FlowJo v9 Manual


Version History

Listed below are the changes made to FlowJo since the release of FlowJo, version 6.4, on November 16th 2005. 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 9.9.6.


Version 9.9.6 Release Notes
Version 9.9.5 Release Notes
Changes since 9.6.2
Version 9.6.2 (Feb 5th, 2013)
Version 9.6.1 (Jan 3rd, 2013)
Version 9.5.3 (Aug 27, 2012)
Version 9.5.2 (May 16, 2012)
Version 9.5 (April 26, 2012)
Version 9.4.11 (February 1st, 2012)
Version 9.4.10 (November 30th, 2011)
Version 9.4.9 (November 22nd, 2011)
Version 9.4.8 (November 16th, 2011)
Version 9.4.7 (November 6th, 2011)
Version 9.4.5 (November 3rd, 2011)
Version 9.4.4 (October 19, 2011)
Version 9.4.3 (October 5, 2011)
Version 9.4.2 (October 4, 2011)
Version 9.4.1 (October 2, 2011)
Version 9.4 (September 19, 2011)
Version 9.3.3 (July 27, 2011)
Version 9.3.2 (June 16, 2011)
Version 9.3.1 (April 18, 2011)
Version 9.3 (March 16, 2011)
Version 9.2 (December 10, 2010)
Version 9.1 (July 27, 2010)
Version 9.0.2 (March 22, 2010)
Version 9.0 (January 15, 2010)
Version 8.8.6 (February 24, 2009)
Version 8.8.4 (November 21, 2008)
Version 8.8.3 (October 24, 2008)
Version 8.7.3 (July 3, 2008)
Version 8.7.1 (March 4, 2008)
Version 8.7 (February 22, 2008)
Version 8.6 (November 19, 2007)
Version 8.5.3 (August 13, 2007)
Version 8.5.2 (June 20, 2007)
Version 8.5 (June 4, 2007)
Version 8.4.6 (April 27, 2007)
Version 8.4.5 (April 13, 2007)
Version 8.4.4 (April 12, 2007)
Version 8.4 (March 14, 2007)
Version 8.3 (January 9th 2007)
Version 8.2 (October 13th 2006)
Version 8.1.1 (July 5th 2006)
Version 8.1.0 (May 17th 2006)
Version 8.0.3 (May 4th 2006)
Version 8.0.2 (April 28th 2006)
Version 8.0.1 (April 13th 2006)
Version 8.0 (April 3rd 2006)
Version 6.4.7 (April 13th 2005)
Version 6.4 (November 16th 2005)
Version 6.3.4 (September 30th 2005)
Version 6.2.1 (March 4th 2004)
Version 6.1.1 (October 11th, 2004)
Version 6.0 (July 5th, 2004)


Version 9.9.5 Release Notes:

tSNE Platform Improvements

  • Increased speed by 3x.
  • Decreased memory requirements.
  • (Together, these two improvements allow tSNE to be run on one million events with 12 parameters! Note that this can take two hours on a laptop.)
  • Can initialize the tSNE algorithm with previously-computed LDA parameters.
  • Can also initialize from previously-added PCA parameters-this means you can compute PCA on a predicate sample, copy the PCA vectors to other samples, and initialize SNEe on those identically-computed vectors for greater cross-sample similarity.


  • v9.9 no longer shows uncompensated parameters in menus by default (unless you hold down option key). But when you concatenated files and add a keyword as a new parameter, it assumed this was an uncompensated parameter and didn't show it. New concatenated files add a notation that this parameter should be shown in menus.


  • Spectral compensation UI: Minor updates.

Layout Editor

  • New "Polychromatic Y by Y" creator in the Layout Editor. Access is similar to the Y by Y platform (select a single graphic and choose Y by Y from the menu or the contextual menu). Select parameters-FlowJo will create a copy of the selected plot with every pair of the selected parameters controlling color in a polychromatic plot. (This tool is useful for exploring a tSNE plot for expression and co-expression of markers-a single click to get tons of info.)
  • Removed limit of 50 overlays in a single Layout graph item.
  • Fix: Reducing dimensions of an LE table containing objects doesn't crash.
  • Fix: Copying or pasting a textbox in the Layout Editor preserves all styling information.

Misc. Fixes

  • Fix (table outputs): Reduce double commas in gate names to one.
  • Fix: Minor UI bugs in the custom transformation editor dialog.
  • Implement smart sorting of groups, tables, and layouts in menus and lists.
  • Fix: Prevent crash if PCA platform shows only one parameter.

9.6.5b Beta Release

9.6.5b Beta release notes:

  • Fix crash when reading certain XML files
  • Allow as many dots as desired in high-res (vector) output graphs
  • Concatenation enhancements:

    ---If files have different compensation matrices, then export compensation parameters

    ---Allow proper concatenation of files with parameters in different order in file

    Recent Release Updates

    Changes since 9.6.2

    • Exporting data files has been enhanced:
    • Dialog has button to switch between compensated/uncompensated parameters
    • Exporting CSV includes parameter name & stain
    • When exporting all compensated (and not uncompensated) parameters, the comp matrix is included in the header
    • Fixes:
    • Changing compensation immediately updates items within LE groups (such as n x n plots)
    • Workspace column preferences are not corrupted by copying non-global preference sets

    Feb 5th 2013, Version 9.6.2 released

    Changes since 9.6.1

    • Tinted gates supported in PDF & SVG
    • Clone gate option possible from command-click on node in WS
    • Fix bug in PDF rendering of quadrant stats legend

    Jan 3rd 2013, Version 9.6.1 released

    Changes since 9.5.3

    • PDF output. FlowJo now creates graphics as PDF format. By default, whenever a graphic is copied, the PDF format is also put on the clipboard. This makes for high-resolution graphs when pasting into PowerPoint and other programs. There are preferences that control what format is included on the clipboard; by default, both the PICT (Mac-native) and PDF will be included. You can also include SVG for programs like Intaglio. In general, most programs will select from these multiple formats the one which is best for them; however, if you find this is not the case, you can change the preferences to not include PDF or SVG. (See Preferences->Output).
    • You can also choose to save a graphic as a PDF file (by preferences). When you do so, the entire graphic will appear as on a single page with no headers or footers. If you want pagination and headers and footers, then simply Print your graphic, and from the Print dialog, choose "Save As PDF" rather than printing to your printer.
    • A few rare fonts (including "Symbol") will not appear properly in PDF outputs. If you find this to be the case, choose a different font in FlowJo.
    • Minor changes:
    • Workspaces can now be sorted on the basis of the Disk Filename (i.e., full path).
    • Create Group dialog will identify all unique stain combinations, no matter how complex
    • Minor bug fixes

    Aug 27th 2012, Version 9.5.3 released

    Changes since 9.5.2

    • Allow FJML gate editing of histogram gate's upper bound
    • No longer opens the Compensation Wizard window with portions off-screen
    • When copying graphics using SVG and pasting into another application, they are always at the same relative scaling
    • Exporting samples from a Group selection allows you to specify number of events to export
    • Fixed disappearing layout when renaming it the same as another layout but with different upper/lower case for some letters
    • Finds the appropriate hardware ethernet address under OSX.8

    May 16th 2012, Version 9.5.2 released

    Changes since 9.5

    • When copying a compensation matrix to create a new one, the transform settings associated with that matrix are copied as well.
    • General bug fixes

    April 26th 2012, Version 9.5 released

    Changes since 9.4.11

      Note: "RMS"in statistics outputs has been renamed "RMSD" (root-mean squared deviation) for clarity.
      New features:
    • RMSV (root mean squared variance) statistic added to cell cycle & proliferation platforms. This statistic normalizes the RMSD by the number of events, providing a value that can be compared across samples with different event numbers.
    • The Compensation Wizard can now compute the "Spillover Spreading Matrix" (SSM). The SSM provides a direct indication of which combinations of fluorochromes result in lower sensitivity from spillover spreading. Higher values in the SSM show spillovers that will reduce sensitivity more than lower values.
    • Export dialog now show stain names when possible
      Bug fixes:
    • Fix an error that occurred rarely after dragging gates from one workspace to another.
    • Fix a problem that led to very inefficient memory usage for 16 bit data files (large workspaces were hard to analyze)
    • Batched overlay graphs show proper headers in the statistics table by the graph
    • Disallow empty layout/table names (resulting in a corruption when workspace is saved)
    • Output to Web does not refer to a FlowJo.com file for the footee
    • Group Duplicate without Data will duplicate all analysis trees, not just the first
    • Fixed menus and menu shortcuts for "add gate vertex” and “show gate vertex numbers"

    February 1st 2012, Version 9.4.11

    • When FJ encounters internal error, it allows you to try an emergency save of all WS files before exiting with error
    • Recalculate menu items from group operations are better named
    • Save as Template adds saved template to Recent Files menu
    • "BSC" is now a scatter parameter
    • Batched overlays show column headers
    • Various bug fixes

    November 30th 2011, Version 9.4.10

      Bug fixes:
    • Copy compensation matrix to layout
    • Various stability fixes

    November 22nd 2011, Version 9.4.9

      Features added:
    • Robust SD added as a new statistic
      Robust CV & Robust SD are now "smart" stats -- if the upper or lower half of he distribution is clipped by the range of the detector, the stat adjusts to report on only the unclipped portion.
    • Bug fixes:
    • Various stability fixes

    November 16th 2011, Version 9.4.8

    • Don't allow page sizes to be too small in layout editor
    • Drawing offset lines for histogram gates (tethered, magnetic) obeys preference setting for whether or not to draw
    • Minor bug fixes to improve stability

    November 7th 2011, Version 9.4.7

    • Major crash fixes

    Versions 9.4.1 - 9.4.5

    • MultiGraphOverlay shows all histograms consistently
    • Remote Transfer of huge data files does not time out unnecessarily
    • Various bug fixes to improve stability
    • Miscellaneous bug fix from beta 9.4.1b2
    • More consistency in the application of preference controls between window perspectives
    • Fix: Reading data files with badly-specified compensation matrix won't crash
    • Do not allow files with only 1 fluorescence parameter to load into the Compensation Wizard
    • Batch to Preview is now the default output. Complex layouts batched to a new layout will suggest using Preview as output
    • A number of bug fixes aimed at improving performance

    September 19th 2011, Version 9.4 released

    Changes since 9.3.3

    • New: FTP/HTTP completely revised and improved, for Lion compatibility
    • New preference to show/hide gate tethers (magnetic or tethered gates)
    • HTTP authorization preference removed - automatically done if needed
    • Fix: Rare crash when drawing gates copied from now-deleted subset
    • Better axis labeling for calibration of transformed parms
    • Fix: Prevent crash when choosing keywords to add to pref for overlays when no WS is open
    • Comp Wizard better handles already-scatter-gated controls
    • Fine-tune peak identification for Calibration platform
    • Better progress monitoring of FTP downloads
    • Fix: Vertical histogram offset for overlays in batched outputs
    • Fix crash on reading some old workspaces using 15 bit files
    • Fix: Mag gate offset drawn to correct origin on resized graph windows
    • Fix: Dragging mag gate annotation on resized windows

    July27th 2011, Version 9.3.3 released

    Changes since 9.3.2

    • Dragging WS node into LE text box inserts sample ID properly for uniterated view
    • Reading LE that have Statistics Tables referencing compensated parameter positions no longer crashes
    • Iterate by nth now creates "missing" graphics if not enough samples present in the list (previously would replicate last sample) -- i.e., iterate by 5th, have 8 samples in list: 8th would appear in position 9 and 10 in batch outputs
    • Concatenating samples with derived parameters no longer crashes if the samples hadn't been opened first
    • FLS on Lion works
    • About box now shows latest downloadable FJ version

    June16th 2011, Version 9.3.2 released

    Changes since 9.3.1

    Workspaces saved in 9.3.2 cannot be opened with 9.2. (As usual, however, you can save a workspace as XML and open that in older versions.)

