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Versions

Listed below are the changes made to FlowJo since the original release of FlowJo, version 2.1, on June 23, 1997. The changes are listed in reverse chronological order. Within each revision are listed the new features (major and minor), and any bug fixes.

Current Version is 2.7.8, posted 10 February 1999

Index:

February 10, 1999: Version 2.7.8 released.

  • Layouts are refreshed better during their initial generation.
  • You could inadverdently resize a layout item to essentially infinite by double-clicking on a graph handle in the layout. This would then cause problems later, like items missing during printouts or other strange behaviors. FlowJo now prevents such an inadverdent resizing from happening.

January 28, 1999: Version 2.7.7 released.

  • You can now purchase USB-compatible dongles for use on an iMAC! Of course, you may also purchase serial numbers for the iMAC as always. USB-compatible dongles will not function on Macintosh computers using ADB keyboards (currently, all other Macintoshes than the iMAC).
  • The FlowJo "Splash Screen" automatically disappears after 5 seconds if no other action is taken.

Bug Fixes:

  • "Copy" of selected items inside the Layout Editor no longer generates an error message; items can be copied and pasted within any layout or pasted into other applications to easily copy graphs.
  • The entire layout is properly drawn while editting a text box.
  • All gates are drawn in layouts if the frequency is shown (previously, only the first gate would be drawn).
  • The resizeable graph view was fixed so that the graph resizes with the window.
  • The annotation text box that associates with graphs in the layout editor is now properly sized at all magnifications.
  • "Scale To Page" in the Batch Layout View now functions properly... use this feature as frequently as possible for easy layout definitions!

January 6, 1999: Version 2.7.6 released.

  • FlowJo serial numbers can now be used on ANY Macintosh running OpenTransport (i.e., any Mac running System 7.6 or later).
  • Statistics belonging to subsets with names including a colon, a "<", or a ">" were not properly shown in the layout editor. This has been fixed for new layouts. To fix existing layouts, delete the statistic from the layout and re-drag it from the workspace.
  • Text box boundaries (used to define a "frame" size in graphical layouts) are defined by the area that is actually drawn over rather than the bounds of the box itself.
  • The Statistics Window doesn't highlight the "Add" button unless there is a valid target.
  • If statistics are hidden in the workspace, you can still add statistics with the Statistics window but they will not appear until you "Show Statistics".
  • A bug was fixed in which some graphs were scaled strangely in complex layouts where some subsets were missing for a given sample.

December 21, 1998: Version 2.7.5 released.

New Features:

  • The number of significant figures in most displays has been reduced to 3 (from 4);scientific notation is used more frequently (i.e., 3.03e-3 = 3.03 x 10^-3).
  • The Graph Tools window name now reflects the graph window to which it refers.
  • You can now Copy, Paste, and Clear subsets & analyses in the workspace! 
    Copy using the option and/or control modifier keys will put a copy of selected nodes(with children and/or parents, exactly like drag-and-drop operations) onto the clipboard.  This can  then be pasted into the layout editor, or onto other subsets in the workspace.  The paste operation will be executed for every selected subset in the workspace; thus, you can quickly copy analysis trees to multiple destinations! If you Copy from the Graph Window, you can Paste into the layout editor to get that graph.
  • You may now specify a font style (e.g., bold) for layout text items
  • As you resize graphs in the layout editor, FlowJo now displays a percentage reduction from the original aspect ratio for both horizontal and vertical dimensions. You can use this to easily resize graphs back to 100%, or to resize multiple graphs to the same ratio.
  • The Preference "Use Filename" for sample identification is now used for displaying the sample name in graph windows, the layout editor, and other locations as well.
  • You can now add keywords to Tables; FlowJo will generate the keyword value for each sample as it creates the table and put them into their own columns.
  • FlowJo now displays a "Splash" screen.

Bug Fixes:

  • Cutting & Pasting rectangles in the layout editor no longer crashes
  • Movie Looping Preference now used for Graph Window movies
  • Closing Statistics Window no longer leaves some menus dimmed
  • A bug causing apparently random crashes on some Macs fixed
  • Choosing "Cancel" in the layout item dialog window could cause later crashes...fixed
  • Choosing "Save" while the Table Editor is active now saves the workspace
  • Various printing fixes:
    • Workspace printout has header, and proper page size
    • Graph window printout has proper header
    • Layout editor printout has complete header
  • Saving movies saves the whole movie
  • Dragging a movie to the desktop copies the whole movie if no frames are selected
  • Quitting FlowJo with a movie window open does not crash
  • Dragging multiple statistics into the Layout Editor adds them all, and formats them properly
  • Dragging items into the top-most 3 pixels of the table editor no longer crashes
  • Resizeable graph window allows more room for axes notation
  • "Edit" menu "Copy" item is now always labeled properly
  • Page Setup... is disallowed when the layout view specifies "Scale to Page"
  • The Page Setup magnification is saved when it is specified in the layout editor view

 

November 18, 1998: Version 2.7 released.

