Current Version is 3.6.1, posted March 07, 2002.

Index:

• Version 3.6.1 (March 7, 2002)
• Version 3.6 (February 12, 2002)
• Version 3.5.5 (January 30, 2002)
• Version 3.5.3 (December 10, 2001)
• Version 3.5.2 (December 1, 2001)
  
• Version 3.4 (April 24, 2001)
  
• Version 3.2 (July 21, 2000)
• Version 3.1.1 (April 2, 2000)
• Version 3.1 (March 28, 2000)
• Version 3.0 (October 17, 1999)
• Version 2 History

February 12, 2002: Version 3.6 released.

Note: Workspaces created by FlowJo version 3.6.1 cannot be read by FlowJo Version 3.4 and older.
However, FlowJo version 3.6.1 can read workspaces created by previous versions.

Version 3.6.1 runs in the Classic environment of OS X.
If you have a USB dongle - download the new OS X/9.2
driver and move it to your system folder.

Changes since 3.6

General:

• Fix: Occasional bug that causes crashing while dragging a gate vertex.
  
• Fix: Inability to find other moved files after pointing to correct one.
  
• Fix: Can edit stain names in columns listed by parameter name by double-clicking on the column.
  
• Fix: Reading linear parameters in 32-bit data files.
  
• Fix: Allow negative numbers in derived parameter offset.
  
• Sorting large workspaces is considerably faster.
  

February 12, 2002: Version 3.6 released.

January 30, 2002: Version 3.5.5 released.

Changes since 3.5.3

General:

• Added the ability to display a column corresponding to the date and time that the sample was collected. This column can be sorted on, resulting in a sample list that was chronological in terms of collection time.
• Sorting large workspaces is considerably faster.
  
• Added an automatic feature to annotate a series of numbers in a keyword.
  -"Copy value to group" command can now be accessed with "cmd-E".
  -"Option-Cmd-E" (an option menu item under the Workspace menu) when you have double clicked a keyword field for editing brings up a dialog where you can specify any arithmetic or geometric series (useful for numbering samples or for creating dilution series concentrations).
  

December 10, 2001: Version 3.5.3 released.

Changes since 3.5.2

General:

• Fixed a serious performance bottleneck, added in 3.5.2
  
• Printer requirement relaxed.
  
• Fixed resolution of aliases if files have moved since last access.
  
• Added ability to reset counter for db export.
  
• Changed menu item to "New Workspace"
  

December 1, 2001: Version 3.5.2 released.

Printer Requirement: You must have a print driver selected in order for FlowJo to run. If you run FlowJo on a newly-setup computer, you should first select the "Chooser" under the Apple Menu, and select a print driver (like "Laserwriter 8"). It is not necessary to select a printer, only a print driver, so this process will work even if your computer is not connected to a network or printer. If you don't do this first, FlowJo will remind you to do so when it launches (and will then quit).

Changes since 3.4.

General:

• FlowJo determines if your OS version is older than 8.5, and automatically disables "live" window operations (live window operations crashes on old OS).
• Print driver support includes Lexmark, HP, and Epson. Page resizing and page scaling in Layout Editor works for any of these printers (and many others). If you find that "Scale to page" or page resizing in the Layout Editor don't work for you, please send us an E-mail and we will add support for your printer.
• Addition of a new menu item (under the Edit menu) to enable/disable tinting for printing. Note: you must regenerate tiled reports after changing this option.
• FlowJo will now create a cache folder only when it needs it.
• FlowJo reads the FCS 3.0 data files created by BD's DiVa.
• FlowJo will read "non-standard" FCS files created by Coulter (Expo 32). The latest version of Expo creates a number of custom keywords beginning with a "$", which is prohibited by the FCS standard. In addition, they use "$PnGAIN" as the name for the parameter gain keyword; the FCS standard specifies that this should be "$PnG". FlowJo 3.5 specifically accommodates these variations to the standard in order to properly process the Coulter files.
• Demo files can now be read without a serial number.
• Rarely, adding a file to a template workspace could cause FlowJo to hang-this was fixed.
• Help buttons have been added to several windows: Table output, Keyword selection.

Layout Editor:

• Clicking on objects immediately unselects other Layout Editor items.
  
• Default page magnification when creating a new layout is 75%.
  
• Textboxes resize better during batch layout operations.
  
• Polygon gates are grouped for exporting to drawing programs.
  
• When saving layout graphics to disk, the default name is the same as the layout name rather than "Off".
  
• Items in grids and groups now iterate properly in batched layouts.
  
• Fixed sporadic crashes caused by rapid, repeated dragging of items to the Layout Editor.
  
• The right border of graph no longer disappears after copying the graph to drawing programs (such as Powerpoint).
  