    New Features:
    • Parameter lists in layout "multi item edit dialog" are now sorted according to preferences
    • Workspaces with large numbers of keywords operate much more efficiently
    • Better refresh on some dialog windows when resizing
    • New PREF for cyTOF files that allows setting uniform range for all parameters. USE WITH CAUTION. FJ will warn you if you are doing this for nonCyTOF file but allows. Used for CyTOF files to set uniform range for all parms... in general, set it to higher than highest of all parm ranges, use power of 2. BE CAUTIOUS
    • Interpolate Kinetics graphs to make smoother graphs
    • If you manually run Sample Validation platform, you can "Copy Detailed Report" which gives the computed value for each check, for all samples & parms. You can use this to determine appropriate ranges for thresholds for failures.
    • Fix reading files with no $BYTEORD (any text-fcs converted file)
    • Fixed loading compensated data files when the parameter name ($PnN) has been edited.
    • Fixes bug introduced into 9.3.1 with 16 bit data (various mfrs)
    • FJML Find function will noe work in all uses

    April 18th 2011, Version 9.3.1 released

    Changes since 9.3

    Workspaces saved in 9.3.1 cannot be opened with 9.2. (As usual, however, you can save a workspace as XML and open that in older versions.)

    New Features:
    • When resizing a Layout graph, you can hold down option key to size to nearest 10% (text appears to explain this)
    • Properly handle remote FTP transfer of 16 bit data files
    • Allow changing layout graph sizing in dialog window
    • Resizing a layout graph shows feedback as to size (as it used to, long ago!)
    • Transparency in SVG now supported

    March 16th 2011, Version 9.3 released

    Changes since 9.2

    Workspaces saved in 9.3 cannot be opened with 9.2. (As usual, however, you can save a workspace as XML and open that in older versions.)

    Major New Features: Other new Features:
    • FJML Gates -- Many new features:
    • FJML Gate editor supports copy/paste operations
    • Gate FJML commands can be shown in workspace, TE, and LE
    • New FJML command to get the center point for any quadrant gate ("Vertex_Q_parameter")
    • Gates relying on FJML get special icon in workspace (circle-F)
    • Gates depending on keyword values immediately change with keyword modification (yes, this means you can change gates from the Workspace!)
    • Option-clicking on a workspace header will sort by that keyword and add it to the sort definition (so you can option-click on successive column headers to do a complex sort). Option clicking on the most recently-sorted column will invert the sort order
    • Improvements to Compensation Wizard when determining color for controls
    • Workspace contextual menu for gate nodes adds "Copy with children" and "Copy with ancestors"
    • "Recalculate" menu commands renamed as "compute" for clarity
    • Preference for precision display adds a radio button to discriminate significant figures from decimal digits
    Bug Fixes:
    • Use all 36 colors in preferences palette for overlays
    • Read workspaces with (some rare) corruptions
    • Changing a keyword value immediately updates LE showing the keyword
    • Templates with LE text boxes containing statistics now work after loading samples
    • FJML Gate editing - when dragging gates into definition, correctly constructs FJML command referencing parameters
    • Quadrant gate vertex numbers are not re-numbered when resizing so FJML gate can correctly refer to them
    • Calibration of parameters using biexponential transformation fixed
    • Histogram range gates appear in SVG output
    • Kolmogorov-Smirnof statistics are properly annotated (titled) in comparison windows
    • Properly handle $TimeStep keyword in special cases
    • Properly update some LE text boxes pointing to statistics that wouldn't invalidate when gate was modified
    • Sorting workspace by $DATE is now correct
    • Quad gates created on parameters containing "slash" will now correctly replace slash with hyphen
    • Table formula entry corrected for some functions (like subtraction, and less than or equal to)
    • Histogram graphs obey the autoselect gate tool preference setting
    • LE displays that are offset from the top left retain proper aspect ratio when printed
    • Editing a compensation matrix will immediately update multigraph overlay platforms and tabular displays of the matrix in the LE
    • Quit is prevented while editing a compensation matrix
    • The LE graph item editor properly sets the "show legend" check box
    • Changing a LE graph to/from histogram updates the overlay legend to show/hide the line style control

    December 10th 2010, Version 9.2 released


    • Changes to layout editor comparison platform graphs are maintained
    • Templates open with "All Samples" group current
    • CXP correction pref only applied to files with $SYS = CXP or $CYT = CXP
    • Changed the number of colors for layout overlays that can be set in preferences from 12 to 36
    • Proliferation Platform: Added EI (expansion index), RI (replication index), & SDD stats, re
    • ordered stats in graph window
    • Added menu / rightclick command "Copy To LE", works on single or multiple selection.
    • Don't highlight (enable) transformation menus for uncompensated samples
    • Allow different transformations for uncompensated parameters with different ranges (Important for CyTOF files)
    • Allow reading (and skipping) layouts that are corrupted (and read other layouts that have not been affected)
    • Comparison Node: Leave enough space to display Overton Percent Positive value. Also, recalculate when switching between univariate and multivariate views to ensure updated display
    • Change percentile calculation for distributions where first channel of events IS percentile (was averaging percentile down)
    • Maintain $PnR on floating point exports
    • Fine tuning Comp Wizard for offscale parameter handling
    • Calibration platform uses smoothed distributions for reference calculations
    • Compensation Wizard provides helpful message when there is complete lack of shared parameters
    • Handle duplicate indexed sort gate wells (gates now include all duplicated events rather than just the last one)
    • Proliferation node allows setting Y axis in LE

    Bug fixes:

    • Recode Gallios FCS3.0 files to correct error in assignment of parameter stain names and recode scaling.
    • Template workspace textboxes retain text
    • Allow concatenation of samples with different stain names when prefs are to sort parm lists by stain
    • Improve Comp Wizard performance & prevent a crash
    • Reopening a workspace with a magnetic gate will show the gate in the moved position upon graph open
    • Fixed template creation for layouts containing groups or grids of samples
    • Backgate displays always show all dots for gated subsets (rather than preference
    • defined setting for dot displays)
    • XML workspaces, when reopened, do not show deleted samples in workspace
    • Selecting "Remove Compensation" when graph window is front-most works
    • Graphs in Layout Grids expand to fill the cells when hiding axis information
    • When selecting multiple cells in Layout Grids and moving objects, the order of the objects is not inverted.
    • Boolean gates that refer to gates that have "G#" in their names (like " gate") are properly shown in the display window when they are edited
    • Multigraph overlay accommodates larger axis text (from prefs)
    • Moving multiple objects within grids preserves order

    July 27th 2010, Version 9.1 released



    • FlowJo now calculates keyword values from formulas involving strings (other keywords) and the usual math operands via FJML.
    • Compensation matrix identifier bar in Workspace (left edge) is wider & brighter for better visualization.
    • Compensation Wizard better handles samples with off-scale scatter measurements.
    • New Preference (on the General tab) to turn off sub-channel randomization of measurements during compensation - makes picket fencing happen but prevents small changes in membership of gated events on compensated parameters.
    • Population Comparison: Overton statistics added to Layout Editor annotation box.
    • Boolean gates that refer to missing nodes now show "RefError" in the Workspace statistic display.
    • Added "?" (Help) button to Custom Transformation Window.
    • Compensation Wizard will use your custom scatter gate if you have pre-defined one.

    Bug fixes:

    Fix: Disallow compensation matrices with same name (will rename them "-1", "-2" etc)
    Fix: Properly scale FCS 3.0 floating point parameters with a $PnR that is not a power of 2
    Fix: Trying to load a data file for which you don't have read privileges now shows error message.
    Fix: FlowJo can now handle the situation where the user sets custom transform visible decades to zero (bad value.)

    March 22nd 2010, Version 9.0.2 released


    • New FJML attribute (property name: "GatePositionArea") to return the center and area of a gate (for table and layout editors). This can be used for QC purposes, by providing a column that can be scanned to identify gates that have been moved (are different).
    • Fine tuned performance specifications, now more efficient.
    • You can now import spreadsheet-based data files with parameter ranges that are not a power of 2 ("FJREALTEXT" format).
    • New menu item to "clear & recalculate" selected items (versus all items in the current group).

    Bug fixes:

    • Batched layouts now obey preferences properly (i.e., layout or workspace or general preferences).
    • Fixed crash if you batched a new layout with an overlay graph that has a layer referring to a missing sample.
    • Fixed crash if you choose to open the graph for a value in a table editor output that has only a single statistic column.
    • Fixed occasional crash on some computers in the PolyChromatic Plot Controller.
    • Fixed crash that occurred when you re-open a saved workspace following a cancelled relocation of a missing data file.
    • Parameter names ending in "Area" (not just "-A") are considered area for scaling purposes.
    • Better axis notation when few decades are shown (i.e., don't show "5x10^3", partial decade values).
    • Derived parameters can be computed on parameters named "P10", "P11" etc.
    • FJML gates allow >255 characters in their specification.

    April 19th 2010, Version 9.0 released



    • New workspace version: workspaces created by v9 cannot be opened by older versions of FlowJo. However, you can "Save as XML" and older versions can read that file (not all options are supported).
    •SVG (Scalable Vector Graphics) is a supported output format. Supports high-resolution vector graphics that can be exchanged into Intaglio (copy/paste or saved file export) or Illustrator (saved file export)
    •Lists of keywords can be navigated by typing (first letter of keyword name)
    •Event number parameter starts with first event = 1 (rather than 0)
    •An expiring serial number is warned about only twice during any session
    •Several main menus have changed: e.g., new Transformation menu; look for new menu commands

    Bug fixes:

    •The correct IP address is shown in the "About" box

    Compensation & Transformation

    •Compensation matrices are sorted alphabetically in the menu
    •Compensation matrix elements can be added as columns in table editor
    •Compensation matrix can be added as separate table in layout editor
    •Can opt to have the current workspace group to recalculate all stats ("live") while editing compensation (helps determine optimal spillover value if manually adjusting)
    When you edit an acquisition matrix, FJ automatically duplicates, assigns to all samples, and then edits the duplicate
    Can remove a compensation matrix
    New user interface to manually adjust Transformations
    •Can remove a transformation
    •Can copy transformation settings from file to file via Adjust transformation user interface

    Bug fixes:

    •Custom transformation re-reads data file to accommodate large negative values
    •Transformation is better computed on datasets with large negative values
    •Autcompensation scripts handle secondary match keywords properly (for multiple matrices per workspace)

    Table Editor:

    •Copying Tables with formulas to Layouts allows creation of "static" tables with all values or dynamic tables with no formulas (static tables can later be changed to dynamic)

    Bug fixes:

    •Formulas can concatenate multiple strings (via the "+" operator)
    •Statistic "Freq of." a subset works when iterating by keyword
    •Fixed significant figures definition
    •Copying a created table to the layout editor works for large tables
    •Statistics based on gates that do not exist are shown as "�" rather than zero

    Layout Editor:

    •Option to show or hide color and line style annotations in legend
    Legends are drawn with a header row that can be customized
    •The interface to edit the legend now has an "Update Layout" button
    • Can create "Y by Y" view for any given graphic (via menu or contextual menu)
    •Backgating history can show fully-gated overlay (a la DiVa)
    •If you drop a node onto a graph to create an overlay:

    -If there are multiple graphs selected in the Layout Editor, all become overlays
    -If the graph is part of a group, then all graphs in the group become overlays

    Bug fixes:

    •Modifying iteration options for layouts in templates does not erase the discriminator
    •Batched movies are properly sized (and pictures are placed properly)
    •Batch to web report functions correctly
    •If black background color is chosen for graph, gate frequency text color is modified to show
    •Fix batched statistics tables created when iterating by keyword value
    •The flag for showing or hiding the annotation or legend item is properly set in the info dialog
    •Printing does not improperly scale to accomodate items that are off-view to the left
    •Grid lines in overlay legends are properly drawn
    •Layout-specific preferences allow specification of gate width on graphs
    •Batching graphs (to printer or preview) obey Layout-specific preferences (if any)
    •Current layout-specific preferences are not replaced by preferences from last layout in a list while saving
    •Creating a new layout makes default preferences and batch attributes rather than copying from current layout
    •Fix: Text boxes in Grids sometimes became invisible
    •Multi-item attribute interface: Making overlay styles consistent works even if they overlas are part of a group


    • Create Series (editing keyword value) allows you to create strings (e.g., "Sample 01", "Sample 02", ...), and/or replace numerical values by specified strings
    •Different color bars are used to annotate samples depending on which compensation matrix they use
    •When concatenating multiple samples, if they do not share a compensation matrix then compensated parameters are exported (otherwise, uncompensated parameters are exported together with the matrix)
    •Exporting data:
    •Event number can be exported to floating point FCS3.0 FCS files
    •Export $PnE keyword for floating point DiVa files
    •Can specify a maximum number of events per file when exporting many files
    • Get Info on Samples: Keywords longer than 132 characters are truncated for ease of viewing
    •Computing a Boolean gate referring to a non-existent gate shows a message (the non-existent gate is
    •considered to include all events)
    •Can show the data file FCS version in the workspace (and, for other places, access via the keyword, FJ_FCS-VERSION)

    Bug fixes:

    •Prevent Find/Replace keyword value from looping if replace string contains find string
    •Allow specifying to export 1M events
    •Fix cache operations supporting netowrked (remote) file transfer (i.e., permissions etc)
    •When you "Create Multiple Groups" from staining panels in the Group definition, the "Live" attribute is obeyed
    •Notifies with an error if trying to read a data file 2 GBytes in size
    •Can now re-find data files that are moved even if their name is 32 characters long
    •Deleting a group-owned gate and choosing �Save with first sample� always works now


    •Can create FJML gates (each vertex can be a formula based on any sample statistics or other gate)
    Can create gates based on event number
    •Can auto-create gates for indexed sorting data files (Supports DiVa keywords)

    Bug fixes:

    •Magnetic histogram gates work properly

    Graph Window:

    •Contextual menu to allow opening parent graph

    Bug fixes:

    •Gate polygon name and subset name are now always identical
    •Copy CDF as text (data values) does not crash
    •Polychromatic plots don't crash in some cases where sample was not yet read in
    •Gating path is displayed in graph window properly


    •Define top end of log scale for 32-bit parameters
    •Read only FCS2.0 portion of data files that have both FCS2.0 and 3.0 data
    Define keyword values to auto-add to legends created in the layout editor
    •Backgating displays shown as fully-gated (a la DiVa) vs. true backgating
    •Force authentication (username/password) when transferring remote data by HTTP protocols.

    Bug fixes:

    •Cache location can be successfully modified
    •Backgating preferences can be properly set via Preferences user interface

    Backgating platform

    •Can optionally display full gated overlay (a la DiVa)

    Bug fixes:

    •Saving settings as preferences are applied to Global (not workspace) preferences

    Multigraph overlay platform

    •If you select all fluorescence channels, only the compensated channel will be shown

    Derive parameter platform

    •When creating linear parameters, the lower bound is explicitly set to zero (not changeable)

    Cell Cycle platform

    •Multiplier constraints on G2/G1 positions must be 0.25 and <4>

    Cluster platform

    •Histogram labels are the $PnS rather than the full name to shorten

    Bug fixes:

    •Histograms are updated if the gating tree is modified
    •"MinSepChannel" refers to the offset from the channel value corresponding to a scale value of "0."or the left-most channel in the display to prevent splitting autofluorescent populations spread by an inadequate biexponential transformation

    Data files

    • Support reading "BCI" files
    •Support reading 32 bit integer data files containing log-transformed data
    •Support a list of URL's as a "Summary File" import

    Bug fixes:

    •Properly scale values from 16-bit integer data files

    February 24th 2009, Version 8.8.6 released


    • "Fit all Windows on Screen" command (under "Windows" menu) repositions windows that are (partially or fully) off-screen

    Bug fixes:

    • Linear compensated parameters were shown with wrong axis scaling
    • Canceling a file search when doing a Get Info on the sample does not lead to a dialog box that can't be dismissed
    • Does not have a crash on certain corrupt layouts
    • Transform all parameters does not lead to a bug when you are compensating 10-bit data files
    • Polychromatic plots can now properly select compensated parameters
    • Prevent crash if entering random (bad) numbers into the Print Settings dialog
    • Fix storing and display of batch outputs in the SciBook
    • New workspaces are named as "YYYYMMDD Workspace" rather than "Untitled Workspace"

    November 21st 2008, Version 8.8.4 released


    • Contextual pop-up menu for groups (control-click or click-hold on a group node)
    • "Duplicate without samples" command for groups. This is a menu item-- creates a new "shell" group that has all the gates and information from the previous group, but no samples (unless samples are auto-added). Similar to a template, but for groups.
    • Sample Info Dialog (cmd-I on a sample): Keywords are sorted in a friendly way; a new popup menu lets you switch to different samples in the same dialog window
    • New Preference to ignore $PnG Keyword (under "General" tab). Can be workspace-specific. Note: this preference may apply only to samples added to the workspace afterwards

    Bug fixes:

    • Layout item information dialog disables the foreground color selector on overlays, since that didn't do anything; disables the "show all layers' gates" checkbox when it's not an overlay.
    • Fix rare crash on reading remote (FTP) data files.
    • Ancestry plots from Layout Editor are not clipped when copied and pasted into PowerPoint (before ungrouping).
    • Site license access made more robust in case of server issues.

    September 29th 2008, Version 8.8 released


    • Sample validity platform has copy report
    • Allows reading improperly-formatted CXP files ($PnB = 10)
    • F5 engages recalculation of workspace
    • Moving existing quads now tracks percentage
    • Spiderweb functionality: mold gates together, option-click common vertex
    • Spiderweb quads: option-click quad gates to move vertices
    • FlowJo Licensing Server allows 2 day-old files for servers that cache web sites
    • Add vertex function (spider)

    Bug fixes:

    • Fixes crash on reading files when using general undo enabled
    • Fixes 8.8 bug that quad gates converted to spider gates did not compute as such
    • Fixes compensation picket fencing on FCS2.0 data
    • Fixes disappearing dots
    • Fixes clicking on a gate without moving it does not remove its group ownership
    • Fixes Comp wizard, if fluorescent events off scale by scatter, fails to create gate and then crashes
    • Edit overlay legend user interface- mapping Insert menu commands to proper insertion
    • Preferences save text color settings
    • Cell cycle remove debris for histograms on >1024 channels
    • Dropping files onto a group node adds data to that group rather than current group
    • Exporting file with specified parameters (bug introduced in 8.7.2)
    • After Batch Layout create, could sometimes corrupt internal layout representation (LIR bug!!! - probably 10 years old!)
    • Allow dragging gates onto comparison nodes to change control
    • Deleting a derived parameter will not cause an exception when reopening graph that showed that DP
    • Export non-FCS format (bug introduced in 8.7.2)
    • Sometimes a magnetic gate would be drawn in its old position until update (always calculated right)
    • Gate annotation position no longer changes when window is resized
    • In setting sample sort order, if you check "Use as default" it will be set in the Preferences
    • When doing Save As, mark original workspace as no longer open (wrt possible double open)
    • Exporting derived parameter doesn't crash if not loaded (beta bug)
    • Workspace preferences for 32 bit reading parameters are obeyed (rather than global)
    • Hiding labels but not ticks -- properly exported bounds on graph
    • MUCH faster (SMP speed up for file reading and compensation)
    • Relocate dialog stays up during browsing operation to see requested file
    • Ctrl-drop node onto overlay reassigns sample ownership of all overlayed nodes if they come from a single sample
    • Concatenate better determines if keyword value is linear or log distributed
    • XML Fine tuning (SD stat, multiparameter compare parms, ws group sort order)
    • Table statistics on subgroups: subgroup name is added to the statistic name in column 1
    • Layout editor Overlay dot plots obey # of dots to draw
    • Prefs "Use as default" from current workspace also copies sample sort criteria
    • XML coding added
    • Find file dialog shows much more information about lost file.

    July 3rd 2008, Version 8.7.3 released

    Bug fixes:

    • Edit menu garbage text (undo/redo) is fixed.
    • The workspace comment column text is properly added to Layout Editor Tables.
    • The Group Editor dialog window doesn't show funky characters for empty parameter stain names.
    • The Kinetics smoothing options are properly initialized in the kinetics window when re-opened.
    • When reading DiVa 3.0 data files, the progress bar better reflects how much is left to read and compensate.
    • Templates with layout editor iteration that depends on keyword iteration and discrimination now work fully.
    • Templates no longer give the error that the file was not properly closed.
    • Allow CellQuest data files with zero events to be added to a workspace.
    • Group Edit Dialog window properly initializes the comparator menu item.
    • In Layout Editor Tables that have a column for "Gate Name" -- for sample-level nodes, the sample name is shown instead of the text "Ungated."
    • Make sure files made from concatenated gates of compensated data have correct number of events in FCS header.


    • Keyword Edit/Replace operations allow searching for blank keywords (so you can replace blank keywords with any given replacement value)
    • Layout Editor overlay graphs can optionally show gates for all overlaid layers (not just the top-most). There are new UI checkboxes in the overlay information dialog to set this.
    • Layout Editor Tables can show the gate name with an "indented" option -- to make it look like the Workspace display.
    • When creating a new Layout Editor Table, you can select (from the popup menu) an option to create a table that looks like the current Workspace (as much as possible); it automatically creates the appropriate columns.
    • When you "concatenate" samples or gates, you can now choose to create new parameters in the resulting data file, the contents of which are equal to keyword values from each of the samples. (Use the option-key when selecting "concatenate" from the menu.) This let's you add identifier information (or other information) found in the keywords as a real parameter, on which you can gate, etc..
    • Empty workspaces show "Drag Samples Here" text.
    • When you drag a population onto a layout graph to create an overlay (or hold down cmd-key to reassign the graphic to that population), FlowJo will now replicate that operation to ALL layout graphs that are currently selected.
    • Added Concatenate User Interface link.


    • The "Recalculate" (Immediate/When Sample Loaded/When Necessary) preference has been removed. All recalculations are now done "lazily" -- when needed. Use the "Recalculate" menu command (cmd-=) to force a recalculation in the workspace display.

