Current Version is 4.6.2, posted August 30th 2004.

Index:

Version 4.6.2 (August 30th 2004)
Version 4.4.4 (Sep. 30th, 2003)
Version 4.3.2 (June 9th, 2003)
Version 4.2 (October 11, 2002)
Version 4.1.1 (August 18, 2002)
Version 4.0.2 (May 21, 2002)
Version 3 History
Version 2 History

August 30th , 2004: Version 4.6.2 released
SUMMARY OF CHANGES SINCE 4.4.4
Important Notes:

Workspaces saved in version 4.6.1 cannot be opened with previous versions of FlowJo.

Major New Features.

• Compensation Matrix Editing. When you create a new compensation matrix, FlowJo no longer automatically saves it to a file. In addition, you can now edit compensation matrices directly from FlowJo, using the "Compensation->Edit/Save Matrix" command. From this interface, you can save matrices to disk (so that you can import them into other workspaces), you can create an entirely new matrix from scratch, or you can modify an existing matrix (and FlowJo will always show you which values you modified). If you have graphs open, they will automatically update to show you the changes you are making. Note that you can edit a hardware compensation matrix by choosing to create a new matrix using the acquisition matrix as the source. You must have that sample selected when you choose to "Edit/Save Matrix".
• Open Recent Items Menu. FlowJo remembers the last workspaces you opened, and lets you open them directly from the "File" menu. A new preference controls how many workspaces you want it to remember.
• Changing Layout Graphs Directly. You can now change the axes on Layout graphs by control-clicking on them (also, you can "right-click" using a two button mouse, and, you can even just click and wait for a fraction of a second): FlowJo shows the standard menu of parameters. If you control-click (or click & wait) on the graph itself, FlowJo shows a menu of different graph types.
• Exporting to Power Point improved. FlowJo now interacts in a much better way with PowerPoint (and some other graphics programs that did not support PICT like they should have!). Graphs can be ungrouped without text moving around! Also, various polygons (like histograms and gates) are now imported into these programs as polygons, not just disconnected lines.

Other New Features.

General

• FlowJo now requests the hardware Ethernet address of the motherboard, irrespective of Airport! No more serial number problems with laptops!

Workspace

• The "All Samples" group attributes (display font & synchronization feature) can be edited now, by double-clicking on the group.
• The workspace can now accommodate more than 100 unique compensation matrices. (See also new compensation editing interface, above).
• The "Frequency" statistic has been renamed to "Freq. Of Total" for clarification.

Preferences

The preferences have been rearranged and a new panel has been added. This was necessary to accommodate the new preferences listed below:

1. Number of workspaces to show in "Recent ItemsŠ" menu.
2. Delay after clicking on layout editor graphs before showing menus.
3. Save dialog settings (i.e., when you choose to "Always use this answer" to a dialog, FlowJo will now remember that across launches). To reset the saved responses, uncheck this preference.
4. Default tiles per page and columns of tiles for batch layout operations.
5. Default position for gate annotation (frequency and/or name).
6. Default auto-save time is now 5 minutes (instead of 10).
7. New popup menu to help select which parameters to maintain as linear when reading 32-bit data files.
8. Default values to specify whether to hide axis ticks, numbers, and/or labels for new layout graphs.
9. Whether or not to jide the white background box drawn underneath gate annotations.
10. Whether or not to create a legend for layout graphs (to specify line style, fill color, etc.).
11. Whether or not to fill new histogram graphs in the layout editor.

Graph Window

• Axes popup menus are now resize to accommodate long parameter names.
• Clicking outside a selected gate only unselects the gate, and does not immediately begin a new gating operation.
• The bottom statistics line reflects the true number of dots displayed (for dot plots, the Preferences may limit the number of dots drawn, e.g., to 8,000).
• You can now have more than 100 subsets per population.