Layouts. 

  • The Layout Editor has changed completely.  An important consequence of this is that FlowJo will NOT convert Layouts created in older Workspaces (they are simply too different).  If you need to use old Layouts, keep version 2.6 of FlowJo around until you no longer need them.
  • Briefly:  the Layout Editor now shows you all graphics "live" on screen.  You can resize them at will; you can change the magnification of the view.  You can copy and paste items (or option-drag them to copy them); you can align them to each other.You can create text boxes, lines, and arrows; you can even add statistics to thelayout (they are also "live").  Batch generation generates the complete view on screen, where you can re-position the "frames" (for each sample) nearly at will, even specifying that they should not cross page boundaries.  You can print, save to disk, copy to clipboard, or even create Web Pages of your graphics (the easiest way to share data with your colleagues!). 
  • To learn about the new Layout Editor, refer to Chapters 7-9 in the new Tutorial; also, go through the web site on the Layout Editor.  To get a brief introduction into the sophisticated features of the Layout Editor, go through the short Introductory chapter of the new Tutorial.
  • There is a new Layout Menu and new Layout Preferences panel.

Preferences.

  • There are many new preferences that give you significantly more control over the default behaviors in FlowJo.  Open the new Preferences to see all of the new features!
  • You can specify whether or not FlowJo should calculate statistics immediately when you drag and drop them on other samples (the default is to only recalculate them when you need them for export or when you select "Recalculate.")
  • You can choose to export abbreviated statistics names from the Table Editor.  This can significantly shorten column names when you read a Table into a spreadsheet. Other new preferences are described in the sections below.

Compensation.

  • A new "drop box" makes creating a compensation matrix much easier: just drag one or more "parent" populations containing the positive and negative gatesfor the compensation stain and drop them in this box:  FlowJo automatically assigns the compensation controls to the correct slots!
  • Confirmation or Notification dialogs.
  • Many of these dialogs now have a checkbox "Use same answer in future".  If you check this box, then FlowJo will remember the answer you give to the dialog and usethat automatically whenever the dialog would have come up in the future (of the same session in FlowJo).

Data Files.

  • FlowJo is better about finding data files if they have moved.  In particular, if it cannot find the files in their original location, it will always search first in the same directory where the Workspace is stored.  It also queries you before it tries to access a Remote Volume (CD or AppleShare volume) to access the data.
  • You can add folders of data to the workspace by the "Add Samples" button.  In addition,there is now the option in this dialog to add all folders of data files within a selected folder--you could, if you wished, add all of the FCS files on your hard drive into a single workspace!
  • You can drag-and-drop files or folders from the finder onto the Workspace to add the data files to the workspace.
  • FlowJo can now read Uncorrelated FCS Data Files (i.e. histogram files collected forDNA/Cell Cycle analysis) FlowJo now takes care of a bug in CellQuest FCS data files.  In CellQuest, thescale of Log axes runs from 1 to 10,000; however, CellQuest specifies thisincorrectly in the data files.  FlowJo "re-interprets" the specification to display the same values as CellQuest.

FlowJo Files.

  • FlowJo now creates a work folder in the same location where the application is. FlowJo will occasionally create files in this folder; it will delete themwhen you quit the application.  If you wish, you can create the FlowJo workfolder in a different location, and create an alias to that folder (name it "FlowJo Work É") and put that in the application directory... FlowJo will resolve the alias and save the data files there.  This is necessary if you put FlowJo on a protected disk drive.
  • The name for the Preferences file has changed.

Workspace.