    March 4th 2008, Version 8.7.1 released

    • Fixed issue with "serial number corruption" and inability to save preferences on certain computers.
    • Fixed edit menu corruption (for undo/redo).
    • Fixed Group Edit dialog. It now remembers all comparator states ("does not contain" etc) properly.
    Changed: CellQuest files with zero events are read into the workspace rather than ignored.

    February 22nd 2008, Version 8.7 released

    Known issues: Files with long names (>31 characters) will not be automatically re-found when moved to a new location.


    • You can now paste in an entire spreadsheet of keyword values into the Workspace for easy editing! (Click here)
    • You can now "Marquee" select (click and drag to select multiple items) in the Group analysis list.
    • Mouse-wheel scrolling is enabled in the Group list.
    • Horizontal mouse-wheel scrolling (shift-key while scrolling) is also enabled.
    • FlowJo has a new Preference to annotate gates shown in graphs with generic FJML, allowing more flexibility on what to show (for example, statistics or annotations).
    • Keyword lists show keywords in a more useful order (with user-defined keywords at the top); also, recently-selected keywords ("favorites") are shown first.
    • Autocompensation Scripting Platform has been updated:  the user-interface has been improved, and features such as compensation gate validation have been added.
    • Site License information (contact information etc) is available to Site Licensees in the About FlowJo window.
    • Layouts can be added and deleted immediately, without having to wait for the current one to finish drawing.
    • Keyword Search & Replace: All instances of a search string within a single value are replaced at once.
    • Keyword values are not subjected to "Significant Figures" preferences when output in Tables.
    • With scientific notation set, all axis values are shown as such (not just exact log ticks.)

    Bug fixes:

    • Layout Editor Batch Discriminator and Iterator keyword lists are now in the same order.
    • Editing a compensation matrix a second time does not falsely flag unchanged values as changed.
    • You can now delete summary statistics in the dialog window with the delete key as you would expect.
    • We now correctly interpret EXPO V2 non-standard files having erroneous keyword values for parameter bit lengths.
    • Batch from layout direct to printer: output is properly paginated even without going through the "Custom..." dialog
    • Kinetics no longer reports (incorrectly) that FJ-created time parameter is not monotonic.
    • Platforms: when using arrow keys to move constraints, FlowJo no longer deselects the constraint.
    • We now allow outputting of all ascii characters (like "�") in keyword values.
    • When group gate are renamed, FlowJo prevents a "/" (slash) in the name.
    • No error is generated if reading an exported data file that has compensated parameters, no uncompensated parameters, and a compensation matrix.
    • Error messages are improved when there is an error reading layouts or if there are too many events on the axis.
    • Robust CV calculations on biexponentially-scaled parameters are optimized.
    • FlowJo allows any length boolean gate specification (It was having problems after 256 characters).
    • Save As Template does not show file as being "currently open" (a bug from 8.7b9).
    • Cell cycle--remove debris gates initially are set to reasonable positions for all cases.
    • Cell cycle--immediately recalculates fit if any constraint for CV is changed.
    • Layout Editor--cannot select pseudocolor or polychromatic plot as graph types for overlays .

    November 19th 2007, Version 8.6 released

    • You can now paste in an entire spreadsheet of keyword values into the Workspace for easy editing!
    • You can now "Marquee" select (click and drag to select multiple items) in the Group analysis list
    • Mouse-wheel scrolling enabled in the Group list
    • Horizontal mouse-wheel scrollling (shift-key while scrolling) enabled
    • New Preference to annotate gates shown in graphs with generic FJML, allowing more flexibility on what to show (for example, statistics or annotations)
    • Keyword lists show keywords in a more useful order (with user-defined keywords at the top); also, recently-selected keywords ("favorites") are shown first
    • Autocompensation Scripting Platform has been updated: the user-interface has been improved, and features such as compensation gate validation have been added
    • Site License information (contact information etc) is available to Site Licensees in the "About FlowJo" window
    • Layouts can be added and deleted immediately, without having to wait for the current one to finish drawing
    • Keyword Search & Replace: All instances of a search string within a single value are replaced at once
    • Keyword values are not subjected to "Significant Figures" preferences when output in Tables

    Bug Fixes:

    • Text boxes created for iterated layouts will have the correct sample ID
      Changing Layout annotation item text contents immediately resizes the bounds to show the text
    • Templates with gates on the "All Samples" group relying on compensated parameters will apply those gates when files are added
    • Cluster platform no longer generates an error if launched on a gated population for a sample not yet read into memory
    • Double-clicking on Kinetics analyses in the Group list does not give an error message
    • Preference for Axis annotation (show parameter stain and/or name) is obeyed for Layouts and Workspaces
    • Preferences for print headers and footers are obeyed for Layouts and Workspaces
    • Create Groups and Show Graph for Table Editor works properly after Table has been sorted
    • Keywords are sorted correctly in Keyword lists
      Layout Editor Menu items are greyed out when Graph Windows are foremost

    August 13th 2007, Version 8.5.3 released

  • Open file dialogs are properly titled (e.g., "Open Workspace" or "Open Samples").
  • The menu item "Create Group From Keyword Value" has been removed; a single user interface is now used for all keyword-related group creations.
  • You can now drag samples from one workspace to another by dropping them on a group in the destination workspace; the samples are added directly to that group.
  • For new workspaces, the Table and Layout Editor windows are by default placed just to the right of the workspace, rather than on the right edge of the screen.
  • There is a new Preference for using generic FJML commands for all gate annotations in graph windows [NOTE: This requires more documentation].
  • General undo preference off by default
  • If general undo is slowing down too much, will warn user to turn preference off
  • Bug Fixes:

  • Comparison Platform: The checkbox for "show difference" is properly initialized.
  • SciBook: Exporting a Layout Batch View does not crash.
  • Polyvariate Graphs: You can no longer select "Histogram" or "CDF" from the contextual menu or main menu.
  • Table Summary Statistics: You can now immediately access the most recently-created table column; changing group names is performed correctly.
  • Derived Parameters: Parameters are no longer randomly renamed on occasion.
  • The Preference for "Show All Keywords in Lists" is obeyed for all keyword selection dialogs.
  • The Preference for "Default number of columns" in Batch Layout creation is used correctly.
  • Opening old workspace could cause undo to crash, until file was saved
  • June 20th 2007, Version 8.5.2 released

  • Fixed crash when creating statistics table object in layout editor
  • Fixed occasional debugging error message on certain operations that were OK (like dragging gates to lots of samples)
  • Truncated (bad) FCS files now generate an error message rather than a crash
  • Fixed crash when reading a kinetics file where the last event's time parameter value is out of range
  • Fixed sorting of file names in workspace (when they had numeric components only)
  • Fixed the scaling factor for linear DiVa data file that are accessed via FTP
  • June 4th 2007, Version 8.5 released

    Note: Workspaces saved by 8.5 will not be read by 8.4. However, you can save a workspace as XML and open it in 8.4 (you will lose information regarding new 8.5 features, but everything else should be fine).

  • Preference Sets: You can now store the current preferences as a "Set" (via the Preferences dialog). You can save as many different sets as you want. Later, you can open the Preferences (for the Application, Workspace, or Layout), and copy from one of the sets to engage those preferences. That way you can keep different settings for different environments. The FlowJo menu has a menu item to directly switch to a given set of Preferences (for the Application). (One application: "Style sheets" for layouts: you could designate the default fonts, graph styles, headers & footers and such for different layouts to be specific Preference sets. Then, when you create a new layout, you can copy the Preference set for the desired view for that Layout).

  • Table Summary Statistics: You can now add any number of summary statistics to Tables, including statistics computed on a subset of the rows in a table. Statistics can include Mean, Median, CV, Minimum, Maximum, Range, IQR, and even T-Tests and Wilcoxon Rank tests on different subsets of data within each column. To define or change these statistics, click on the "Sigma" (Statistics) button in the Table Editor (each table can have different summary statistics).

  • Statistics: Statistics computed on distributions (e.g., median fluorescence, mean, CV, etc) are now considered "invalid" if there are insufficient events on which to compute the statistic. By default, the minimum number of events is 1 for most statistics (or 2, for CV and SD). In addition, the statistic "Frequency of parent" (and similar) are considered invalid if there are no events in the parent subset.

  • There is a new preference, under "General", where you can increase the minimum number of events on which to calculate these statistics. "Invalid" statistics are represented by a bullet ("�") in all output places. "Invalid" values are ignored by the Table Editor when computing summary statistics or formulas (a Table formula that has an invalid statistic as one of its inputs will generate an invalid output value).

  • Compensation Wizard: Performance enhancements; better identification of positive controls.

  • Minor additions:
    • Workspaces store a history of all versions of FlowJo that they were saved with (accessible when "Save As XML" is chosen).
    • Pseudocolor graphs obey dot size (2, 4, or 8 only) preference
    • FlowJo's file reading has been optimized to take advantage of multiprocessor machines for faster data loading

  • A number of bug fixes:
    • Compensating DiVa data that has linear parameters now properly stores and re-reads the information when the workspace is saved.
    • A situation where layouts could be saved in a corrupted fashion has been fixed; workspaces that have this issue will now be properly read.
    • Accommodates new Coulter-generated files
    • Layout Graphics now obey Layout-specific preferences
    • Workspaces can only be opened once simultaneously
    • Statistics tables in Layout Editor obey significant figures preference
    • Allow data files with more than 128 parameters
    • Fix reading $COMP keyword compensation matrices (e.g., Coulter data files)
    • Properly initialize Preferences on new computers
    • Fix reading FlowJo Collector data files
    • Fix: Show scientific notation preference was being re-set everytime the Preferences was launched

    April 27th 2007, Version 8.4.6 released

    • Fix: Behavior where files/gates would disappear from the workspace.

    April 13th 2007, Version 8.4.5 released

    • Fix: Bug could lead to crash while reading some workspaces.
    April 12th 2007, Version 8.4.4 released

    • Fixed an occasional crash on the Compensation Wizard
    • Fixed a bug where (on Intel Macs) the Proliferation Platform would not compute a model for some fits
    • Fixed a bug where keyword values from BioTrue-generated workspaces might have an extra character at the end

    March 14th 2007, Version 8.4 released

    • Table columns can now have custom significant figures assigned (in the formatting dialog for table columns)
    • Compensation Wizard is significantly improved:
      • Graphical display uses smaller graphs if there are a lot of compensation parameters
      • Much better (if not perfect!) identification of unstained samples
      • Refers to unstained as "Unstained" rather than "Universal Negative"
      • You may have multiple unstained controls (for example, cells, different kinds of beads); the platform will automatically select the appropriate control based on the Forward Scatter matching
      • You can choose to have the Wizard add "Clean-up" gates, which will add tight gates around the fluorescence distribution of the positive controls
      • You can choose to have the Wizard add scatter gates to identify lymphocytes or singlet bead populations
      • There is a menu that controls what happens when you create the matrix: by default, the matrix will automatically be applied to all samples and the Wizard finishes
    • Concatenating files does not export the compensated parameters (re-compensate after concatenating)
    • You can now choose to show the full data file path on the disk, as a column in the Workspace window
    • A number of bug fixes:
      • Derived parameters (and Calibrated parameters) created on Intel Macs are properly saved in workspaces
      • The Calibration platform manual definition will draw only one axis scaling
      • Grouping in the Layout Editor preserves front-to-back layering
      • Intel Macs can now update purple (version 6) dongles
      • Derived parameters dialog properly enables log and linear parameter menus
      • General Undo crashing repaired
      • Table Editor summary statistics shown with desired number of significant figures
      • Table Editor formulas that referred to specific rows of a column now work
      • Boolean gates allow parentheses in the gate specification
      • Showing gate coordinates for Boolean gates in the workspace shows the full specification
      • Group gate synchronizing was fixed to handle a case where multiple gates, derived from different groups, were modified; the entire gating tree was incorrectly synchronized to one of the groups

      January 9th 2007, Version 8.3 released

    • Fixed:Unknown corruption leading to bad keyword values causing an error building tables with those keywords.
    • Saving incrementing file name versions will tag the number before the filetype ("abc.001.jo"); will only keep most recent in "recent items" menu;
    • Save as will not create extra blank file.
    • Auto dialog answers will generally not store 'Cancel' answers to prevent confusion.
    • Tweaked Compensation wizard auto-assignments.
    • Exporting histograms includes a third column as scale fluorescence (bin / fluor / count.)
    • Fixed: Edit comp matrices on intel macs wouldn't allow non-integer values.
    • Long gate names are abbreviated in graph windows (abc/ad...def/fjd/).
    • Fixed: Annotation items automatically resize to accommodate changing info!
    • Text boxes can now be set (default) to resize automatically to text. If you resize via drag, then the flag is set off. Old textboxes do not acquire this flag.
    • Fixed: reading packed data files (e.g., 9 bit files.)
    • Modified: storing keychain information for servers with multiple names will store under original & modified host name.
    • Preferences: changed how they are stored. Workspaces store data transform prefs with WS; not affected by global prefs.
    • October 13th 2006, Version 8.2 released

      Known issues: Files with long names (>31 characters) will not be automatically re-found when moved to a new location.