Layout Editor

• The proliferation platform shows %Divided and proliferation index statistics in the layout graphic annotation item.
• Axes labels are moved in closer to the graph if ticks and/or numbers are hidden. This allows for larger fonts to be accommodated by the graphs.
• Text boxes can be rotated 90 degrees left or right.

Proliferation Modeling

• Previously-calculated fits are no longer recalculated when the model is re-opened or used in the table editor: significantly improves throughput!

Kinetics

• FlowJo now gracefully handles bad LSR I files (that have bad time parameters).

Derived Parameters

• When creating a ratio parameter, FlowJo much more intelligently selects the parameter scaling (when you don't specify the scale manually).

Bug fixes.

• Proper reporting of the current available version
• Supports version 6.0 dongles and serial numbers
• Fixes crash that occurs while modifying gates and autosave kicks in
• Kinetics: maximum time steps increased to 4,096 (from 512)
• Default OS9 memory allocation increased to 120 MBytes
• Double clicking a workspace when FlowJo is not running will actually open the workspace!
• Occasionally, strange characters should appear in axes labels of new layout graphs. We believe this has been fixed.
• You no longer have to agree to the License Terms every time you save a new set of Preferences.
• Compensation parameters created from hardware-stored matrices are now immediately available for gates (previously, they were only created when the file was opened for the first time).
• You can no longer drag a quadrant gate off the graph window, rendering it impossible to retrieve.
• In the overlay platform, you can again click on any population and press the delete key to remove it from the overlays.
• Hitting "command-S" ("Save") in the Layout Editor no longer causes the alignment function to enact (should only happen with the "S" key).
• Editing of header and footer values from the Preview (tiled report) immediately take effect.
• You can now specify graphic centering and sizing even when 1/page is selected.
• Fix the time scale shown on graph windows, which was rescaled after the kinetics platform was opened.
• Fix the Y axis scale (numbers) on Kinetics analyses performed on transformed parameters.
• Empty templates that are re-saved will not crash FlowJo.
• Concatenating 32-bit floating point files now works.
• MultiSample comparison platform can use calibrated or compensated parameters without crashing
• Double clicking on an overlay legend presents correct dialog window
• Adding samples to a workspace when a "live" group is currently shown will not add the samples to that group unless they belong
• On OS9, you only have to agree to the license terms once
• Create group dialog wouldn't show reagent panel of last tube in workspace
• Synched group gates will synch at all levels (was only working for top-level gate)
• Click on any page boundary in layout view to properly resize
• Open original node from layout view: axes & labels are shown even if they were hidden in the layout graphic
• Offset overlayed histograms when a minimum scale value >0 is chosen will be properly displayed.
• Handle DiVa 3.1, 4.0.0, and 4.0.1 data files that incorrectly specify the compensation matrix
• Fixed: cell cycle model statistics calculated on derived parameters
• Fixed: reading old workspaces with cell cycle analyses in the groups
• Fixed: error that arose when layout overlay legend items were grouped separately from the parent graph
• Fixed: Slight scaling problem that happens when printing in Landscape mode, causing pages to be broken in the wrong place
• Fixed: Reading workspaces with cell cycle analyses at the group level.
• Fixed: Ability to read data files by FTP that are larger than 100 MBytes.
• Printing from layout view does not change aspect ratio of plots
• Occasional corrupted workspaces occurred when cancelling layout generation no longer occurs
• Group versions of Proliferation and Cell Cycle analyses which specified constraining ranges are now properly saved in workspaces
• Resizing graph items happens properly when "suppress live updates" preference is set
• Fixed: Workspaces with cell cycle or proliferation gate regions on compensate parameters can now be read without crashes
• Fixed: Annotation information for overlay graphs is complete (some items were missing)
• Fixed: OS9.2 no longer gives an error when creating a new compensation matrix
• Fixed: DiVa 32 bit files with compensation matrices are no longer improperly compensated upon the second reading of the file (only happened with large data files)
• Fixed: Exporting data files with acquisition-defined compensation matrices will no longer cause confusion when re-loaded into new workspaces
• Fixed: OS9 crash for layouts with cell cycle or proliferation graphics
• Changed: Histogram smoothing for very low event numbers slightly changed; equivalent pre-version 4 smoothing
• Fixed: Crash when saving a workspace that has group cell cycle or proliferation analyses with constraining gate ranges
• Changed: FlowJo can now find files that have been moved to a different parent folder after being shown once.
• Fixed: If you cancel a relocated file search, FlowJo will exit the batch operation more gracefully.
• Fixed: A bug that caused occasional random crashing; more stable now
• Fixed: An inefficiency that caused layouts displaying gate frequencies to be computed twice
• Fixed: The layout name will now always appear in printed header/footers as specified by "#batchname"
• Fixed: Problem that occured when trying us the multigraph overlay platform with 1-parameter files
• added support for Summit V4 compensation matrices
  