• Overlay graphs make room for larger fonts.
  
• You can now drag PICT files into the layout editor to provide background graphics (or additional graphics).
• Grids:
  • You can turn off grid lines.
  • If you reduce the number of columns in a table causing a selected cell to be deleted, FlowJo no longer crashes.
    
  • Grid drawing was made far more efficient.
    
  • Fixed Grid drag dividers problem.
    
  • Textbox borders are removed when dropped into Grids.
    
  • Generating a batched layout containing an empty grid no longer crashes.
    
• Iteration of a layout containing textboxes but no graphs now creates a batched layout with the correct statistics.
  
• Dragging a related family of nodes into a Layout grid adds all graphs and statistics rather than only the top node.
  
• Contour plots without outliers are always copied as vector graphics (not bitmap).
  
• Unify Analyses now immediately updates all displayed gates in the Layout Editor.
  
• Statistics in batched layout outputs no longer show the first sample when a statistic is missing from a sample in the batch.

Tables:

• Fixed the problems with live resizing the Table columns.

Workspaces and graphs:

• Clicking on objects immediately unselects gate.
  
• Doesn't leave a segment on the graph when you abort drawing a gate after 2 segments.
  
• Parameter "Event Number" does not appear in Create Group panel.
  
• Improved automatic scaling of smoothed histograms.
  
• New keywords are automatically added as a new column in the workspace window.
  
• For quadrant gates created on parameters with a blank stain name, the parameter name is used in place of stain name.
  
• Does not crash if you print from a Graph window twice.
  
• Event Number parameter is fixed for large (>65K) event collections (note that previous gates based on the event number will now be invalid).
  
• Switching groups while editing workspace column values now stops the edit rather than copying to random sample in the new group.
  
• Quadrant gate names start at Q1, not Q0.
  
• Unselecting a gate immediately unhighlights the select child graph button (down-arrow).
  
• Fixed movie appearance when the event # parameter is selected and "equal channels per frame" is checked.
  
• Altering a gate automatically updates all statistics (if the preference to "recalculate immediately" is on).
  
• As quadrant center position is moved, the x and y location numbers track with the center position.
  
• Allow the changing of a name even if that involves case change only.
  
• If the location of the data files changes, and you use "Browse" to find the new location, deleting a file from the workspace does not cause FlowJo to crash.
  
• Will not choose Event Number parameter as a default parameter for new graphs.
  
• Gates that overlap the edge of a graph are not drawn with segments on the edge.
  
• No longer allows you to rename nodes with "/" in them. Gate names are not allowed to have a "slash" in them.
  
• All statistics are recalculated and displayed in the Workspace window after manual recalculation.

Kinetics Platform:

• Can draw range gates in the Cell Cycle, Kinetics, Proliferation Platforms even if your preferences are set to "not autoselect a gating tool".
  
• Kinetics window saves and restores timeslice coloring properly.

Cell Cycle Platform:

• Y axis label is now correct.

Proliferation Platform:

• Changing the number of peaks to model requires the model be recalculated.

Compensation:

• Compensation window only shows fluorescence parameters and not scatter or event#. Note: "SSC-W" is included in the Compensation window because this parameter is used to collect fluorescence on some machines.
  
• Changing the stain name for a parameter also changes stain name of the compensated equivalent parameter.
  
• Reads compensation matrices edited by MS Excel.

Derived Parameters:

• Derived parameters replace the existing parameter of same name (rather than adding new ones as "-1, -2" etc.).
  
• Fixed copying derived time parameter to other samples.
  
• Handles the FCS 3.0 keyword "$TimeTicks" properly when creating a Time parameter.
• Can immediately delete the offset derived parameter from derived parameters list.

Comparison Platform:

• Multi-parameter Comparison: no longer crashes if window is closed during computation.
  
• Event Number parameter does not show up in Multi-Parameter Comparison Platform.
  

April 24, 2001: Version 3.4 released.

General: Most operations affecting window displays are now performed "live"; i.e., when you resize windows, tables, etc., the window refreshes as you perform the operation. If the refresh process takes too long, then FlowJo automatically switches to a faster, non-live operation. If you don’t like this behavior, then select the Preference "Don’t use live window operations" in the "General" Preferences panel. (Note: if you previously selected the preference "Use live window drags", then you must now uncheck this preference). If you use "Live window operations", you can hold down the shift key while resizing any window to maintain its current aspect ratio.

Known Bug: If you launch FlowJo on a computer on which you have never selected a printer (for example, a new Macintosh), it will crash on launch. To prevent this, select the "Chooser" under the Apple Menu, and select a print driver (like "Laserwriter 8"). It is not necessary to select a printer, only a print driver, so this process will work even if your computer is not connected to a network or printer.