    • Linear axis values are abbreviated with "K" (like 100K) to make them shorter
    • When overlaying more than 12 items in a Layout Editor graphic, the colors continue to rotate (rather than being only red)
    • Cumulative records for FlowJo analysis times (under "About FlowJo") are properly incremented
    • There is a new Platform, "Sample Validity Testing."  This platform allows you to determine if the events collected during acquisition are uniform (i.e., unchanging over time).  You can identify files which have clogs, discontinuities, or other problems.  The platform can be automatically invoked for every data file through a Preference; the settings which fine tune how FlowJo identifies potential problems are set in the Platform window.
    • Boolean gates that do not contain "or" operators (for example, as created by the "Create Combination" platform) now compute 30 times faster!
    • In the Table Editor, there are now contextual menus (click and hold, or control-click, on table column definitions) which allow you to modify a row: move it to the top or bottom of the list; delete it; edit it; or change it to a different kind of definition.
    • FlowJo will now rename duplicate parameter names (in Dako files); duplicate names led to a lot of different problems.  For older workspaces that refer to such files, open them in this version, and just save them.  Any error messages will now go away.
    • Transformations defined on DiVa-generated compensation matrices will be applied to all files with "similar" compensation matrices.  DiVa generates compensation matrices that have trivial differences that caused FlowJo to think they were actually different.
    • If you copy a table with formulas to the Layout Editor, FlowJo now informs you that formulas are not supported in Layout Editor Tables.
    • Linear axis values are abbreviated with "K" (like 100K) to make them shorter

    • Bug Fixes:
    • Several stability issues were addressed.
    • Proliferation statistics will now appear in Tables even if the Proliferation model has not yet computed.
    • If the files were loaded in the Compensation Wizard which did not have fluorescence parameters found in other files, then the Wizard could crash.  Now only parameters that are common to all files are selectable for generating compensation matrices.
    • Biexponential transformation parameters are correctly initialized in preferences.
    • Correctly reads workspace files that were modified on an Intel Macintosh using an early 8.0 version of FlowJo, but caused a crash when reading.
    • Selecting "Save" menu when "SciBook" is open will save SciBook entry to disk; changing a SciBook comment will mark the Workspace as having been changed so it can be Saved immediately.
    • When overlaying more than 12 items in a Layout Editor graphic, the colors continue to rotate (rather than being only red)
    • Cumulative records for FlowJo analysis times (under "About FlowJo") are properly incremented
    • A number of bugs that only occured on Intel Macintosh computers were fixed:

      1. Correctly reads workspace files modified on an intel Mac using an early 8.0 version of FlowJo that caused crashes while reading
      2. Does not crash when double-clicking on layout graphs that have long gating path names
      3. Correctly copies table outputs to layouts
      4. Properly saves statistics tables created in layouts
      5. Drop-down menus in Compensation wizard work  
      6. Polyvariate gates are saved such that they can be read on non-Intel macintoshes   
      7. Linear parameter scaling does not change with each workspace save for remote-access datafiles

      July 5th 2006, Version 8.1.1 released

      Known issues: Files with long names (>31 characters) will not be automatically re-found when moved to a new location. Copying layouts between workspaces crashes

    • Fixed: Quadrant gate statistics in tables and layouts
    • Fixed: Copying Graphs from Layouts with history gating are properly cropped when pasted into other applications
    • Table Editor Formula entry window is now resizeable
    • Derived Parameters: New "Edit" button allows you to edit a previously-defined algebraic formula.
    • May 17th 2006, Version 8.1.0 released

    • Prevent crash in Multi-Sample Distancing Platform dialog if no sample files are available for comparison.
    • Changed name of dialog box from "Layout Item Definition" to "Graph Definition", to be consistent with the Windows version.
    • A "workspace" created from the BioTrue server contains translations of the original FCS file headers. If the original FCS header file contained a keyword with a blank value, the BioTrue translation of that header would confuse FlowJo, causing it to incorrectly read the header information after that value. If multiple Samples were included, this would cause some samples to have incorrect names. This condition has been corrected. FlowJo will now read the translated header correctly.
    • The FlowJo Workspace window created from a BioTrue ".jo" file, is now given the name of the file instead of being an unnamed workspace.
    • Added preference to enable SFTP file transfer.
    • Added dialog box to ask for SFTP User name to initiate file download from BioTrue SFTP server.
    • Added dialog box to ask for user, workspace, and destination information to initiate SFTP file transfer when saving a Workspace to a remote SFTP server.
    • In the About Box, changed "Serial: " to be "Serial: Dongle" when authentication is via a dongle.
    • Now works with V8 "purple" dongles on an Intel Mac.
    • Changed the Graph Window so that the text, "Warning! More than X% of events on the axis!", appears above the graph pane, rather than touching it.
    • May 4th 2006, Version 8.0.3 released

    • Fixed crashing bug when calculating the Kinetics Platform.
    • Fixed crashing bug while attempting to quit with the Kinetics window still open.
    • April 28th 2006, Version 8.0.2 released

    • Fixed: Cell cycle statistics overlay: axis label does not overlap with axis ticks.
    • AutoCompensation scripts now generate exactly correct matrices when universal negative is used.  Previously, off by a small amount for low fluorescence controls.
    • MultiDimCompare: Does not crash when computing multiple chi square.
    • Batch creation (to preview):  Only warns on too-large layout size if ... too large!
    • FlowJo properly sets picture boundaries for graphics copied from layout editor to show all axes without needing to ungroup.
    • Workspace files with Derived Parameters will display correctly on an Intel-based Mac.
    • Renaming a gate at the group level is properly handled so that all references to the samples' gate are also updated.
    • Fixed several instances where old (PowerPC) workspace files might not open properly on Intel Macs.
    • Fixed dongle-upgrade URL to paste the old dongle ID into the upgrade web page.
    • Added check box to select SFTP for file download and upload.  Currently disabled.
    • Fixed a problem on Intel-Macs where some older workspace files would not load properly, resulting in the dreaded "You've uncovered a defect in the program" assertion-failure dialog box.
    • Fixed a few more instances of handle-based I/O not being "swapped" properly on an Intel-Mac.
    • Fixed problems on Intel-Macs where older workspace files would "lose track" of sample files in some instances. That is, if you load an older workspace and double-click on a sample, a Graph Window will display the expected graph, rather than asking the user to find the FCS file.
    • April 13th 2006, Version 8.0.1 released

    • Fixed problem with LE text annotation edit dialog, which caused all menu items to be disabled, and prevented the program from responding to further command events. Changed PPob resource #4319.
    • Removed second, unused "Workspace" "Rename..." menu item, #2023.
    • Removed "Extended" attribute from menu items:
      "Edit" "Select equivalent nodes" (#2032)
      "Workspace" "Add Samples into Group..." ('AddG')
    • Changed "ValidThumbDrive" to set "gDongleAttached" so that the "FlowJo" "Serial Number" menu item is disabled. This now disables the "Serial Number..." menu item when a valid thumb drive is found.
    • Fixed uninitialized variable in "MultiDimCompare::MultiChiSquare", causing a crash on an Intel Box when the first sample in a Multi-Sample Compare is not selected.
    • Fixed printing problem on Intel-Macs, where the Y-axis labels were rotated by other than 90 degrees.
    • C
    • hanged FlowJo.rsrc "Miscellaneous Strings" (resource #2100), string #240 to read:
      FlowJo does not support a HASP key (purple dongle) on an Intel-based Mac. Please click on "About Dongles" to view our trouble-shooting web page.
    • Added version resource "8.0.0" to the SNConverter tool, so we can tell when it has been updated.
    • Fixed problem in "FTableViewer", where the "fNodeForCell" was not being completely initialized, nor was it being indexed incorrectly. When trying to create a new Group from a list of cells in a table, via "FTableViewer::CreateGroup", function "FTableViewer::GetPopulationForCell" would loop forever looking for the last cell.
    • Fixed problem where an exception would occur on an Intel-Mac when reading workspaces with Calibration tables.
    • Fixed problem that would prevent FlowJo from recognizing a black dongle if another USB device with a serial number was also attached.
    • April 3rd 2006, Version 8.0 released

      Does not support OS9.x. Minimum version is OSX.2.
      Minimum workspace readable is version 20 (2.7 or beyond)...
      For old Workspace, read using version 6.x and save
      Need new serial number or dongle
      Now built as a fat binary (runs on Intel mac and PPC Mac in native mode)


      • New Table Editor: much faster, new formatting options, computed columns, iteration...
      • Drag Tables and Layouts from WS to WS
      • Can now define Page size (Page Setup)--saved via preferences
      • Different scale, orientation for each layout, otherwise global
      • More performance enhancements (particularly, batch >generation)
      • New Table Menu (Layout/Table menus changed)
      • Keyword selection dialogs now show keyword values for any selected sample

      • Stain name mismatching is no longer considered (always allowed) [old groups--obeyed]
      • Menu item changed to "Define BiExponential Plot"
      • Define Transformation dialog has disclosure triangle for "advanced" options
      • Changing factory settings for advanced options is saved in preferences
      New Graph Option:
      • PolyVariate Plot: Gateable, Displayable "PolyVariate Plot"
      • New: Obey PnDisplay keyword (DiVa only currently, FCS3.0 suggested)
      • New: Size of large dots in low resolution dot plots (Great for publication)
      • Removed: Stain Name mismatching in LE (always allowed)
      Table Editor:
        UI has changed
      • Drag Tables from WS to WS
      • Building big tables is hugely faster
      • Specify special formatting for any given column (including hiding it)
      • Iteration like Layout Editor
      • Double click table name to edit iteration attributes
      • Double click column to edit formatting
      • Table Editor Formulas! (NOTE: Formulas are NOT copied to Layout Editor when table is copied there)
      Layout Editor:
      • Drag Layouts from WS to WS
      • Double-clicking layout does a get info
      • Can set iteration group from get info dialog
      • Can Show gate coordinates & offset vector in Layout Tables
      • Cmd-E (Graph->Transpose Axes) now works for graph items in layout editor
      • Create Group From Keyword Value--can always be chosen in menu now; can choose keyword to select from
      • Show gate coordinates & offset vector in Workspace
      • Sort dialog pre-loads existing sort order
      • Statistics node indentation increased
      • Can now rename group-based gates
      • Allow more than 16 time slices to have colors
      Bug Fixes:
      • Transformations computed on hardware-compensated data only apply to other files with same matrix
      • Kinetics: Can delete multiple time slices simultaneously
      • Workspace: Node icons are drawn to left of name column even if too narrow
      • SciBook: Editing text entries is saved!
      • XML: Save graph options re hide Ticks/Numbers/Labels in axis specification
      • Groups: Membership changes affected by keyword editing happens immediately
      • Group editing: disable "More choices" button when 4 sets of criteria already shown
      • Fix: reading color palette preferences for layout overlays
      • Fix: Deleting first level of LE overlay left "selection" above; pressing delete would cause crash
      • Intermittent Site License validation problems have been corrected.
      • Allowed FJ to run with a v6 or v4 Site (FLS) License.
      • Fix: Badly-formatted compensation matrix in data file does not cause crash
      • Fix: FlowJo doesn't crash when a workspace is closed with an open Batch Movie output
      • Boolean Gates: if creating a large number of gates (which can take a long time), FlowJo provides feedback on the progress
      • Statistics Window shows larger fonts and doesn't allow "Add to all compensated parameters" if no compensated parameters exist
      • Intermittent Site License validation problems have been corrected.

