Weasel Development: Present and Future

Weasel users are offered the opportunity of guiding future development of the program. We invite you to comment on and vote for your favourites among the many suggestions for enhancement received from users. Email your comments, mentioning "Weasel" in the subject line, to .(JavaScript must be enabled to view this email address)

NEW 06 October 2011. Bug fix Weasel version 3.0.2 is now available! 

For download, go to Weasel Install.  Some of the many new features in version 3, including a significant speed increase, are as follows:

  • Significant speed increase over the previous version: typically 2.6 times faster at loading a large data file.
  • Enhanced handling of multi-block data by extension of the main menus.  This is particularly aimed at Guava multi-sample FCS v3 data.
  • Added options for multi-block data in the fluorescence compensation dialog.
  • Expanded user-setable Preferences section includes plot label font and default display sizes.
  • Expanded region formatting options including line weight and colour and the font of the region name which may now be dragged to a clear area of the display.
  • More compact dialog boxes for small screen laptops.
  • Faster fluorescence compensation adjustment facilitated by a new "Quick Trial" feature.
Bug Fixes:
  • 06October11: Fixed digitizing errors when reading 256-channel log scaled data.
  • Improved colour coding on dot density for low dot counts.
  • Fixed bug in reading DiVa analysis templates with imbedded spaces in gate names.
  • Fixed bug in reading saved presentations with background subtracted histograms.
  • 11March11: Fixed digitising errors when reading 1024-channel log scaled data. 
  • Exported FCS data and text are now both gated on their display's gate.
  • File names that are a truncated version of other file names are now recognised.
  • Improved the reading on Mac Weasel, of presentations saved on PC and vice versa.
  • Fixed batch mode issues when processing multi-block data files.
  • Batch mode displays showing attached stats no longer have over-sized stats drawers.
  • Histogram marker stats now include the section from the lower display edge to the first marker.
  • On PC, in batch mode, attempts to delete a display from the layout or to set a file as a control by right-clicking no longer fail.
  • Now distinguishes CellQuest instrument settings files from FCS data files.
  • Fixed error reading presentations with regions defined on linear parameters in MoFlo XDP data.

 

Possible Future Enhancements (not yet included):

  • Draw in the graphical display the percentages of cells enclosed within regions.
  • Add user-composed, on-screen text boxes not attached to any graphic display.

Enhancements Included in version 2.7.4 (Released 13th November 2009)

  • Important! The order of operations in evaluation of gate logic expressions has been made more intuitive.
  • Cell cycle modeling for extraction of G0/1, S-phase and G2/M percentages has been added.
  • Gating regions matched to the populations defined by CFSE or other tracking dyes may be automatically created.
  • Graphics can be exported in an additional format: scalable vector graphics (.svg).
  • Information buttons  are distributed among several control panels for contextual user help.
  • Graphics copied to the system clipboard for pasting into other applications is now in vector format (Macintosh only).
  • FCS parameters are now identified by name, not sequence number. This facilitates comparison of files with differing parameter lists.
  • The editing of polygon gating regions is simplified: double click to close an open region, double click to add a vertex to a closed region.
  • Semi-transparent histogram fill colours are an added option.
  • Dot plot displays may have a requested maximum number of dots regardless of the number of cells in the data file.
  • Dot sizing on Macintosh has been improved.
  • Y-axis labels of plots in exported graphics files are now in vertically rotated text.

Bug Fixes:

  • Fixed an error in reading MoFlo 2-byte files.
  • Now correctly handles user-defined time scales for Time as a parameter.
  • Stats numerical lists from all displays are now correctly correlated in the Stats Window. 
  • 08Oct09: Fixed bug in "Read all files in sequence" mechanism.
  • 08Oct09: Fixed bug in batch processing section.
  • 13Nov09: Fixed failure of dash patterns in histogram plots.
  • 13Nov09: Fixed occasional failure to properly apply compensations "..to current and new displays". 

Enhancements Included in Version 2.6.1 (released 18th November 2008)

  • Further speed increases: Typically 2-fold faster in loading DiVa analysis templates. Also 30% faster in reading fixed log scale files from conventional cytometers.
  • Now reads MoFlo XDP files.
  • Now reads any data block from a FSC file that contains multiple data blocks (e.g. BeckmanCoulter .LMD files, Cell-Dyn* files).
  • Reads and merges multiple data files into a single display.
  • Compensation setting changes applied in the context of one screen display now immediately apply to all on-screen displays of the same data file.
  • Histogram plots show mouse-sensitive colour-coded titles for all overlays.
  • One or more files among overlaid histograms are selectable as fixed controls; only the others respond to "next file" commands.
  • Current colour palette is now stored with each presentation for later (optional) retrieval.
  • Display annotation positions are now scaled to the display size.

Bug Fixes:

  • Comma vs. point confusion in European number input has been resolved.
  • More visible colour palette displays when using more recent Java versions.
  • Dialogs protected from irretrievable loss off screen.
  • Presentations prevented from being stored with negative screen coordinates for displays.
  • 18th November 2008: Corrects an inaccurate translation of DiVa analysis template regions.

Enhancements Included in Version 2.5 (released 11th December 2007):

  • Speed increases for many operations (in particular, up to 2.8-fold faster for data file re-reading and processing).
  • More time-efficient calculation of colour coding obviates the need for many file re-read operations.
  • Automatic fluorescence compensation.
  • New, automated "Weaseltracks" population-encircling regions.
  • Enhanced batch mode operation for numerical and/or graphical output from data collections, including "ad hoc" presentation creation.
  • User can set the negative range of "split" displays to better mimic the cytometer's biexponential display.
  • Save a graphics file including any number of selected displays.
  • Increased memory allocation for the Macintosh version.
  • Double-click a region name to fine adjust the region.
  • Double-click quadrant intersection to fine adjust the quadrants.
  • Display titles truncated on the left instead of the right and duplicated within displays, mouse-sensitive for requesting change to a new data file.