September 30th, 2003: Version 4.4.4 released
SUMMARY OF CHANGES SINCE 4.3.2

Important Notes:

• FlowJo now requires you to agree to licensing terms whenever you launch a major new version of the program. Please read and understand these terms.
• Workspaces saved with version 4.4 cannot be opened with previous versions of FlowJo.
• FlowJo 4.4 uses a different preferences file. After you launch FlowJo, you will need to enter your serial number and then set all of your desired preferences. The new file is named “FlowJo Preferences.plist” under OSX, and “FlowJo v4 OS9 Preferences” under OS9. (instead of “FlowJo v4 Preferences”). On OSX, FlowJo now users Apple’s built-in Preference Manager for better performance and consistency. This Preferences file can now be directly edited just by double-clicking on it; however, we do not recommend this as FlowJo may not be able to recognize the values you change.

Major New Features.

• New Printing Model. Printing layouts and layout outputs has been completely revised. One of the best ways to see how this functionality can be used is to create a “Tiled View” batch report, and choose to Print this view—the new interface will show you the various options you have. These options are also available when you choose to directly print a batch output.
• The new printing model has enhanced the speed of performance in the Layout Editor, as well as printing itself. In older versions of FlowJo, the Layout Editor would have to query printer settings for many operations (ex. drawing page breaks).
• Importantly, you no longer need to (or can) do “Page Setups…”. Rather, FlowJo will automatically adjust printouts to whatever printer you select when you print. By default, FlowJo will also automatically position your graphics to fit best on each page (i.e., Portrait vs. Landscape, centered, and sized as large as possible). There is a new interface that lets you exert complete control over how you want the outputs to look—including the number of panels per page, the orientation, whether or not to suppress headers and footers, etc. The “Page Setup…” command from the Layout Editor now lets you select only whether you wish Portrait or Landscape mode, and whether you want headers and footers printed. Note that when you click to resize the page boundaries in the view, FlowJo will switch between Portrait and Landscape mode automatically as needed. Printing is now a breeze!
• In addition, printing of Workspaces and Tables is also completely revised. These are always scaled to print no more than one page wide (although they can be several pages long). FlowJo chooses the best layout to print this abular data; no “Page Setup” is needed. Finally, printing of analysis platforms and graph windows is significantly improved along the same lines.
• All printed pages can be customized through the Preferences selections. You can define a variety of header and footer information (for example, the user, computer, date, time, workspace, layout name, group name, etc.) as well as a graphic that is to be displayed within each header, footer, and/or body of every printed page!
• Template functionality. The functionality of template workspaces is significantly improved. Previously, when you created a template workspace (and all samples were thereby deleted from the workspace), FlowJo would no longer be able to remember attributes about those samples which helped it define complex layouts. This has been changed—FlowJo now records all sample attributes in workspaces even after files are deleted.
• Synchronized Group Gates. Groups now have a new attribute, a checkbox that can be selected in the group efinition window, labeled “Synchronize Group’s Gates.” When this is set, anytime you move, resize, or otherwise change a gate that belongs to this group, then all samples will automatically get the updated gate. (Note: if you select the preference to “Recalculate Immediately”, then this can slow you down significantly while FlowJo updates and recalculates all gates for all samples… you might consider changing the preference to “Recalculate Only When Needed”. This preference is in the “Workspace” set.)
• Multiple Graph Windows per Subset. You can now open up additional graph windows to show different views of the same subset simultaneously. After opening a graph window for a subset, you can choose to “Open New Window” (under the graph menu). Each window is fully functional. The graph window has a new button (“plus” sign) that will automatically open a new window of the same population.