      Known issues:

      Files with long names (>31 characters) will not be automatically re-found when moved to a new location.

      April 13rd 2006, Version 6.4.7 released

      • Fixed problem that would prevent FlowJo from recognizing a black dongle if another USB device with a serial number was also attached.

      November 16th 2005, Version 6.4 released

      Bug fixes:

      • No more hanging when the Tree Star web site is impossible to reach
      • Can create derived parameters on Cyan-acquired data
      • Workspace statistics don't disappear when a recalculate is performed
      • Read all Coulter data files
      • Cell cycle: constraining peaks to gate positions is now correctly saved
      • Cell cycle: option to use pattern fill for graphs is correctly saved
      • Annotation items in layouts are properly filled for batch outputs
      • "FS LIN" and "SS LIN" parameters are now recognized as scatter parameters
      • Improved performance and stability


      September 30th 2005, Version 6.3.4 released

      Important Notes:

      Note: workspaces created with this version cannot be opened with older versions.

      New Features.

      New in 6.3.4 (cumulative changes since 6.2.1):

      • Significant performance improvement noticeable when compiling large layouts or tables-particularly when hundreds or thousands of samples are involved!
      • Fix text issues in dialogs on some computers running OS9.2.2.
      • Summit 4.x files with incorrect data location specification keywords are now read in properly.
      • The compensation definition window can now be resized to allow for long parameter names.
      • Fixed: Memory was slowly being used up by doing large numbers of text boxes in the Layout Editor
      • Fixed: Tables with negative numbers in the statistics will now show means & standard deviations.
      • A number of optimizations and bug fixes were done to prevent crashes that occur during large computational demands; stability should be much better.

      General Operation:

      • Site licensees are validated more efficiently Preferences:
      • There is a new preference to define the default sort order for samples in the workspace Workspaces:
      • Workspaces are now read in and saved much more efficiently. Note: the first time you read in an older workspace, it may be much slower; as soon as you save in the new format, it will be considerably faster!
      • Workspace sort criteria are now "persistent": if you add new files (or for templates), the files will be automatically sorted according to the last selected criteria. In addition, when you define the sort criteria, you can make them the default for all new workspaces.
      • Workspace sort criteria can be individually set to be increasing or decreasing values.
      • Unreferenced samples are now removed from workspaces (making templates much smaller).
      • XML format has been modified (more similar to PC version). This format is still being updated and is not guaranteed to be consistent with future revisions of FlowJo.


      • Tables with keyword values that have or display properly
      • You can copy a series of custom column heading names (from Excel or Word, separated by returns) into any column heading name – the entire series is copied to the subsequent table columns (hit return or tab after pasting). In this way, you can edit the column names in a different program and then copy them in all at once.
      • The mean and std. dev. are filled in only for valid calculations (e.g., they are left blank for text columns)

      Bug fixes:

      • reading newest Coulter data files
      • Cell cycle models that constrain to a region--constraint is saved after closing & reopening
      • Cell cycle platform option to display pattern filled models is properly saved
      • Annotation items for Layout Graphs are properly built in batch reports "FS LIN" and "SS LIN" are recognized as forward and side scatter parameters
      • Fixed bug that could cause crash during gate computation while other tasks were happening-improved stabililty!
      • When directing a batch output directly to the Printer, the page information is properly initialized without having to go through the "Custom" settings button.
      • Fix: Preferences correctly reads layout color palette for overlay colors
      • Fix: Bug that could cause rare occasional crashes when reading files
      • Fix: When choosing to sort the workspace, the current sort criteria are displayed
      • Templates that refer to compensated parameters now add all gates & statistics
      • Renaming a gate will no longer cause a Layout (referring to that gate) to crash
      • Opening graph windows no longer occasionally reset the Layout iteration value
      • Cycling graphs (next/previous) no longer cause a rare crash that happens when gate frequencies were shown
      • Modifying a series of gates that are all group-synchronized no longer causes a rare crash
      • $SPILLOVER keyword values are properly supported
      • Allow dragging gates from one workspace to another if the destination sample is selected
      • Crash no longer occurs if changing a graph while an outlier plot is computed
      • Selecting a graph from a sample not in the current group does not make that sample temporarily appear in the workspace window
      • Double clicking multiple samples in the control definition list for an overlay graphic now sets all selected samples as controls
      • Grid lines are displayed in histogram overlays
      • Histogram overlays will not occasionally display parameter names for the Y axis label
      • Boolean gate specifications are no longer case-sensitive
      • The Layout batch Preview will not crash if the display is too large to show on-screen
      • The line color for boxes drawn around text is correct in batched layouts
      • Summit data files with badly-formatted $SPILL keyword (Summit version 4.1) are now read in (an error message is shown) but no compensation parameters are added. These files can be compensated the usual way in FlowJo, using appropriate compensation controls.
      • FlowJo does not crash if you try to delete the only layer listed in the Legend Item for a Layout Graphic.
      • Batch layout generation: if Iterate by Nth (n > 1), the resulting layout's discriminator is properly set.

      Known issues:

      • Files with long names (>31 characters) will not be automatically re-found when moved to a new location.
      March 4th 2005, Version 6.2.1 released

      Important Notes:

      The format of the workspace file has changed. Workspaces saved in 6.2b3 and beyond cannot be read by older versions of FlowJo .

      New Features

      Graphs and Gating:

      • There is a new preference to control the default naming scheme for new Quadrant gates (you can choose to have only "Q#", where the number increments for each new quadrant set; you can choose to add the stain names; and, as before, you can choose whether or not to ask for a prefix to the gate name).
      • The Backgating analysis now shows a legend of gates applied for each graphic, to better illustrate what is being shown. In addition, the last graphic in the window is no longer a backgating analysis (as there as no useful information for that level), but rather shows a simple overlay of the gated population.
      • There is a new gating tool to create two gates that bisect a histogram; while tracking with the mouse with this tool active, the graph window will show live statistics (like the quadrant tool).
      • A new menu item, "Show defining gate", allows you to quickly access the graph that defined any selected subset.
      • Contour plots can no longer be drawn as unsmoothed.
      • Log contour plots do not allow you to select "show outliers", which was meaningless for this display.
      • Kinetics analyses now show the threshold value used for calculations in the kinetics window.
      • Grid lines for linear parameters are now drawn to match major axis tick marks.

      Data compensation and transformations:

      • Corrects Summit Compensation matrices (for all versions of Summit).
      • FlowJo now supports the FCS3.1 keyword "$SPILLOVER" as specified in the proposal.
      • The compensation matrix name (if FlowJo was used to create the compensation) is now stored in a keyword ("FJ_CompMatrixName"),
      • The compensation definition window has new buttons to calculate and close; to clear all positive & negative gates from the boxes; and has better selection of gates in the boxes.

      General Operation:

      • FlowJo keeps statistics of how many different kinds of operations you perform (number of files analyzed, gates created, events read): Choose "About FlowJo", and click on the disclosure triangle near the bottom of the window.
      • All "Confirmation" dialog windows have button names that better explain what the two choices are (instead of just "Yes" or "No").


      • When editing the attributes of platform graphics in the Layout Editor, you can now set additional options such as the colors and size of the graph.
      • Scrolling large layouts is much quicker.
      • You can now change fonts for individual layout items.
      • For overlay legends, the cursor will change when targeting the color or line style controls to aid in identifying where to click.
      • Generation of Batch Layouts was made more efficient (faster).


      • Tables can be saved as XML (for import into LIMS systems, for example). Choose "Save As XML" while viewing a completed table.


      • Preferences reorganized (a 'Platforms' preferences panel added)
      • The preference for copying the FCS Comment keyword into the workspace annotation was removed
      • A new button clears all memorized auto-answers for confirmation dialog windows

      New preferences to define:

      • 1. Default statistics that are added to layout editor when Cell Cycle platform is dragged in (and the 'auto-create statistic table for platforms' preference is enabled).
      • 2. Default statistics that are added to layout editor when Proliferation platform is dragged in (and the 'auto-create statistic table for platforms' preference is enabled).
      • 3. Default columns to be created whenever a new overlay legend is created in the layout editor.
      • 4. Default colors and graph types for Backgating analysis (these can be set either through the Preferences dialog, or by selecting the checkbox before closing a Backgating window).
      • 5. The default scheme by which to name new Quadrant gates (you can choose any of 'Q#', where the # increments for all new quads for a subset; the stain names (e.g., CD3+CD4-); a prefix that is asked for when the quads are created).

      Bug fixes.