Layouts:

• The font traits of the overlay legend can now be set (double click on the legend).
• When changing the magnification of a layout view, the current position is maintained.
  
• You no longer have to wait for a layout to finish drawing before switching to another layout.
  
• Dragging a Kinetics, Cell Cycle, Proliferation, or Comparison Platform node to the Layout Editor now creates not only the graphic, but a Grid of statistics as well. You can delete the whole Grid, portions of the Grid, transpose it, or edit it. The Grid values will update as the Platform is modified. The Grid is a separate object from the Graph; deleting the graph does not delete the Grid.
• If you choose "Show Gates" for an overlay graphic, then the gates for the top-most sample are drawn in the overlay.
  

Workspaces and graphs:

• You can now display a new column, "Gate parameters", which shows which parameters were used to create the gate.
  
• You no longer have to select a sample in order to define a new Compensation matrix.
  
• When you create or open new graph windows, they are automatically positioned below and to the right of the parent gate’s window, as well as ensuring that they do not exactly overlap another graph window.
  
• When you create a quadrant gate, FlowJo now asks you to enter an optional prefix for the newly-created quadrant gate names. Enter a short value; entering a prefix will ensure that the quadrants are sorted together in the workspace list.
  
• A new parameter, "Event #" can be viewed for any sample. This parameter’s value is the number of that event in the ungated data file (the first event = event number 1). You can use this parameter for gating. View plots of a parameter vs. event number to see if there were unexpected changes (clogs?) during the collection—if so, you can use an exclusionary gate to remove those events from analyses. If you make a Graph Movie (from any GraphWindow) using Event Number to control the progress of the movie, FlowJo will display the event number(s) in the movie. For sites that have "index sorting" enabled, you can create a movie with as many frames as events (typically, 96), unselect "use equal number of channels per frame", and then view a movie of the desired graph showing the position of each specified event. The best graphic to view for this purpose is a smoothed pseudo-color graph.
  
• Samples with derived parameters show a light-blue bar next to their name in the workspace.
  You can use the page up or page down buttons on your keyboard to cycle to the next or previous samples when view a graph window.
  

Calibration Platform: Now uses a Mean calculation (rather than Median calculation) to compute the peak position of a reference standard (such as bead positions).

Kinetics Platform: Automatically asks for a new threshold value when switching to a statistic that uses thresholds. The default absolute threshold is the lowest value of the current parameter being analyzed, rather than zero.

Comparison Platform: A new statistic, "Super-Enhanced D-value Subtraction" is a new sophisticated algorithm by Bruce Bagwell to compute %Positives when comparing histograms.

Proliferation Platform: Two new statistics were added. (1) Proliferation index, which is the average number of divisions that those cells which divided underwent. (2) %Divided, which is the percentage of the cells of the original sample which divided (assuming that no cells died during the culture).

Networking: All network activities (site license network validation, remote data file transfers) now use Apple’s newest URL support. For remote data file transfers, this means that authentication is required (FlowJo will store usernames and passwords during a session, so you only have to enter them once). FlowJo now supports FTP, HTTP, and HTTPS access of data files (ask Tree Star for more information).

Preferences: The meaning of the "Live Window Operations" preferences is opposite of what it was in previous versions. Some Factory Default preferences have been changed (these only affect new users, or when you select "Reset Preferences" under the "Edit" menu when viewing the Preferences). New default preferences:

• Forward Scatter is on the X axis
  
• Graph type is unsmoothed pseudo-color plot
  
• Gates are included in copied graphs and in layouts
  
• Autosave is on, and the default autosave time period is 10 minutes
  
• Gate frequencies in the workspace are "Frequency of Parent"
  
• Gate frequencies are shown on graphs
  

Bug fixes:

• The preference for automatically tinting gates now works.
  
• A bug causing an occasional crash while drawing layout textboxes containing multiple statistics from the sample node was fixed
  
• Inverted dot plots, contour plots, and histograms are no longer drawn as black on black in the Layout Editor
  
• Copy to clipboard in the Layout Editor no longer asks for Batch output options.
  
• Summary statistics in the Table Editor (mean, sd) ignore missing values rather than treat them as zeroes.
  
• Graph Items in Layout Grids no longer resize inappropriately for no apparent reason.
  
• The default window size for movie outputs now shows the movie at 100% scaling (if possible) rather than ~90% scaling.
  
• The default window for Graph Window movies also shows the movie at 100% scaling.
  
• Graphs in batch layouts use the same font as specified for the Layout Editor.
  
• If an object in the Layout Editor is selected, but below another object (you can command-click to select items below other items), you can now click on the selection handles to resize it (and still keep its layer position).
  
• Switching any parameter to "unfixed" (in the Proliferation platform) highlights the "Recalculate" button.
  