  • You can now copy samples from workspace to workspace (just drag & drop them!).
  • You may sort the sample list by the keyword "$DATE" or the value "Collection time", and FlowJo will correctly sort the samples in the order in which they werecollected on the Cytometer.  In addition, the sort order is now preserved whenthe workspace is saved.
  • AutoSave.  There is a preference that has FlowJo remind you to save the workspaceevery few minutes.  The reminder has a checkbox that will tell FlowJo toautomatically save (or not save) every time the interval expires: so youcan make sure that the workspace is saved every few minutes.  Never riskthe loss of a significant amount of work!  We highly recommend that you setthe preference to remind every 2-5 minutes, and then select the checkbox atthe first reminder, so that FlowJo saves your workspace almost continually.

Groups.

  • The Sample Group creation dialog has been extended significantly.  In addition, Groups can now be specified to be "Live."  A live group will automatically add new samples added to the workspace if they meet the appropriate criteria... thereby adding group-specified analyses as well.  See the Introductory Chapter of the new Tutorial for an example.  Finally, you can now double-click on a group to rename or change the criteria of the group.

Graph Windows.

  • You can choose to annotate gates with the percentage of displayed events falling in that gate (i.e., Frequency of Parent).  Set this in the Preferences window.
  • You can change the font that FlowJo uses to display graph axes & numbers.  The font you choose is also used when you export the graphics to other programs.
  • There is a new preference that lets you draw "Large" dots for dot plots and Outlier plots... this may improve the quality of graphics in publications.
  • When you export graphs to another drawing program, you will find that the "grouping"of items has changed a little, to make it easier to manipulate the graphs.
  • You can double-click on a gate in a graph window to open a new graph window for that subset.  Many of the functions under the "Workspace" menu (such as Rename, etc.), are now accessible when you have a single gate selected in the Graph Window.
  • The function of "Invert" (an option to all graph types) has changed slightly. It now generates graphs (white on black, or equivalent) that can be betterdisplayed in slide presentations.

 Floating Graph Specification Dialog.

  • This window now appears next to the graph window when you click on the "i" button.If you hold down the "option" key while clicking on "Apply", then the graphtype and options you specify will be applied to all graph windows thatare currently open.

Kinetics.

  • There is now a menu command for copying the table in the Kinetics window ontothe clipboard. This aids in the automation (using, e.g., Quickeys) of exportingthis information to spreadsheets.
  • You can now put Kinetics graphs into the Layout Editor--even to overlay kinetic analyses from different gates or samples.

Statistics.

  • The statistics window is now a Floating window.  Thus, you can leave it open onthe screen... go back to the Workspace and click on other gates to which to applystatistics.  If a Graph window is front most, then the Statistics window will applystatistics to the subset displayed in the Graph Window.

Progress Bar.

  • You can move the Progress Bar to a different location on the screen; later, itwill remember where you moved it and use the same location.

Exporting Histogram and Kinetics data.

  • FlowJo by default includes both the graphic and the text data for histograms andkinetics when you "Copy" from the graph window.  You can set a Preference to notinclude the text data (this is necessary if you use a Graphics program that incorrectly interprets the contents of the clipboard).
     

Bug fixes:

  • When recompensating a group of compensated samples, FlowJo only asks once for confirmation.
  • FlowJo used to crash if you deleted a sample from a Workspace and a subset ofthat sample had an open GraphWindow... no longer!
  • The Robust CV calculation for linear-scale parameters has been fixed.  (In general, you should only use Robust CV for log-scale parameters).
  • The problem wherein sometimes some menus were not accessible has been fixed.  sometimes some menus were not accessible has been fixed

Changes in Version 2.7.1 (first CD ROM version)

  • Works correctly directly from the CD
  • Handles locked volumes and no printer available correctly

Changes in Version 2.7.2 (first public release):

  • Much faster when using very large workspaces
  • Better memory management when creating movies

Changes in Version 2.7.4: (CD-R Master)

  • Added Preference to show Frequency of Parent in the workspace
  • Saving graphs as disk files from the Batch Output no longer saves scaled graphs,but saves the full-resolution graphics.
  • Creating tables with abbreviated statistics names fixed.
  • Printing from the Graph Window will draw the gates (depending on thePreference"Include Gates when Exporting Graphs").
  • Adding a gate to a subset will immediately be reflected in the Layout windowif that subset is being viewed.
    Animated Frame Movies are not created until you switch to that view (this cansave time & memory if you have set the Preference to view tiled frames by default).
  • "Scale To Page" and "Auto" scaling in the Batch Layout View have been fixed:they occasionally positioned graphs incorrectly.
  • Fixed a bug where FlowJo would crash if you created a Quadrant and deleted the Q4 gate while the window was still open.

 

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