Delta2D Changelog

Delta2D 4.8

4.8.2 Final 06 (201911292109)

• Warping has been improved by refering to the pixel center instead of its top left corner. The effect is only noticable in transforms with a very high scale factor, but increases warping precision there.

4.8.2 Final 05 (201910251939)

• The Java version shipped with Delta2D is updated from Java8u144 to Java8u202, which is the last free update for Java8. Following Java Versions have been emitted by Oracle under a  more restrictive license. Note: Java is only included in full installers, not in updaters.
• Under Linux the launcher is now ensured to be executable after installation. Before it could happen, that the user had to set the executable bit himself.
• A potential problem with SSL handshakes is now fixed, which could occur with future SSL versions.
• In the analysis window, the info (help) button did not react in some dialogues. This is now fixed.

4.8.2 Final 04 (201905211550)

• Fixed a problem with reopening a project, which was saved empty (containing no gel images) in a previous session.

4.8.2 Final 03 (201905061325)

Usability

• The labels and the group ratio columns of the Quantitation Table can now be controlled in the Visibility Dialog (button with the eye).
• Determining the Ratio Master Group for Statistics Tables has become more transparent:
  Before, the group on the top most position in the Project Manager was used as the reference for the group ratios in the Statistics Tables. To use a different group as reference, you had to move that one up to be on the top most position in the Project Manager.
  Now the Ratio Master Group follows the Ratio Master Gel: the group containing the Ratio Master Gel set in the Visibility Dialog (again: button with the eye) is also used as Ratio Master Group for the Statistics Tables.
• In Gel Standard images are now hidden by default in quantitation tables, except if they are the only image representing their very gel.
• On the Light Table, In Gel Standard images are now easier to identify: they are marked with a little cross in their gel icon.
• The Labels tab in the Options dialog now lists all Label Scouts potentially providing numeric data for pI/MW Estimation. Before it contained only those scouts actually containing data, which could lead to an unintended shift of this setting, when you modified other options and confirmed this dialog with OK.

Features

• A new project type has been introduced, including its own warping strategy: Mercator.
• The visibility of columns of your table is now saved along with your project, so that you can now use independent visability settings for different projects. Before it was a user setting, where you had to change the visible columns every time when changing the project if you had different demands in your projects.

Fixes

• The titles of the spot tables now better express which spots of which gel images they show.
• Small problems with the enabled state of the buttons in the Visibility Dialog (the one with the eye ...) are solved.
• Debug + Audit: added info about image size and warping problems to debug output and removed superfluous other info.

Note: the versions 4.8.1 Final 01, 02, 03,  4.8.2 Final 01 and 02 have not been released.

4.8.0 Final 23 (201809271707)

• The CSV/Excel-export of quantitation tables can now be enhanced by additional pI/MW columns for all visible gel images with existing pI/MW estimation. Please have a look at Options: Delta2D: Labels, make sure to set the correct data source for pI/MW estimation, and set the checkmark to Include pI/MW data when exporting tables.
• Multiple exceptions and NPEs in connection with changing warp mode and regions view were fixed.
• A new report, "debug.py", was included to enable in case of problems also end users to create debugging output, which can be saved and sent via email to support@decodon.com.
  It can be produced by clicking on the link:
  http://127.0.0.1:2007/Delta2D/debug.py
  Please use your browser function (press the keys CTRL + S simultaneously on your keyboard) to save the report.

4.8.0 Final 22 (201809061502)

• The uniprot scout now has two extra options, applicable in the scout configuration in Delta2D's installation folder: "IgnoreTemplatesWithMissingParameters" and "IgnoreTemplatesWithMissingSubstitutions".
• Fixed problems which prevented the uniprot scout from working since an update of the uniprot site.
• A problem was fixed, which could occur when saving project on changing pool.
• The Western Blot report now does not show error messages any more in sections 'Transferred Spot Pattern' and 'Fused Images' when you want to see the support images as well.

4.8.0 Final 21 (201808171336)

• A problem with size and position of a drop-down menu in the reports was fixed.
• The manual has been updated.

4.8.0 Final 20 (201808151949)

• We fixed some Exceptions when switching Warp Mode on fresh imported images directly to a different one, especially implicit mode without having such an implicit warp path.
• Fixed links to Fused Images in the workflow, which were all pointing to the newest Fused Image.