• The workspace now properly scrolls when dragging the horizontal "thumb" scroller.
  
• "Show Ancestry" in the Layout Editor no longer generates white squares when the Layout item is overlayed on a darker background.
  
• Platform statistics in the Layout Editor are automatically updated when necessary, including those in the
• Annotation boxes below graphs.
  
• The clickable area for workspace disclosure triangles (to the left of gates) is now correct.
  
• Clicking on the "up arrow" in a graph window (to select the parent gating view) now selects the gate that created the original population.
  
• If a Layout tiled view is too large to draw, FlowJo properly notifies you of this. You will not be able to view or print areas of the view outside the maximum size.
  
• A rare bug causing cell cycle models to be drawn in the wrong part of the window after resizing the window was fixed.
  
• Create Group dialog doesn’t show multiple instances of the same keyword.
  
• Scale to height in Layout views fixed.
  
• Printing the Layout View does not relocate objects to the top left of the page.
  
• Fixed rare bug that could cause inability to save a workspace after replacing a group’s version of a cell cycle or proliferation platform.
  
• Fixed the ability to iterate on workspace groups other than the current one from the Batch creation dialog window.
  
• Saving a workspace as a template now resets the sample count for groups (to zero).

February 10, 2000: Version 3.3 released.

Major Changes

Population Comparison Platform

• Univariate: Overton subtraction statistic added.
• Multivariate platform added.
• Distancing platform (for comparing multiple populations) added. This platform is not an analysis associated with a single sample (and therefore does not appear in the workspace list of analyses); it is used to compare several different samples or gates, possibly using any or all of them to form an aggregate "control" or comparison population.
• Gates can be created based on differences between samples. These gates can be copied to any other samples to help identify which contain more or less of the cell types that are of interest.

Proliferation Platform

• Models proliferation data (such as CFSE experiments) to fit the number of cells in each division, as well as a "division index"—the average number of divisions any given cell in the original sample underwent by the time of analysis.
• Can automatically create gates for each cell division for further analysis.

Cell Cycle Platform

• Can automatically create gates for G1, S, and G2 regions.

Kinetics Platform

• All buttons, checkboxes, etc. that control kinetics analyses are now shown in the Kinetics window itself (rather than the floating tools window).
• Kinetics overlays in the Layout Editor now allow you to set the line color, as well as defining a "control" sample that does not vary during batch iteration.

Workspace

• "Copy samples as Text" in workspace: Copies a properly-tabbed text representation of the workspace that can be pasted into a word document or spreadsheet.
• "Save as Template"—saves the workspace minus all samples. This is useful for creating template workspaces into which samples can be added for automated analysis.
• Can be displayed in any desired font & font size (see Preferences).
• FlowJo can now read specially-formatted ascii (text) data files for display. Contact us for more information.
• You can edit almost any keyword value simply by double clicking on the listed value in the Sample view. (For example, you can choose to display the FL1 reagent; double-click on it to edit its value). Edited keyword values are associated with the sample only for that workspace, but are added to any exported files from that sample data.
• You may also define new keywords for samples. This may be useful for full control over Layout Iteration, where you can define "Iteration" keywords (that control generation of frames) and "Discrimination" keywords (that control selection of tubes within a frame).

Table Editor

• Allows custom column name specification (click in the fourth column of the Table Editor and type in a name—that name becomes the column head for all created tables).
• Created table can be sorted in either ascending (double click on column head) or descending (option-double-click on column head).
• Allows selected cells to be copied (for pasting elsewhere) even before computation has completely finished for the table.
• You can click & drag the boundary between the list of Tables and the table specification to resize these two lists.

Layout Editor

• Batch creation now brings up a dialog, in which you can specify the output format, the iteration to use, the group from which to select samples.
• Batch output can now be directed to a new layout. This allows the creation of persistent batch views which can be further edited.
• Batch output directed to HTML files can now specify default header and footer files to be included (see Preferences).
• In addition to specifying an "Iteration" keyword (the batch processor generates a frame for every unique value of this keyword in the list of samples of the iteration group), you may also specify a "Discrimination" keyword. When there are multiple different tubes corresponding to a single "Iteration" keyword for a given graph or statistic, FlowJo will select the one which has the same value for the "Iteration" keyword as the original. See Iteration Documentation (http://www.flowjo.com/…) for more information.
• The page size (for printing) can be easily resized by clicking near any page corner (the mouse changes shape) and dragging to the desired size. In addition, the page size can be automatically changed through a popup menu near the bottom similar to the same menu in the batch view window (e.g., "Scale to page").
• Histogram overlays can either be exactly on top of each other, or offset by a small fraction to create a pseudo-3D effect.
• Default overlay colors have been changed slightly.
• A PICT file can now be dragged & dropped onto the layout editor (in addition to adding to the layouts via the "Add Picture" command).
• You can click & drag the boundary between the list of Layouts and the layout view to resize these two areas.
• Layout Grids can be Transposed via the "Transpose Grid" menu command.