      • Correct sorting of file names that have the format 'name.#.#' (like abc.040602.001)
      • Line color of histogram was sometimes forgotten when the graphic info dialog was opened in Layout Editor
      • Distribute horizontally in Layout Editor works even if items are too close together
      • Selecting 'About FlowJo' no longer puts application in Demonstration mode
      • Layout items now correctly show cell counts after batching
      • Resizing Proliferation window properly draws the model histograms
      • Copy table from Multisample compare platform fixed
      • Inserting keywords for specific samples in Layout Editor Text chooses correct sample (was one off)
      • Occasionally, 10.e-4 would be displayed as 10.e-3 for frequency in Workspace
      • Correctly displays time parameter for BD files using the 'TimeTicks' keyword
      • Copying from layouts no longer clips the right or top edge of certain graphs
      • Fix Copy/Paste of a single textbox in the Layout Editor creates a new text box, not a picture of a text box
      • Group-synchronized gates don't crash if more than 1 is simultaneously changed (like quadrants)
      • Layout text boxes with a line width of 'none' will not show the box line in printouts
      • Fixed obscure bug where rarely a Layout textbox could lose the last statistic in its text
      • Layouts with statistics tables won't crash during batching
      • Open Graph Sets will properly tile windows (and resize if necessary) on the screen
      • Holding down 'option' key while selecting a sample in the 'go to sample' menu button on graph windows will advance all open graph windows to that sample
      • Fixed a memory allocation bug that could cause apparently random crashes
      • Reading old layouts with legend overlays will now properly initialize the legends instead of leaving them blank
      • Changing the threshold value for a Kinetics analysis forces an immediate recalculation
      • Thick lines in the layout editor are better handled (selection and arrows)
      • Avoid page breaks in the Layout Editor will not cause a graph and its annotation or legend to be put on different pages
      • Create group window: Removing a criterion clears it; complex formulas doing comparisons on string values now work
      • Clicking escape while drawing a gate now cancels the gate creation
      • Selection of gate constraints in Cell Cycle platform was corrected
      • Histogram gate lines in layout editor (and exported graphs) don't extend beyond edge of graph
      • Adding a statistic to a group based on a parameter that has a ')' in its name no longer crashes
      • Putting commas in custom table column names no longer alters the formatting of table headings
      • Dragging a PICT file into the Layout Editor now refreshes the view immediately
      • Tables dragged into the Layout Editor now automatically refresh statistics when gates are moved
      • Double-click timing to open graphs from the workspace window restored to proper functioning
      • Changing a gate does not reset the Layout Editor iteration to 'off'
      • Only the 17th parameter in a file could not be compensated: now it can!
      • Scrolling while entering table editor custom headings improved
      • Fixed: Changing a gate does not reset the Layout Editor iteration to 'off'
      • Fixed: You can again edit custom column headings in Layout Editor statistic Tables
      • Fixed: Scrolling of window while editing custom column headings in Table Editor
      • Fixed: You can now compensate the 17th parameter in a data file
      • Fixed bugs that crept up in beta versions:
      • Contextual menu for gates restored
      • Group-based synchronizing multiple gates (like quads) fixed

      September 10th 2004, Version 6.1 released

      Important Notes:

      Workspaces saved in FlowJo v6.1 cannot be directly opened with earlier versions of FlowJo.  However, you can save a workspace as XML (File->Save As XML...); that file can then be opened in FlowJo v6.0.  Please see notes on XML under "Workspace" below.

      New Features:


      • Version Locking.  You can now "lock" a version of FlowJo on a given computer (which will apply to all users on that computer).  This lock ensures that no other version of FlowJo will be used for data analysis on that computer.  This feature is useful for laboratories who have validated a given version of FlowJo and want to ensure that no analysis is done by a different version.  To "Lock" a given version, choose the Lock command under the file menu, enter an Administrator username and password, and then follow the instructions.  Locking can be performed in a password-protected fashion (if desired).  NOTE: "Locking" a FlowJo will not prevent versions 6.0 (or 4.x) from launching, because they cannot check for this feature.  However, these older versions of FlowJo cannot read workspaces saved by this (or future) versions of FlowJo, so there is no risk of analysis by the wrong version.  NOTE: Because the "lock" feature will apply to all users on that computer, you must have Administrator privileges.  When you choose "Lock", you will be asked by the Macintosh operating system to authenticate a Username with Administration privileges.


      • Complex Group DefinitionsSample Groups can now be defined based on arbitrarily complex combinations of keyword information.  In the Group Definition Dialog, you can convert current keyword restrictions to a formula, and continue to extend this formula to be as complex as you wish!  Formulas can contain complex string manipulations, so you can search for substrings within keyword values, etc.
      • Opening sets of graphs.  Through the preferences, you can now define one or more "Graph Sets".  These are predefined sets of graphs (with specific X and Y parameters defined for each).  Any defined graph sets will appear in the contextual menu when you click on a sample or subset; choosing that Graph Set will cause one window for each defined parameter pair to be opened for that sample.  This allows you to predefine combination of parameters to view simultaneously for each subset.  (Use "option-Next" or "option-previous" to move all graph windows forward to the next or previous sample simultaneously).
      • Copying Boolean gates will now notify you if the subsets on which they depend are not found in the destination.  In addition, if you delete a subset on which a Boolean gate depends, you will also be notified that this is the case.
      • FlowJo will now read badly-formatted legacy Cytomics FCS files.
      • XML Workspaces :  Versions 6.x give you the option to save as XML (and can read such workspaces as well).  At this time, Tree Star does not guarantee that the XML format will be compatible with future versions of FlowJo; we are in the process of evolving this format to be consistent with the PC version.  If you have suggestions or questions regarding the FlowJo XML format and/or future plans, please contact us!


      • You can now calculate the standard deviation ("SD") on any parameter.
      • When adding a statistic calculated on a parameter (e.g., mean, CV, SD), you can choose to add that statistic to all parameters, all fluorescence parameters, or all compensated parameters at once, by choosing those in the parameter menu of the statistics dialog.
      • The order of the statistics in the Statistics Dialog window was changed to group them better.


      • Printing:  For batched outputs (either direct to printer, or printing from the Preview output), you now have the option to use the original pagination as defined in the Layout Editor.  This means that you can print batch reports where each panel crosses page boundaries—for example, if you spread the page boundaries such that each iteration of the batch is on 3 pages, you will get 3 pages times the number of samples in the group for your output. To choose this option, select "Use Layout's Pagination" where offered.
      • Batched layouts are no longer grouped after being created.
      • Keywords are better handled in layouts (particularly, for batched layouts and/or templates).
      • When entering a keyword into a text box, you can select which sample for which to display the value (and single text boxes could have keywords from multiple different samples).
      • You can now set the text style for axis labels differently from axis numbers (see Preferences); you can make the axis text as large as you wish and it will no longer be "clipped" (see Bug fixes).


      • There is a new contextual menu popup for when you click on a gate in a graph window that allows you to perform operations on the selected gate.
      • The "Create Manual Gate" interface has been extended to allow you to create a series of gates that are adjacent (non-overlapping) across the entire range of the displayed parameters.  The series can be specified to step by equal channel numbers, equal intensity levels, or equal percentile levels.

      New Preferences

      • Gates and Graphs preferences were split into separate panels.
      • A preference can be specified for how FlowJo exports histograms as graphs.  The default is to export as polygons, which is useful for changing their characteristics; this works well in programs like PowerPoint.  Deneba's Canvas does not interpret Mac PICT polygons properly; thus, changing this preference will cause FlowJo to export histogram graphs as connected lines.  This makes it show up properly in Canvas (and other programs), but the histograms cannot then be filled in those programs (exporting of filled histograms will still work from FlowJo in all cases).
      • Graph Sets can be defined in order to simultaneously open multiple graphs; these sets can be chosen from the contextual menu when you click on a sample or gate in the workspace.
      • The text style for layout editor graph axes labels can now be defined differently than that for the axes numbers—you can have large axes labels!
      • The location of FlowJo's Cache folder for transferring data from remote servers can now be specified to be either in the User's directory (default) or in the local shared directory.  The latter is preferable for computers where User directories are kept on remote computers.
      • The Preference for Hiding or Moving "clipped" axes numbers has been removed (see bug fixes below).


      • You can now zoom in and out of graphics in the SciBook.
      • Workspaces saved with many SciBook entries now read in faster.
      • A new option for Groups can be set ("Allow stain mismatch") that forces the group to add analyses and gates even if the stain names for the parameters are different than for the original sample's analyses.
      • FlowJo now corrects the improperly formatted compensation matrix in Summit v4.0 data files.
      • When files are moved and need to be found by FlowJo, you now have the option to ask FlowJo to perform an exhaustive search of all mounted disks for the data file (this may take several seconds).
      • The text color for Print output headers and footers can be set in the Preferences.
      • New quadrant gates will ignore the Preference for gate annotation position; the frequency will always be placed in the graph corners.
      • The "Edit Annotation" menu item has been removed (annotations can be edited by simply double-clicking on them in the workspace).
      • If you misidentify a file that has been moved, FlowJo will show you the name of the file before asking you again to locate it.
      • Layouts will now show at least one additional page, horizontally or vertically, when scrolling, to allow you to better place new objects.
      • A new Preferences lets you use the Bi-exponential/Logicle transformation on uncompensated height parameters ("-H") in addition to the area parameters. Click on the button: Preferences->Workspaces->DefineÉ (32 bit options).

      Bug fixes.

      Layout Editor

      • Axes labels and numbers are no longer clipped in the Layout Editor or upon export to other programs. Finally!  You can now have axes labels & numbers as large as you want!
      • Layout Statistics Table tool doesn't crash if there are no samples in the workspace
      • Overlaid histograms with auto-scaling have exactly correct Y axis values (previously, these "relative" numbers were off by 4%).
      • Text boxes in the Layout Editor can have braces in them again "{}".
      • Gate frequencies are not duplicated underneath the graph (after ungrouping an exported layout).
      • Printing a specified range of pages from the Layout View now works (previously, would print all pages).


      • Double-clicking in the workspace sometimes didn't open a graph; this now works.  (Although if you double-click too fast, it may not).
      • You can now delete a keyword value in the workspace and leave it blank.
      • The Time parameter is properly retained on saved and re-opened workspaces.
      • Italicized text in the workspace and Table output is better displayed on-screen (not clipped).
      • A crash could occur if graphs and statistics were selected in the workspace, and the contextual menu "Open graphs" was selected; this was fixed.
      • Workspace mousing (click & drag, etc) is more responsive.
      • Save As Template does not crash when the preference for incrementing workspace versions is selected.
      • Occasional mis-sorting (or poor sorting) of samples fixed.
      • No more unnecessary recalculations of subset gates that occurred in some circumstances (despite a Preferences setting of "Only recalculate when needed").
      • Concatenating events from different 32-bit data files (e.g., DiVa data) is now handled properly.

      Graphs & Gating

      • Autogating will now place the resulting gate properly in windows that are not the standard size.
      • Autogating tool is not active until the data has been loaded and displayed.
      • Autogating will occur on the correct parameters after axes are changed.
      • Boolean gates will immediately recalculate upon creation, if the Preferences are set for "immediate recalculate."
      • Boolean gates work more reliably when copied from sample to sample.
      • FlowJo will not crash if you choose to create Boolean gates on a group of selected items including Statistics.
      • Possible bug causing crashes during gate adjustment fixed?


      • Contextual menu for graphs & gates no longer appears for Platforms (causing a crash)
      • Cell cycle and Proliferation platforms no longer crash if something happens to invalidate them during their computation (like a parent gate moving).
      • Cell Cycle and Proliferation: Copy table to text will always work now.


      • The "Application Lock" contact information and hint information are no longer switched for new Lock commands.
      • After batching a layout, the graphics are properly reset to the "off" iteration state (previously, they were reset to show the first sample in the current group rather than their original state).
      • Layout axes will now correctly adopt the color set by the Preferences.
      • Layout overlay graphs will obey the specified background color (including transparency).
      • Gate trees added by groups (i.e., when you add samples to a workspace) would not add an entire tree if any gate was based on parameters with stains that did not match the original; now only the mismatched gates are not added (unless the group option is to allow mismatches--see new feature above)
      • Coulter ".HST" files are properly read and loaded.
      • Cell cycle: The remove debris, remove doublets no longer crashes
      • If a Boolean gate was opened without first opening the other gates, then the Boolean gate could show the wrong events.
      • Fixed crash that could occur on very first use of autogate tool on first dotplot graph.
      • Fixed: Opening graph sets places graph window below the menu bar.
      • Fixed: Contextual menus in the workspace window show the platforms & Boolean gate options.