4.8.0 Final 18 (201807182158)

Usability

• A new project type "Western Blots", dedicated to 2D Western Blots, was introduced.
• You can import your images now directly into your project.
• In Western Blot projects, Delta2D can sort your images automatically into the according groups, based on their names and their assignment to a sample, gel or channel.
• The different roles of the images are considered in Western Blot projects when applying the warping strategy.
• Importing images now first shows images already imported into your pool, but not yet used in the current project, and if there are none of these, opens the Import Wizard.
• The 2D Western Blot warping strategy can be extended for realizing stripped Western Blots (Western Blot 2, Western Blot3, Western Blot Contour 2, Western Blot Contour 3).
• A new visualisation now shows at a glance in the Project Explorer, the Light Table and the Warping Setup, which sample, gel and channel are assigned to your images. And when pointing on this visualisation, a tool tip tells you details.
• The job manager now shows automatically if you create jobs by defining automatic warps for the first time in the session.
• The progress of an autowarp job now shows even if the job was started implicitely by clicking on "Warp" or "Find Match Vectors" in the Dual View.
• Now you can change the warp mode also in the context menu if exactly two images are selected in the Project Explorer.
• When clicking on "Review" of one of your image pairs in the Work Flow pane, the Dual View now activates the match vector tool automatically.
• A new column called "Labels" is available on every Quantitation Table and shows labels from ALL images of the current project, not only those being visible in the current table. With its filters you can control the labels of which images you want to see or hide, regardless of the visibility status of the images themselves, and also regardless of whether the spots of these images are included in the total spot set or not.
• On spots having labels also on matching spots on other images, the labels are now sorted corresponding to the sorting of the images of their origin in the project manager. This way, by moving the images up or down in the project manager, you can control their sequence in the combo box of the table rows yourself.
• Administrators in regulated environments, where e.g. CFR-compliance is relevant, can now benefit from syslog based audit trails.

Reports

• The Western Blot report recognizes the different roles of the images and initially does not show the support images.
• If you defined filters in the Quantitation Tables, the report now applies these first, and uses its own defineable filters if not.
• The report now validates your project setup on calculating results, and tells you, if something is not as it should be.
• You now have the option to only show image pairs with the same gel.
• If there are multiple gels in your Western Blot project, the images are now matched first by their gel and then by their order in the group.

Fixes

• A problem with the overlay rollup was fixed, where switching back to automatical visibility of spot or label layers did not always work.
• Several rarely occuring NPEs were fixed.
• Small cosmetical issues, typos etc. were corrected.
• The native look-and-feel under Mac OS X was recovered by updating the involved libraries.
• Some small problems with the Western Blot report were fixed.
• The job manager now refreshes more accurately and empties and populates its list and controls accordingly when closing and opening projects or the complete application.
• When clicking on the status button in the Dual View and an image pair with automatic warping is opened, where the match vectors are not yet calculated, Delta2D now does not start finding match vectors any more.
• The Blotting Report now computes Mean and RSD of coverage values between groups for all image pairs instead of only for the first six pairs.
• A deadlock could occur on importing images.

Note: the versions 4.8.0 Final 01 to 15 have not been released.

Delta2D 4.7

4.7.3 Final 05 (201809261413)

• The UNIPROT scout now works again with the modified uniprot homepage.
• Multiple exceptions and NPEs in connection with changing warp mode were fixed.
• A new report, "debug.py", was included to enable in case of problems also end users to create debugging output, which can be saved and sent via email to support@decodon.com.
  It can be produced by clicking on the link:
  http://127.0.0.1:2007/Delta2D/debug.py
  Please use your browser function to save the report (press keys CTRL + S simultaneously on your keyboard).

4.7.3 Final 04 (201802271505)

• Import and handling of gel images modified and saved with Adobe Photoshop in TIF format is improved.
• Im- or exporting projects now includes the project properties properties as well.
• The selection status of the buttons for foreground and background of image in DualView is now better visible.
• A problem with an NullPointerExcetpion when opening quantitation table for a pair is now fixed.[7985]
• Deleting of image attributes like gel, sample and channel is now enabled again. [7968]
• Another NullPointerException on interacting with a project which is already about to be closed is fixed. [7966,7990]

Note: the versions 4.7.3 Final 02 and 03 have not been released.