Preferences:

• New interface design
• Default browser for help documentation can be specified in the preferences.
• Dragging windows can drag just the outline or the whole content
• Font to use for the workspace
• Font to use for layout graphs (separate preference from graph window font)
• Log axis labels can be drawn in scientific notation (e.g., "102, 103, …").
• Dots to display in dot plots can be an absolute number or a percentage of the total
• Specifications for translating 32-bit data files (i.e., conversion from linear to log)
• Specification of header & footer file to include in batch HTML layout outputs

Minor Changes

• Next/Previous sample buttons added to all platform windows.
• Between next & Previous is a sample selection popup: click on the "o" and select any sample with equivalent platform from the popup menu.
• The Edit menu now supports a "Select every nth" sample—this aids in creating groups of samples that are evenly distributed.
• The workspace will now re-open with the sample & group portions sized as they were at close. Also, the preference that sets the default workspace display will save these sizes as well.
• FlowJo uses a new Cache Manager. All temporary files and network-accessed files are saved in the same "FlowJo Cache" folder, located in the same folder as the FlowJo application. The "FlowJo Work" and "Export" folders can be deleted.
• A different, more intuitive dialog box is shown when group analyses are deleted.
• The serial number entry dialog and demonstration explanation dialog boxes have been changed to be more intuitive.
• "BD$…" keywords are no longer shown in keyword value selection lists (such as the Table Editor or Layout Editor text boxes), as they do not contain values of interest to most users.
• All platform statistics (Cell cycle, proliferation, kinetics, comparison) now work in the Layout Editor. The easiest way to get them into the layout editor is to drag a table from the Table Editor containing the desired statistics into the Layout Editor.
• Compensated data no longer shows "striping", a visual artifact of digital compensation. "Striping" is removed by uniform distribution of data within a single channel—this is a purely visual effect and has no impact on statistics, gating, or other analysis.
• Shaded gates are not printed as shaded (currently, printers do not support the "translucent" shading that can be shown on screen).
• Nearly all printouts include a "footer" area that identifies the printout, date, and version of FlowJo. The footer will now appear at the same size irrespective of the page scaling used to enlarge or reduce the graphics & tables.
• Performance enhancements:
• Large workspaces are drawn much faster
• Sample exporting is now done as "Tasks", allowing you to work on other FlowJo items during the export process

Bug fixes

• If a batch layout view is too big to display, you are notified and whatever can be drawn is shown (previously, only a blank window would be shown).
• Fixed bug that could cause occasional crash while drawing gates in the layout editor.
• Layout editor text box fill pattern and box now get drawn in batch layouts as well.
• Statistic nodes deleted from groups now properly delete all equivalent nodes in the samples (if that option is selected).
• Fixed minor drag-selection bug in sample list that cause strange selection behavior when moving back and forth over several samples.
• Several rare and seemingly random crashing bugs were fixed.
• You can once again double click in any part of a sample or gate row in the workspace window to open the graph (except clicking in the annotation column allows you to edit the annotation for that row).
• Dragging a comparison node to another workspace now clears the control sample.
• Dragging rows within the Table Editor now properly re-orders them.
• Dragging data files into the workspace in Demo mode would sometimes fail; this has been fixed (and allows only Demonstration data files to be added).
• Dragging an item into a Layout Grid will now drop it into the selected cell rather than the first open cell of the Grid.
• The keyword list in the Table Editor (shown when adding keywords) is now complete. Previously, it would show keywords found only the first sample which may not include keywords in other samples.
• Layouts & Tables can no longer be renamed identically at any time.
• "Recover" command added to File menu to allow reading workspaces without reading in layouts—this acts as a work-around for workspaces corrupted by a bug (since fixed) that resulted from layouts named identically.
• The color popup palette for defining overlay colors now shows up in the correct position under the mouse.

July 21, 2000: Version 3.2 released.

New Features:

(1) Comparison Platform: you can now select a new platform that allows you to compare two different univariate histograms. In addition to providing the K-S statistic, FlowJo also provides you with a much more powerful statistic, the Chi-Squared T value. This value not only gives you an indication of the significance with which two histograms are different, it also provides a metric that you can use to determine how different multiple histograms are! As with all platforms, the Comparison platform can be dragged into the Table Editor or the Layout Editor, and can be dragged to other samples or groups for batch analysis! Click here for more information.

(2) New Preferences:

• "Turn sounds off"–lets you turn off the audio feedback that FlowJo provides after certain operations.
  