Other New Features.

Preferences.

• New preference to show all FCS keywords in lists by default
• Removed the “Use Large Dots” preference; the “high resolution” setting now controls whether or not all dots are drawn small or large (for dot plots, density plots, and pseudocolor plots).
• You can now define header fields in addition to footer fields for graphical printouts. Up to 6 fields each can be displayed. You can have each field show a variety of values, including things like the current date, the workspace name, your username, your computer’s name, etc.
• In addition, you can define graph images to be displayed as the background within the header, footer, or body region of every printed page. These must be loaded from graphics files saved in “PICT” format.
• You can now choose “Direct Print” as the default destination for batch graphical outputs.
• Default preference for reading 32-bit data: SS is left as linear.
• New preference to define which parameters should be left as linear when converting 32-bit data files.
• Memory monitoring preference removed.
• Default graph window size preference removed.
• Interlaced graphic output preference removed.
• Export histogram data as text preference removed (it’s now a separate menu command).
• On OSX, a FlowJo serial number is stored in the system preferences so all users can access it.
• Gate annotations (drawn by gates) can be the gate frequency and/or the name (previously, the name could only be displayed if the frequency was).
• Correctly saves application to launch for tables and layouts
• Saving graph style preferences (like high resolution, etc.)
• Layout annotation boxes show population frequency when desired
• In Demonstration mode, gives proper error message when reading non-demo files

Editing Groups.

• Selecting “Apply changes”, “Cancel”, or “Create Multiple” all perform their function and then close the window immediately, rather than forcing a two-step process (unless a box is checked to keep the window open).
• Groups can now have “synchronized gates”… see above.
• Changing the criteria for which samples should be included in a group will now cause samples that don’t match the criteria to be removed from the group.
• Keyword value search & match operations are now case-insensitive.
  

Layouts.

• Newly-created empty textboxes are deleted (they were invisible and caused hard-to-diagnose layout sizing issues).
• View scrolling speed is increased for large layouts.
• You can now choose to output a batched graphic directly to the printer, without having to go either to a new layout or to a “Tiled View” for previewing.
• Printing is dramatically improved… see above.
• Gate annotation can include name or frequency—can be set independently from preferences.
• HTML batch output files are named according to the specific batch iteration value (rather than “image###”).
• Movies output files are given a suggested name from the batch rather than “untitled”.
  

Tables.

• Printing of tables is dramatically improved… see above.
  

Graph Windows.

• Gate drawing is improved (no more lines on the edges)
• New menu command, “Copy as Text” under the Edit menu, will copy the univariate or bivariate data to the clipboard as text for pasting into a spreadsheet. Data can be exported as columns (x, y, z) or as a matrix of counts (z only).
• A histogram annotation (frequency and/or name) can be positioned anywhere, not just above/below the gate.
• Printing from the graph window is improved.
  

Workspaces.

• Dragging a Finder folder into a workspace will add any data files contained within folders of folders.
• Adding folders of data contained within other folders will create group names that reflect the folder hierarchy.
• Printing is dramatically improved… see above.
• The sort order of samples is preserved in saved workspaces.
  

Analysis Platforms.

• Printing from the Cluster platform now generates a second page with the cluster information table.
• Exporting (print, copy, save) from the MultiGraphOverlay platform will include the legend identifying subsets.