4.7.3 Final 01 (201709252002)

• In Delta2D's Statistics Table you already could configure the spot attributes and the aggregation for the values you want to see in the table. While as default the statistics is shown for the Normalized Volume of the spots and the ratio is based on the groups' Mean value of each spot, you could change this to see the statistics of e. g. the Absolute Volume of each spot, and the group ratio based on each spots' median in every group. The handling of this configuration has now been improved in several ways:
  • This setting is now saved persistantly with the project data.
  • You can change the statistical reference (the spot attribute the statisitics are based upon) now in the Project Properties dialog as well.
  • Dual View's Scatterplot window and the Expression Profiles (both rollup and window) now consider this setting as well.
• In the Image and Table Column Visibility dialog the table headers now reflect the status better by also indicating in their check box if columns are only partially selected. Before you only could distinct empty and not empty columns, and the header boxes were initially all checked, regardless of the column's status.
• The Spot Profiles Rollup now refreshes correctly.
• The reports did not always notify the user if subsequent modifications in the project rendered the report inconsistent; e.g. in importing a new image not yet containing labels in a labels report.
• Some Error messages rarely occuring on generating a report were fixed. (NullPointerException, IndexOutOfBoundsException)
• The histogram sliders are now positioned more exact and so better to use.
• Some small cosmetical issues are now fixed.
• The installer did not save the Auto Update frequency correctly, now it does.
• The included Java engine was updated to Java 8 Update 144 (JRE 1.8.0_144) under Windows and MacOSX (not yet under Linux).

4.7.2 Final 03 (201705081334)

• The included Java engine was updated to Java 8 Update 131 (JRE 1.8.0_131) under Windows and MacOSX (not yet under Linux).

4.7.2 Final 02 (201704281529)

• Added interpolation as alternative method for mW estimation. Usually regression is the most suitable method, but the results sometimes are not satisfying, e.g. when you included precise markers in your gel. In this case, interpolation produces better estimations.
  To use interpolation, please make sure Delta2D is not running and append the following line to your Delta.ini in <your userhome>\.Delta2D:
  calibration.mw.interpolate=true
  If you start Delta2D again, it will use interpolation for estimation of mW on your gel Images.
  To revert this behaviour, simply set the above value to 'false' in the Delta2D.ini or remove the line completely.

4.7.2 Final 01 (201704121723)

• Added support for gel image type *.mel produced by ImageScanner / LabScan
• DualView now opens gel image pairs with respect to their order in the Project Explorer: the upper sorted image will always be the the unwarped master image and the lower will be the warped sample image in the DualView. Pressing the SHIFT key while double clicking on a image pair still swaps the roles.
• Fixed an error occuring occasionally on moving images around in the Project Explorer.

4.7.1 Final 01 (201703281946)

• The stability of pI estimation has been improved.

4.7.0 Final 16 (201703241352)

• Fixed a problem where installation on Mac OS finished with an IO-Error in some cases.
• Installation on Windows can now be done also without adminstrator rights in private places on the computer.
• Manual was updated to current version.

4.7.0 Final 15 (201703101213)

• Fixed a problem where Delta2D did not always use the system default browser for showing reports under Windows 10.

4.7.0 Final 14 (201703061509)

• Improved usability: When opening Gel Image Pairs in Dual View by clicking on the pair connection in the Project Explorer or the Warping Setup window you can now open the image pair with inverted roles by holding the Shift key while clicking.
  Example: Klicking on the Pair GelA_vs_GelB normally opens GelA as so called 'Master Gel', the gel out of the two on which the other one, GelB in this case, will be warped to. If you now press Shift while clicking on the same pair, GelB will be the unwarped 'Master Gel' and GelA will be warped onto GelB.

4.7.0 Final 13 (201702231806)

• Fixed problems with transferring spots when a modeled spot could not be computed. [7917]
• Gels in Gel Image Attributes dialogue are now sorted alphanumerically instead of alphabetically before.

4.7.0 Final 12 (201701301758)

• Improved labeling: When labeling spots with numbers, they are assigned according the position of the spot from top to bottom.
• Sorting of Gel Attributes is now alphanumerical instead of alphabetical before.
• Fixed a problem where in new, not yet saved projects the quantitation table opened initially empty.
• The spot numbers (all/visible/selected) at the bottom of Quantitation Tables was not always correct.
• Fixed a problem with right click on column header without filter in Quantitation Tables.
• Fixed a problem with representation of ratio filter dialog.

4.7.0 Final 11 (201611031939)

(cumulated changes from versions 4.7.0 Final 01 through Final 11)

• Blotting Report was introduced.
• Numerous improvements, mainly of performance, related to generation of reports.
• Numerous small glitches and problems related to reports were fixed and details polished.
• Installation routines were cleaned up, unnecessary elements removed.
• Updated some third party elements.
• Updated included Java engine to Java 8 Update 102 (JRE 1.8.0_102).
• The installer got a new 'EV' signature to avoid Windows Smartscreen warnings.