• "Show Summary Stats"–lets you show the mean and standard deviation of all numerical columns in a Table. As well, FlowJo will automatically mark entries in that column that are more than X standard deviations from the mean by changing their color.
  
• "Canvas 7 Export"–instructs FlowJo to create exported graphics that Canvas 7 (from Deneba) can handle without problems. This is a work-around for two different bugs in Canvas 7.
  

(3) You can now select one or more Layout Graphs, and choose "Open Original" (cmd-R) to open the graph window for that graphic.

(4) You can now choose to add data files from a folder (or series of folders) only if the data file meets the criteria specified by a Workspace Group.

(5) The Derived Parameters dialog adds a new option for adding Offset and Gain to the new parameter. There is also an additional option to the ratio function, that will put the sum of the parameters into the denominator.

Other changes:

• You can no longer rename Kinetics or Cell Cycle platforms.
  
• Medium size graph windows now display cursor coordinates in an area not occupied by other information.
• Double-clicking on an FCS data file that FlowJo has created will launch FlowJo and add that data file to a new workspace.
• Deleting analysis from a group has been made more intuitive.
• FlowJo can now read 32-bit data files. Currently, there are no preferences for how these are handled; the default is that forward scatter is left as linear and all other parameters are displayed as log parameters (with 4 decades).
• FlowJo now resolves aliases when receiving a drag & drop from the Finder.
  

Bug Fixes:

• Histograms are now tinted in Layout displays.
  
• Moving a gate will be immediately reflected in a Layout graph showing that gate
  
• Deleting a time slice in the Kinetics Platform no longer causes a crash
  
• Kinetics & Cell Cycle platforms show axes names when first created
  
• Kinetics & Cell Cycle window don’t automatically show floating graph tools window
  
• Layout histograms with autoscale will properly autoscale all graphs immediately. In addition, autoscaled overlays now show a "Percent of Max" Y axis rather than # cells.
  
• Fixed Layout Annotation box display if any given line of text was too wide (would
  inadvertently overwrite the subsequent line)
  
• Gates now move correctly when using the arrow keys to move them (occasionally they would step too far or not at all on log-scaled plots)
  
• Dragging the gate frequency outside of the graph area no longer makes it impossible to re-position the gate frequency text.
  
• Fixed crash that occurred if a workspace was given a name exactly 31 characters long.
  
• Fixed crash that could rarely occur on Quit when the "Next Sample" command was used from a graph window during heavy calculations.
  
• Fixed cosmetic user interface issues in the Layout’s multi-item information dialog.
  
• Creating a new folder while selected the export file destination now works.
  
• Resizing a graph window now redraws the graph at high resolution.
  
• Fixed bug that made FlowJo think it hadn’t finished computing a layout when in fact it had (occurred only with overlay graphs and a particular selection of preferences).
  
• Statistics shown in Layouts are immediately refreshed if a parent gate is moved.
  
• Fixed Drag & Drop bug – sometimes FlowJo would not recognize that data files or folders were dropped onto the workspace.
  
• Fixed operation of group drop: when a gate is dropped on a group, FlowJo now checks to make sure that the gate’s axes are drawn on the same stains as all of the group’s samples–if not, FlowJo will confirm whether you want the gates added to those samples or not.
  

Additional bug fixes:

• Fixed kinetics analyses applied to uncomputed populations
  
• Fixed histogram gate display when graph is changed (i.e.,fixed <-> auto)
• Fixed gates not always showing up in Layout batch windows
  
• Fixed random crashing bug
  
• Added kinetics gets time info from fcs header and correctly converts time axis to seconds
  
• Added population naming popup to Rename dialog

April 2, 2000: Version 3.1.1 released.

Additional bug fixes:

• Fixed kinetics analyses applied to uncomputed populations
  
• Fixed histogram gate display when graph is changed (i.e.,fixed <-> auto)
• Fixed gates not always showing up in Layout batch windows
  
• Fixed random crashing bug
  
• Added kinetics gets time info from fcs header and correctly converts time axis to seconds
  
• Added population naming popup to Rename dialog

March 28, 2000: Version 3.1 released.

Version 3.1 has a number of improvements over 3.0, including both bug fixes and significantly increased execution speed. In addition, we are pleased to announce the release of a Kanji translation of FlowJo. For more information on Kanji FlowJo, click here. Version 3.1 changes are listed below:

New features in FlowJo version 3.1:

We have optimized several important routines in FlowJo to make gate computation, statistics, and graph generation significantly faster. The improvements is most notable when analyzing many or large files--and can be anywhere from 2 to 5 times faster, depending on how many events you have collected.

The functionality of the Derived Parameters section, has been improved. You can now specify the number of decades as well as a fixed upper bound in the calculated ratios.