Templates:

• No longer show old (removed) files in layouts
• Can save empty templates
• "#groupName" tag in headers & footers properly filled
• Frequency of Parent statistic in layout now correctly updates even if there is no node for that statistic present
• Sample selection popup in Kinetics and Cell Cycle window does not crash

Bug fixes.

• (4.4.1) Fixed bug to allow printing more than one page from layout view.
• Occasional font problems have been fixed.
• Corrected a bug that would sometimes display negative values for percentages in quadrants only while dragging a potential quadrant gate around a graph window.
• Proliferation platform: Copying graphic to clipboard is easier (before, once you adjusted the number of peaks, the copy command would always copy the edit field’s number; now, you can click in the graph to ensure the graphic will be copied).
• Using a large font size for layout graphs no longer causes uncontrolled graphic resizing problems. Hint: if you wish to display large fonts for axes labels, then choose to hide axes numbers in the layout graphs to allot more space for the label.
• Adding a graph to the layout editor copies the current state of the “show grid” option for that graph.
• Fixed a bug that pinned most events on the axis, of a ratio computed on 32-bit data (DiVa export data).
• Fixed a bug that caused problems when layouts of empty template workspaces were viewed.
• Fixed a bug that caused blank workspace displays with more than 32,000 samples and gates (now that is a power-user!).
• Proliferation platform now works with 32-bit data files (e.g., DiVa).
• Fixed a rare bug where a crash could occur if a workspace display column was added, removed, and then added again.
• Fixed: gates that were modified through group operations didn’t always immediately show the frequency on graphs immediately.
  

June 9th, 2003: Version 4.3.2 released
SUMMARY OF CHANGES SINCE 4.2

Major New Features:

• FlowJo now gives you the option of displaying your data using a transformed scale that provides a much more intuitive distribution! This is particularly important for compensated data, where negative values can arise. For more information on this exciting display option, please visit our display transformation web pages.
• The newest version also reads in compensation settings defined at the instrument—so if you export raw data (and the software saves the compensation settings), FlowJo automatically compensates for you. You can still define your own compensation if you need to override the original.
• Finally, FlowJo’s compensation interface provides better support for the use of“antibody-capture” beads in compensation (see below).

New Features:

Workspace:

• Workspace file version changed… therefore, workspaces saved with 4.3 cannot be read by older versions.
• There are new buttons in the workspace window and Table View window that will auto-resize columns to fit the contents (same as option-double-click column separator bars).
• Creating groups: a criterion based on a value found in any keyword can be selected to define a new group.

Compensation and data transformation:

• Acquisition-defined compensation matrices are used if present.
• FlowJo warns when lots of events are on channel zero in bivariate plots. New preferences control how many events need to be on the axis before the warning is displayed.
• The compensation definition window has a slightly different look to make it more useable.
• The“auto-assign” drop box in the compensation definition window will now accept a population that has either one or two child gates. If there are two, it assigns one as a negative control and one as a positive control (as it has previously). If there is only one child gate, it assumes that it is the positive control.
• If the data files are raw (floating point) format, then any area parameter will be displayed using a minor transformation to allow the display of negative values.
• When you use the“multi-comp” feature (i.e., dropping a gated sample that has single-stained controls for all colors mixed together), FlowJo will now present a dialog in which you select which parameters are to be compensated. In addition, this feature better finds the individual controls.

Proliferation Platform:

• You can now create overlay of CFSE vs all parameters for gated peaks—just click on the“overlay” button after creating gates.
• Peak numbers are now optionally shown on the graphic.
• If computation of the model fails, the platform gives an explanation in the statistics table.