Note: The versions 4.7.0 Final 01 to 4.7.0 Final 10 have not been released.

Delta2D 4.6

4.6.3 Final 08 (201610131247)

• Updated developer certificate in installer to avoid complaints by Windows SmartScreen on attempting installation.

4.6.3 Final 07 (201607141842)

• Fixed a problem with saving all reports at once (Reports Index).

4.6.3 Final 06 (201606031858)

• Fixed several small problems with reports.
• Fixed problems with reopening projects with saved filters or importing filters.

Note: the versions 4.6.3 Final 04 and 4.6.3 Final 05 have not been released.

4.6.3 Final 03 (201605111742)

• Fixed a problem loading Fuji files with uppercase file suffixes.
• Fixed a potential deadlock on closing Delta2D.
• Fixed problems with saving a project when only filters have been modified.

4.6.3 Final 01 (201603171119)

• Fixed a problem where some windows were not resizable in certain constellations of windows.
• Changed initial values for filters activated from the context menu (right click on column header in tables).
• Fixed a problem where project was not saveable if 'Clear all filters' was the only modification.
• Fixed a problem with deleting all labels if there were groups of labels before on the same gel.
• Continued preparation for future enhancements.

4.6.2 Final 02 (201603041621)

• Fixed a problem with spot matching in reports when gel images without spots were included in project

4.6.2 Final 01 (201603031925)

• Fixed a problem where the Quantitation Tables were not resizable in certain constellations of windows.
• Improved filter dialog to show infinity ( ∞ ) values as well.
• Fixed several problems (technical and cosmetical) with negative values and logarithmic representation in filter dialog.
• Modifications of filters now also enable project saving, even if they are the only modifications on project.
• Fixed problems with inverse filters saved in previous sessions.
• Several mostly cosmetical issues were fixed in reports.
• Several enhancements, improvements and fixes for special reports (not included in standard installation)

4.6.1 Final 06 (201601251000)

• Fixed a problem in Quantitation Tables where actions for selected elements sometimes were not available.

4.6.1 Final 05 (201601181129)

• Some cosmetic issues were fixed.
• Improved usability of update installer: does not ask unnecessary questions any more.

4.6.1 Final 04 (201601141759)

• Adapted size of Warping Strategy dialogue to fit larger description texts as well.
• Fixed Delta2D asking whether to use logarythmic values when opening an empty DIGE project.
• Fixed a problem with the filter active checkbox and an sometimes inactive apply button in filter dialogues.
• Fixed a problem with initial color of table cells with negated filters.
• Impoved usability: main quantitation table is now opened and activated after spot transfer
• Fixed a problem with initial spot filter state when creating report after opening project or transfering spots.
• Started preparation for future report enhancements
• Small fixes and adaptations for special reports.

4.6.0 Final 30 (201510281938)

• Fixed a problem with opening and saving certain statistical analysis (TMEV).

4.6.0 Final 29 (201510231917)

• Updated Java 8 from version 8u60 (8u45 on Mac OS X and Linux) to 8u66 in full installers on all platforms.
• Updated 3D library (JOGL) to version 2.3.2 to fix problem with Java8u60 under Mac OS X.
• Fixed problems with proxy settings for update checks and web-based license-check.
• Significally reduced size of deployed Java Runtime by stripping libraries not needed by Delta2D anymore.

4.6.0 Final 28 (201510061526)

• Fixed a bug for consumable mode: proxy settings are now used properly.
• Fixed a bug for exporting presentation slides: fill state of label arrow heads is now considered.

4.6.0 Final 27 (201509152320)

• Unified hover effects for spots, spot markers and labels using the corresponding layer color.

4.6.0 Final 26 (201509142039)

• Show mouse-over effect (hover) for spots and spot markers, too.

4.6.0 Final 25 (201509111948)

• Fixed active (mouse-hover) positions for label groups.

4.6.0 Final 24 (201509102326)

• Label Management: Group and select labels, create multiple labels during translation.
• Increased performance of reports.
• Adjusted synchronous spot matching status across different views.
• Delta2D now based on Java 8.
• Fixed a couple of exceptions.

Note: The versions 4.6.0 Final 01 to 4.6.0 Final 23 have not been released.

Delta2D 4.5

Delta2D 4.4

Delta2D 4.3

4.3.0 Final 01 (201108171453)

• Introduced project import / export.

Delta2D 4.2

4.2.0 Final 01 (20101201)

• GenoList/AureoList scouts did not show result of fetching in editor.

Delta2D 4.1