      July 5th 2004, Version 6.0 released

      Important Notes:

      • Workspaces saved in version 6.0 cannot be opened with FlowJo v4.6

      Major New Features

      Autogate tool . Point… click… gate. It shouldn’t be any harder. And, with FlowJo’s new Autogating tool, it can’t get easier! FlowJo’s autogating tool has an almost prescient knowledge of where you want the gate—an effect made possible by the instantaneous feedback of where the gate will be as you mouse over the graph! Choose the new autogating tool in the graph window, or simply hold down ctrl-option as you move the mouse over any bivariate graphic. (Note: if you hold down the mouse button as you click to create the gate, you can then track the mouse to inflate or deflate the gate to size it with even more precision!)

      SciBook . The SciBook is a place where you can store pictures, text, tables, or custom annotations. The SciBook is stored with the workspace; you can use it as a permanent record of your analyses, as a temporary holding place for outputs, or just to keep notes for yourself. You can paste graphics, text, or tables from anywhere in FlowJo into the SciBook (the Graph window, Platforms windows, Layout Editor, Batch Layout View, and Table View all have buttons that will directly copy their contents into the SciBook). Contents in the SciBook do not change-therefore, if you change a gate, delete a sample, or make other modifications, the SciBook contents will not be modified. Once in the SciBook, you can copy into other programs, print, or simply just view. The SciBook gives you an interface to add comments about each item that you insert, and records the date and time that the item was inserted.

      The SciBook is meant to evolve; we look forward to your comments regarding which features you use the most, what features you would like to see in the future, and what you do (and don't) like about it!

      Backgating Analysis . Validating gate positions is one of the most important aspects of multiparameter Flow Cytometry. FlowJo now provides you with a tool to view the effect of every gate on your final gated population! In any graph window for a subset that is gated more than once, you can choose “Backgating Analysis…” under the Graph menu (or, click on the Backgating button that appears near the top right of the window). FlowJo shows you a window where each level in the gating hierarchy is displayed, with the final gated population overlaid at each level. This overlay is a backgating overlay: in other words, it shows what the final gated population would look like without that level’s gate! Therefore, you can quickly scan to see if any one of your gates is positioned incorrectly. The backgating display can be printed, copied, or saved in the SciBook (see below). Note that the Layout Editor can also show a version of the backgating analysis, by choosing “Show Ancestry” and selecting the “Backgating” option for a graph

      Boolean gates . You can now create a gate which is a Boolean combination of any existing gates (i.e., "and", "or", and "not" combinations). Boolean gates are "live", meaning that they will reflect any changes to the gates on which they depend. FlowJo can also automatically create a series of Boolean gates that represent all combinations (plus and minus) of a set of gates. For example, if you have a sample which was stained on different parameters for IL2, TNF, and IFNg, you can create a positive gate for each of the three cytokines (for example, a histogram gate). Then use FlowJo's Boolean Combination to create the 8 gates that represent all combinations of expression of the cytokines (e.g., IL2+TNF+IFNg+, IL2+TNF-IFNg-, etc.). To create or edit Boolean gates, choose the parent subset(s) and select the menu item "Boolean gates..." under the "Platforms" menu.

      Derived parameters . You may now create a derived (computed) parameter that is any algebraic combination of existing parameters. FlowJo allows you to specify arbitrarily complex formulas, and includes a wide variety of mathematical functions that you can use to transform the data. This platform can be used in FRET calculations to create a parameter that reflects the efficiency of resonance energy transfer.

      Layout Editor: New Statistics Table. FlowJo now renders tables of statistics in a beautiful and highly customizable way in the Layout Editor. You can copy tables (either by dragging them from the Table Template Editor to use with Batch iteration, or directly from a completed table). Or, you can create them from scratch, adding your own statistics and keywords and other information. Statistics Tables in the Layout Editor come in two flavors: (1) Each row is from a single sample: this is like the output of the table editor, where statistics for subsets or the whole sample are all represented on the same row; (2) Each row can have subsets from the same sample: this allows you to view a number of statistics (e.g., MFI) on many subsets from a single sample in column format. Note that you can copy Layout Statistics Tables directly to spreadsheets (as tabular data) or to graphics programs (as their graphical representation).

      Layout Editor: Overlay legends . The legends for overlays in the Layout Editor can now be customized to show statistics, keywords, or other pertinent information from each subset that is overlayed in the graphic. Simply double click on the legend to specify what should be shown.

      Layout Editor: Iterate by "nth" sample. Sometimes you just want to do batch iteration where the order in which you collected the samples defines how you want the output to appear-for example, every three tubes comes from a single sample, where the first of the three is a control, and the other two are two different panels. FlowJo lets you easily specify such a design by using the "Iterate by nth" option. (Choose "Iteration options" under the layout menu). In this example, you would iterate by "every 3rd sample", telling FlowJo to group tubes into samples of 3. This significantly simplifies batch operations. All new Layouts are created with the “Iteration by nth” (n = 1, i.e., every sample) by default.

      Templates: Improved functionality. This "Iterate by nth" Layout Editor feature also means that Template Workspaces that contain batched layouts will work well. A batched layout is now automatically defined to have the appropriate iterator (and discriminator) values; when you batch a layout over every sample and save it as a new layout, the new layout is automatically defined to iterate by "nth", where "n" is the number of tubes in the original batch.

      In addition, sample identification is significantly improved in FlowJo. This means that Template workspaces will fill out layout graphs as expected-FlowJo tries very hard to overcome any ambiguities that might arise because of multiple samples fitting the criterion for a single graphic.

      Other New Features.


      • The FlowJo icon is properly displayed on all workspace files (that have names ending in ".jo", ".ws", or ".flowjo").
      • There are new “Help” menu items to provide quick links to documentation and contact information.
      • Lists of FCS Keywords are sorted better, with user-defined keywords appearing first, and standard FCS keywords arranged in better order.


      • The workspace auto scrolls to show the sample corresponding to the front-most graph window.
      • The number of samples in a group is now shown in the first column after the name, not aligned with the "Statistic" column.
      • Template workspaces are now saved with the default extension of “.jot”.
      • While editing a keyword value, you can paste a selection (copied from another program) that has a series of values (tab- or carriage-return-delimited, as from Excel). FlowJo will fill out successive rows with these values.
      • You can now ctrl-click (or click-and-wait) on analyses in the sample list to show a menu of actions appropriate for the selected items.
      • The column resizing button has been moved from the top of the workspace window to the middle bar.
      • $PnE keywords (log/linear scaling of parameters) can now be edited.
      • When sorting on keyword values, FlowJo looks to see whether a keyword value is numeric, alphabetic, or mixed, and sorts appropriately. For mixed values, FlowJo will sort “A-2” before “A-10” (even though this is not alphabetical); it recognizes the presence of both strings of letters and numbers and treats them independently when determining sort order.

      Graph Window

      • Graph windows now use the "ctrl-click" (or click-and-wait) to show a menu to change the graph attributes (graph type, options, etc.), similar to the Layout Editor graphs.
      • Cloning a graph window (“+” button, or “Open New Window” menu) now creates a new window that has exactly the same settings.
      • You can specify (for dot plots only) the number of events to display, on a graph-by-graph basis.


      • Compensation: When editing a compensation matrix, you can now copy it (to the clipboard) or print it.
      • Cell cycle: There is a new preference to choose a Pulse Area parameter as the default for new analyses, and new preferences to control the default modeling characteristics.
      • Cell cycle: The cursor coordinates are now shown in the window.
      • Proliferation: The modeling algorithm has been improved to better find good fits. (The formula for the model has not changed, only the approach to the fit).
      • Derived Parameters: Older derived parameters for Ratios, Gain/Offset are now automatically converted to Algebraic derived parameters with the correct formula shown.
      • Derived Parameters: You can double click a previously-defined algebraic parameter to edit it.


      • Overlay Legends: You can now click to select any row in the legend; press the "delete" key to remove it from the overlay; drag to re-order the overlay.
      • Show ancestry plots: You can choose to make all ancestry graphs show at equivalent size, rather than scaling them to fit in a single row or column.
      • Text boxes: If you select a text box and choose "Copy", then the contents of the text box are put on the clipboard so you can paste them into other applications.
      • Arrows: If you create a line with arrow heads, you can now specify the shape of the arrow head to customize its appearance.
      • Graphs: You can now specify the number of events to display (dot plots only) on a graph-by-graph basis.
      • Graph Item Annotation: The dialog window in which you can specify custom contents for a graphic item annotation box now has a menu to choose keywords to insert into the annotation text. Also, graphic item annotations can be edited for multiple graphs simultaneously from the "multi-item attribute editor" window.
      • Batch Iteration Dialog: The dialog window that appears when you create a new Batch output has been made easier to understand; the iteration controls have been removed from this window (to specify iteration options, you must choose them via the "Iteration options" menu item).
      • Text boxes, annotations: In addition to specifying FJML commands for items like statistics (" ") and Keywords (" "), you can also specify information about any given subset using the "Property" command. Properties that can be displayed include: "Comment" (any comment in the workspace for that subset), "GateName" (the name of the subset), "SampleName" (the name of the sample), and "Path" (the full gating path for that subset). For example, " " will be translated into the subset's sample name.


      • Editing column names: While editing a column name, you can paste a selection (copied from another program) that has a series of values (tab- or carriage-return-delimited, as from Excel). FlowJo will fill out successive rows with these values.
      • Hold down the option key while clicking on the "Copy to clipboard" button and a transposed version of the table is copied onto the clipboard.

      New Preferences

      • Pulse-area parameter should be the default for Cell cycle analyses.
      • Newly-created histogram overlays in the Layout Editor should be scaled to a fixed value by default (rather than scale-to-max).
      • Specify the default line styles for histogram overlays.
      • Default graph window size for newly-created graphs (brought back from Version 3.x of FlowJo!).
      • Text traits for gate frequencies shown in graphs in the Layout Editor
      • Text traits for headers and footers in printouts
      • Specify the default statistic that is added to the Table Editor when a gate is dragged to the Table.
      • Specify whether axis numbers, on graphs that are near the edge and would appear clipped as a consequence, should be moved slightly or hidden.
      • Cell cycle platform preferences can be defined.
      • Proliferation platform model display preferences can be defined.

      Bug fixes

      • Suggested output file names are chosen better.
      • Sample Information window can be resized to show keyword values better.
      • Deleting a sample from the workspace will close its graph window.
      • Create Value Series (while editing a keyword value) now obeys the maximum number of values to fill in, and better remembers the previous values you used for it.
      • Cell cycle and Proliferation analyses immediately recompute a model if a parent gate changes.
      • Proliferation: If create a constraining gate to position the undivided peak, you can now select it without having to close the window first.
      • Layout graph items with oversized text (from the preferences) no longer randomly resize themselves. However, large text will still be clipped if it is too big. (You can choose to hide ticks or axis numbers to provide additional space for label text).
      • Cell cycle: Remove apparent constraints that allowed positioning of peaks by absolute values (this was never a possibility).
      • Cell cycle: Fixed synchronous peak constraints for DJF model.
      • Cell cycle: copying analyses to groups or other samples retains the preferences for how models are displayed
      • Workspace: Fixed editing a keyword value for workspaces with >1000 samples.
      • Kinetics: Fixed an issue that could cause a crash for files with corrupt data at the end of the time series.
      • Layout Editor: Multiple graphs dropped in from the workspace are now positioned better (so as not to overlap).
      • Workspace column resizing no longer occasionally resizes the window height.
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