Graph Window:

• In Graph windows: cmd right arrow = next sample, cmd-left arrow = previous sample; cmd-up arrow = parent; cmd-down arrow = drill down on a select gate

Preferences:

• Preferences->Workspace text changed to better help with "Sample Identification" options
  New preferences:
• You can ask FlowJo to let you know when there is a new beta testing version available if you are using the commercial release version (this happens automatically if you are running a beta version already).
• Define the threshold percentage of events on the axis in a bivariate plot to bring up a warning dialog (default = 2%) or graph window warning (8%). If you never want to see these warnings, set the threshold to 100%.
• You may disable showing subset frequencies in the workspace.
  Preferences removed:
• You can no longer re-open graph windows automatically when reading in workspaces.
• GIF is no longer an option for saving files.
• Automatic gate tinting preference removed

Miscellaneous:

• Reads floating point FCS data files.
• Better grid line position selection
• The Time parameter is now rescaled to be shown in much better detail on graphs (i.e., the graph is "zoomed" with regards to time).
• FlowJo now tries to get help from the internet site first, even if you have a local copy of the documentation—to make sure that you are getting the latest help possible.
• FlowJo automatically disables“symmetric multiprocessing” for operating systems before 9.2.
• FJML (e.g., <key $tot>) fully supported in the editable box of LE annotation items
• Layout grids by default: force contents to resize, don't adjust to new drops.
• Statistics window has "close" button.
• Dialog windows (like renaming gates and so forth) are now opened on same monitor as front-most window; before, they would be placed on the main monitor.

Bug Fixes:

Layout Editor:

• Tiled report printout no longer puts workspace name with layout name in footer field #batchname. Layout text box editing properly sets up scroll bars.
• "Freq of: " statistic now works in batched layouts.
• Scale to page functions in layout editor (layout view and tiled view) now properly reflect page size at any magnification (previously, at very low magnification, page boundaries were not drawn exactly right).
• Empty text boxes don't prevent tiled report generation.
• LE Annotation items are better sized in batch outputs (to include all text!).
• Overlay graphs in layout editor that aren't dot plots now maintain their type instead of resetting to dot plots.
  Layout grids now save the state of certain flags (like auto-resizing).
• Fixed: If a layout had a grid with a graph whose annotation was not in the grid, then canceling a print of that layout caused a crash

Workspace:

• Auto-incrementing workspace version numbers don't roll over from 100 to 1... they go to 999.
• Editing an annotation (keyword) in the workspace will now make a sample re-add to live groups if possible.

Kinetics:

• Fixed an occasional crash when cycling back or forward sample.
• No longer crashes when selecting a file in the pulldown arrow of kinetics graph window.
• Adding gates to kinetics grows window instead of shrinking graph.
• Changing axis of kinetics doesn't change label in layout.
• Layout editor overlay graph now updates when gates are adjusted.
• Kinetics“time slices” no longer turn blue when copied to new node.
• Time slices no longer obscure graphic when exporting.
• Cell cycle: Now displays correct X axis name the first time it is launched. Copy/paste exported axis labels only once.

Proliferation platform:

• Creating gates based on divisions now properly takes into account background parameter.

Graph Window:

• Enable/Disable tinting (under edit menu) didn't work if graph window was foremost

Derived parameters:

• Deleting derived parameters (from edit parameter dialog) no longer crashes
• Can no longer select a derived parameter as an input to make a new gain/offset parameter
  Preferences:
• 32 bit options dialog doesn't throw an error in OS9.
• Default gate color is now obeyed. Select the default gate color to“N” to have FlowJo automatically change the gate color according to the graph type.

Miscellaneous:

• Concatenating gates which hadn't been computed no longer generate improper FCS file.
• Choosing to replace an existing file when outputting concatenated files will now actually do so.
• Concatenating samples with compensated parameters does not export the compensated parameters—when reloading this file, just assign the appropriate compensation matrix to it.
• Exporting files that end with sequence numbers is now handled properly.
• Splash window correctly displayed during startup. Cache management made far more efficient; bug associated with caching files fixed. Gates are always drawn as closed polygons (even if segments are off the graph).
• Fill & line color of layout boxes and textboxes is not lost after saving
• Cell Cycle models: range constraints are initialized in menus when re-opening window
• Cell Cycle does not crash when you move a constraining region
• Compensation: Autoassign function doesn't bring up erroneous message
• Log contour plots don't crash
• Dragging table editor items to a different WS table editor no longer crashes (and is not allowed)
• Create group dialog properly sets FCS keyword attribute menu values when editing an existing group
• Layout editor annotation box boundaries are set better
• Proliferation platform doesn't recompute for tables if already valid
• Occasionally, gate frequencies wouldn't be drawn in graph windows until the next action
• A bug that could cause "random" crashing when closing computing items (like windows, platforms, etc.)
• bug that caused batch layout crash if a graph didn't exist for subset
• bug that caused crash when recalculated command issued on a sample node
• Correctly display forward scatter on DiVa-exported "experiments" saved as workspaces
• Network site licenses will validate network connection on multiple sites (not just Treestar.com)
• Magnetic histogram gate algorithm improved dramatically
• $PnV (voltage keyword) is shown in keyword menus
• Can export floating point FCS files
• About box shows IP address
• CFSE modelling algorithm improved
• Future date and version checking turned off if program is force-quit while date checking hang
• If defining a visual transformation, and your preference is set to not use transformations, FlowJo will ask if you want to override it!
• Platform statistics tables created in layout editor are now placed to the right of graphs rather than below (to avoid overlap)
• Fixed CC: Doublet removal & debris removal crashes
• Fixed occasional crash during edit colors in LE overlay item
• Fixed: Handling time parameter scaling in DiVa data files
• Default pref is to not check date/version

October 11th, 2002: Version 4.2 released.
SUMMARY OF CHANGES SINCE 4.1.1

IMPORTANT NOTES

• Workspace file format has changed: workspaces saved by this version cannot be read by older versions of FlowJo.

Major New Features:

• Graphs have several new features to make them more aesthetic and meaningful. You may choose to show
  a light background grid to help guide interpretation of the distributions.
• In the Layout Editor, grids can be turned on or off for individual graphs.
• There are new preferences that give you more control over how gates are displayed in graphs: you can choose a uniform specific color in which all gates are drawn, you can draw gates with thicker lines, and you can choose to annotate gates with the gate name (in addition to the frequency). Finally, we now support the ability to show "outlier" dots for smoothed pseudocolor, density, and zebra plots (approximately 2% of all events will be shown).
• The MutliGraph Overlay platform has a number of new options to automatically show your data in a variety of ways: For example, all parameters vs. all others (with or without histograms, or only fluorescence parameters); or one parameter vs. all others.
• FlowJo will now check the Tree Star web site to see if there is a new version available! This way you can be sure to have the latest free upgrade with new features and bug fixes. (If you wish, you can disable the automatic checking via a preference setting; however, we recommend that you leave it on so that you are immediately aware of any bug fixes or new features).

Other New Features:

General:

• The "About FlowJo" window shows how many days are left on the serial number (if applicable)
• Added more helper text to identify fields under the mouse
• FlowJo's cache folder is now created in the User's cache folder (OSX) or in the Temporary Items Folder (OS9)
• Support for "scroll wheels" available on some types of mouse

Workspace:

• Save as template: by default, the new file name ends in " template"
• Can choose "Show Histograms" from any selected gate
• New workspaces suggest a ".jo" ending for file names. Files ending in ".jo" will automatically launch FlowJo as their application
• While editing a keyword field, you can now choose menu items (may need option key) to:
  (1) Create a new group containing samples from the current group with the same value of
  the keyword you are editing
  (2) Create a series of new groups, each containing those samples with equivalent values
  of the keyword you are editing
• Option-click in the header of any column sorts the workspace by that column's values
• Can now create "concatenated" files, in which several files (or gated subsets) can be exported into a single file.If there's a time parameter, then it is modified to show the relative time since the first event of the first file in the series
• Exported files that are too large for FCS2.0 format are created as FCS3.0 files

