zooming gels
- Improved cropping option
- Adjust contrast in 3D view
- Measure histogram in spot report