FlowJo can now display a popup menu of "standard gate names" whenever you are creating a new gate. This can used to ensure consistent naming across samples, workspaces, and experiments. To create this list, click on "Set Standard Gate Names" in the "Gates" preference panel. You can cut and paste from a standard word processor file into this list. FlowJo only shows the gate name popup if there are names defined.

You may hold down the "option" key while clicking on the up- or down-arrow in a graph window to display the parent or child population in the same window--this allows you to navigate up and down the gating tree without having the windows appear in different locations.

Bug fixes in Version 3.1:

Overall, several bugs have been fixed that caused the program crash at seemingly random times, especially when using the Layout Editor. As a result, the program is considerably more stable.

The Table Editor no longer gives an error message when first opened; the occasional crash as a result of this error has also been fixed.

Derived parameters dialog no longer crashes occasionally when creating or deleting parameters.

Dragging layout items put them precisely where you let go of the mouse (there was a 1-2 pixel offset in some cases).

The preference to automatically add comments from the FCS data files now works properly.

Kinetics overlays in the Layout Editor now properly scale the graphs when "Auto" scaling is chosen.

FlowJo would crash if exporting multiple different files simultaneously from the same sample. This has been fixed.

October 17, 1999: Version 3.0 released.

The changes from version 2.8 of FlowJo to version 3.0 are numerous. However, the basic user interface has not been changed. Rather, we have added a host of new features that make FlowJo even more powerful than before. In addition, we have fixed various bugs as noted.

The changes listed below are grouped by topic.

New features in FlowJo version 3.0:

• General
  • FlowJo now does most calculations in the "background." This means that you are free to perform other operations while FlowJo calculates graphs, layouts, tables, etc. You can have FlowJo create as many Layouts and Tables simultaneously! This can actually increase the efficiency of analysis, because FlowJo intelligently schedules its tasks to use available resources. With this feature, you can now switch axes or graph types before a graph is even computed for the first time, start a table or layout batch analysis and go back to do more gating, etc.
  • Undo is supported in some operations (like moving gates or layout items).
  • Most items can be dragged to the Finder trash to delete them.
• Workspaces.
  • You may now annotate any row in the Workspace. Simply add the "Annotation" column to the workspace; double-click on the space to enter a new annotation. (You can also shift-click multiple items to add the same annotation to all, or copy an annotation to multiple rows). By default, FlowJo will add the contents of the "$COMMENT" keyword in data files to the Annotation field (although you can reset this via the Preferences). The workspace can be sorted by the value of the Annotation field. Annotations are copied to Layout Items for display in the annotation box.
  • Gates that are Magnetic or Exclusionary are displayed with special icons.
  • You may use the Page Up/Down, Home, and End keys to navigate the workspace window.
  • The "Create Group" interface has been modified. You can select multiple different panels of stains and click on "Create Multiple" to create one group for each different panel selected.
• GraphWindows.
  • A gate frequency drawn on graphs can be dragged to any other position on the graph (just click and drag it).
  • There is a new graph type, "Zebra" graphs, that may be useful for publication purposes.
  • Invert mode for graphs will export axes text in inverted colors as well.
  • Histogram gates can now be set to be Magnetic.
• Statistics.
  • The statistics floating window now preserves your selections when you add statistics to subsets. Statistics added from the floating window are immediately calculated if required by the Preference related to recalculation after drag & drop.
  • Statistics to be displayed in Tables or Layouts must now be attached to every sample that is being analyzed.
• Tables.
  • The Table Editor has substantially changed. The Table Editor now has only a single create button; it creates a window on-screen with the table. The table is shown as it is built. The table view can be saved, copied, printed, or launched, like layout views. This view is "live": if you move gates, affected cells in the table will be recalculated! You can have as many tables calculating and open at the same time as you want.
  • The table window shows the full population path name (including ancestor gates) to aid in identifying rows.
  • You may launch any other application with the output of a table: FlowJo will save the table to disk and then open it with the selected application.
• Layouts.
  • Editing text boxes is now accomplished in a new Dialog window. Using this window, you can easily create Statistics and Keyword commands to insert "live" statistics and keywords (i.e., that change as you view other samples or move dependent gates). You can drag statistics into this window to add the text, or select keyword values from a popup menu of keywords.
  • You can now drag Tables into Layouts! FlowJo will create a "Grid" containing all of the appropriate statistics in the Layout Editor.
  • You can create "Grids" in layouts. Grids are tabular arrangements; each cell of a grid can contain any other Layout element: a statistic, text box, PICT item, graph, or even another Grid! Grid columns and rows can be resized (as well as the whole Grid at once). Grids are useful for arranging multiple items in an ordered fashion.
  • You may now group (and ungroup) items in the Layout Editor. The grouping is preserved when you export the layout to another program.
  • Histograms (and overlays) can now be set to have a dashed line style. To set the line style for a non-overlay histogram, select "Show Legend" from the Layout Item Information Dialog (Select "Get Info" from the layout menu with the graph selected or double click on the graph). From within the Legend Box, you can change the color or line style of the histogram (or overaly item) by clicking on the color/line boxes and selecting an option.
  • CDF plots can now be colored and filled like histograms.
  • A new interface allows you to you to change attributes for multiple layout items simultaneously: if more than one layout item is selected, when you double click or do a Get Info, then Multi-Item UI is launched. There is also a new Preference that lets you see this dialog by default even when doing a Get Info (double-click) on a single item.
  • You may align or distribute multiple items in the layout to a regular grid arrangement. FlowJo tries to arrange them as well as possible in a cartesian format.
  • You may import any PICT object (by Pasting it into the Layout, or choosing "Insert Picture…" to open a PICT file) into the Layout Editor. PICT objects can be resized and can then serve as a backdrop for layouts (for example, for adding a form or company logo to each output).
  • You may launch any other application with the output of a Layout: FlowJo will save the table to disk and then open it with the selected application.
  • You may select whether Layout graphs should show or hide gate frequencies.
  • You can manually specify the scaled size of a Layout graphic (double-click on the graph and change the settings in the Attributes window). You can easily rescale all graphs to 50% by selecting all of them, double-clicking, and entering 50 in both the horizontal and vertical scaling boxes.
  • When FlowJo draws PlaceHolders for layout graphs, it will include some text to explain why PlaceHolders are shown (for example, it couldn't find a subset specified by the layout for the current sample).
  • Invert mode for graphs shows axes & labels in inverted colors.
  • You may now command-option click on a Layout Graph (or on a Legend item) to open the original graph for that Layout item.
• Batch Layout View.
  • A new "Custom…" dialog makes setting the tiling pattern more intuitive. Use this if the "1-up", "2-up", "3-up", or "4-up" don't suit your needs.
• Preferences
  • The name of the preferences file has changed. When you install FlowJo 3.0, you will have to set your preferences as you like them.
  • The order of the preferences has been modified slightly.
  • While viewing the Preferences, you may reset all preferences to the Factory Default (choose the menu item under the "Edit" menu).
  • Your serial number (if you have one) is now stored in the Preferences file–so when you update to newer versions of FlowJo, it will automatically find the number for you.
• New Preferences for:
  • Select the graphics format for any graphics (layouts) exported to disk: PICT (default), JPEG, GIF, or TIFF. You must have the helper application "clip2gif", supplied with FlowJo 3.0, to use the alternative formats.
  • Which interface to choose when changing attributes for layout items
  • Whether layout annotations should include the full gating path name or only the name of the subset being viewed.
  • Which programs to launch when launching from created tables or layouts
  • Default gate tool can be either a rectangle or a polygon.
  • Default layout item attribute interface can be either the standard interface or the multiple-item interface even when only one item is selected.
  • Whether or not to copy the value of the "$COMMENT" keyword into the annotation field in the workspace display.
• Bug Fixes:
  • A bug causing FlowJo to occasionally crash when it could not fit a Cell Cycle model to the data was fixed.
  • Graph annotation boxes and overlay legend boxes are now properly "Layered" when creating batch views (i.e., above/below other objects).
  • Layout statistics and keyword commands have been changed. Statistics and keyword values will now be properly selected from the correct sample (when the batch iterator is set to something other than "Sample".)
  • Page breaks are properly drawn in "Auto" scaling mode for the batch layout view.
  • The workspace displays frequencies whenever they are computed.
  • The "mousing" of legends (for overlay graphs) has been fixed.
  • Text box widths when including long keyword values are now correct in batch layouts.
  • Cmd-C for copying now works again from graph windows.
  • FlowJo informs you if QuickTime has been disabled (you will not be able to view or create Movies).
  • Creating groups by finding text in sample titles may not have always worked… now fixed.
  • Distribute by… function in the layout editor has been fixed.
  • Saving the default workspace view (in the preferences) now works. In addition, when you select "Default" in the workspace view setup window, you will get what you have saved as the default, not the factory default.
  • The floating graph tools window interface for cell cycle analysis has been fixed (sometimes fields would be unhighlighted or unselectable at incorrect times).
  • Printing the Workspace window no longer cuts rows off the bottom of the page.
  • "Distribute by…" function in Layout alignment fixed.
  • When copying a "Time" parameter created based on collection times to other samples (or group of samples), each sample's individual collection time is now used to compute the new Time parameter.
  • Text boxes containing Keyword commands are properly sized now.