    Bug fix:

  • Fixed poor matching of fluorescence compensation values imbedded in DiVa v5 files.

Enhancements Included in Version 2.4:

  • Additional graphics save formats Windows Bitmap (.bmp) for bitmap graphics and Enhanced Metafile (.emf) for vector graphics.
  • Re-introduction of the BIPLOT display form deleted from Weasel version 2.
  • User-selectable colours and colouring hierarchy for marking cells within regions or gates.
  • Increased maximum parameter count for FCS data files.
  • Revised "Help" section.

Bug fixes:

  • Fixed misreading of fluorescence compensation values imbedded in DiVa v5 files.
  • Fixed failure to read large files (>100MB).

Enhancements Included in Version 2.3.1:

  • The gate creation dialog may be launched from the "Gate" item of a display's popup menu.
  • Newly-drawn regions are shown on display by default.
  • Allow printing of displays with dark backgrounds intact.
  • Allow File and Batch dialog to be reduced to an accessible on-screen icon.

Bug fixes:

  • Fixed bad Histogram fill colouring in side-on displays.
  • Fixed non-intuitive application of fluorescence compensation and the overriding of settings imbedded in the FCS file.

Enhancements Included in Version2.3:

  • Enable batch processing of a dragged-in list of files or a folder.
  • "Next File" commands don't require strict numerical or alphabetic sequence.
  • Collect numerical statistics from all displays on screen; copy to clipboard or save as text file.
  • Allow Weasel's canvas to display several pages, to exceed monitor screen size and be scrollable.
  • In connection with the previous, allow printing of multiple pages or "fit to 1 page".
  • Maximum numbers of defined gates, 1D and 2D regions, number of parameters read from each FCS data file and number of displays on screen all increased.
  • Full file name and gate can be made to appear as a "tool tip" at each display edge.
  • Read gates, regions and display layouts exported as analysis templates from DiVa software.
  • In Region Stats; allow choice of which regions are to be reported.
  • Display selectable individual keywords in the numerical statistics list.
  • Export gated FCS data files.
  • The user's fluorescence compensation settings may be set to override those imbedded in the FCS file.
  • Explicit instructions for 3D stereo display pairs are included in the "Help" file.
  • Animation of population-linked 3D dot plots is now optional.

Features and bug fixes introduced in version 2.2.3:

  • Optimized split linear/log display axes for smooth binning distributions.
  • Corrected the extraction of stats from derived (curve fitted) histogram overlays.
  • Improved the application of DiVa* embedded Spill matrix for fluorescence compensation.
  • Corrected CFSE curve fitting on fcs version 3 floating point data.
  • Fixed file "Select.." error when choosing files containing fewer parameters.
  • Corrected display sizing on Mac OS X with AquaLookAndFeel.
  • Improved display of dot plots colour coded on cluster designation assigned by the ACluE program.
  • Allowed the positioning of annotations on 3D contour displays.

    Enhancements introduced in version 2.2:

  • Fluorescence compensation spillover array is now read from the file header.
  • New command File->New clears displays and/or/not gates and regions.
  • Flexible choice of linear and log scale display axes which now reflect the original data range.
  • Regions and stats markers are transformed to suit the display axes.
  • Floating point text exported from dot plots is for linear or linearised data.
  • The "Windows List" dialog box can now retrieve displays dragged off screen.
  • Folders containing data files and a saved presentation are now portable to all Weasel systems.
  • Graphic display enhancements:
    • Probability density displays show outliers with selectable dot format.
    • Probability density displays may be plotted in pseudo colour.
    • Probability density displays and 3D rendered hills and valleys may plot in grey scale.

    Enhancements introduced in version 2.1:

  • Export of text representation of fcs list or 1D or 2D histogram data for import into XL, Matlab, etc.
  • Permanently-enabled mouse dragging of rotation and tilt of 3D displays.
  • Global dragging of all 3D displays simultaneously.
  • Fine control of the numerical statistics calculated for defined populations and for synthetic curve fitting.
  • Improved handling of saved presentations to allow their use as templates.
  • Revised handling of the "time" parameter including a selectable full scale.
  • Also, a version suitable for Mac OS X v10.3 now allows graphics copy and paste and shows greatly improved graphics.

Known bugs beyond our control:

  • Bug: Under MacOS X, Weasel hangs when printing one file per page in batch mode.
    • Fixed by internal workaround on most mac systems.
    • Workaround: Print all files in one operation but set "Actual Size" in File->Page Setup..
  • Bug: Graphics copy and paste is broken in MacOS X v10.4 / Java v1.4.2.
    • Workaround: Save a graphics file using File->Save Graphics As.. and insert it in the target application.
  • Bug: Under MacOS X v10.3+ when printing, any change from the default printer is ignored.
    • Workaround: Set a new default printer before Weasel launch.
  • Bug: Printing fails on MacOS X, using MetalLookAndFeel when stats windows show scroll bars.
    • Workaround: Use AquaLookAndFeel (see Edit->Preferences..).
  • Bug: Erroneous display sizing under WindowsXP using WindowsLookAndFeel.
    • Workaround: Use MetalLookAndFeel (see Edit->Preferences..).

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