MultiGraph Overlay

• The "Set up graphs" menu has many new options, including the ability to show all parameters against
  all parameters, to show only fluorescences, or to show one parameter against all others
  

Graph Window:

• Will display grid (if preference set)
• Can now show outlier events for smoothed pseudocolor, density, and zebra plots
  New menu commands (or use option-arrow key) to shrink or grow selected gates

Preferences:

• "Draw dots as circles" renamed to "Draw dots as filled boxes", and moved to export graphics area
• A new preference to specify whether or not to draw grids on graphs, as well as how dark or light the grid should be ("contrast"). Note: this preference will automatically apply to all graph windows, and to all NEW layout graphic items.
• Old layout graphs will not have the grid unless individually specified
• You may now specify whether fluorescence channel axis names should include both the channel name (e.g., "FL1") and the stain name (e.g., "CD3"), as has been the case, or to only show one or the other
• The "Use Large Dots" preference now applies to pseudocolor and density plots
• You may now choose to annotate a gate with its name in addition to the frequency on graphs
• You can choose a universal default color to use for drawing gates, as well as a thicker pen width
• You may choose to disable automatic new version checking

Layout Editor:

• 3D histogram overlays: Default angled offset changed to 10 degrees
• Deleting a layout automatically makes a different layout active
• You may now duplicate a layout ("=" button)
• You may now choose Histogram or CDF from the Y axis popup menu
• Several new line widths for histogram overlays can be chosen
• Several new line widths for boxes & lines can be chosen
• The layout editor is not automatically re-opened when opening a workspace
• A background grid can be turned on or off for individual graphs (independent of the Preference setting)
• The default color order for new overlays has been changed to Red-Blue-Green (from Red-Green-Blue)
• Adding a new layer to an overlay selects an unused color if possible
• Choosing "Avoid Page Breaks..." will resize the page if any of the items wouldn't fit on a single page

Table Editor:

• The Table editor is not automatically re-opened when opening a workspace

Compensation:

• New "drop" boxes that allow you to (1) drop a single negative control that applies to all
  samples; or (2) to drop a single samples that has a mixture of single-stained populations
  (currently, will work best with bead compensation sample).

Cell Cycle:

• Automatically selects the first linear fluorescence parameter when first created
• Choosing to overlay a statistic automatically turns on the Overlay Statistic Graph feature

Kinetics:

• A new button under the graph will create multiple time slices spanning the entire data collection

Derived Parameters:

• A new function, "Sum of 2 parameters" is available

Data Export:

• When exporting less than the total number of events, events are selected from the entire data set
  (Previously, only the first "n" events were exported)

Population Comparison:

• Changed "ChiT" to "T(X)" in windows to be consistent

Bug Fixes

General:

• Rarely, resizing a window caused the window to grow enormously--now resizes properly
• Browser launching for help buttons fully working. (Note: in OS9, IE is always used; in OSX,
  whatever Browser is specified in the System Preferences is used)
• Double-clicking a workspace opens that workspace when FlowJo is launched (previously,
  it was only opened if FlowJo was already running)
• Scrolling controls no longer "jump" to slightly different positions than desired
• Fix handling of parameters that have colons in their names (Cytomation)

Layout Editor:

• When adding item to grid, on immediate double click on item, was unable to change attributes
• Exporting graphics to Canvas 8 (etc) as "vectors" (rather than bitmaps) now works
• The Y axis is not labeled on offset histogram overlays\
• The X axis label is drawn at normal resolution for 3D histogram overlays
• Dotted and dashed lines now work for 3D histogram overlays
• Creating an overlay no longer resets the color of the first layer if it had been changed
• The multi-item inspector dialog correctly turns off "show count", "show graph title", and
  "show ancestry" features if specified

Table Editor:

• Deleting a row from an output table no longer resizes the columns
• "Print" menu option is disabled until you are actually viewing a table

Population Comparison:

• The "?" button now stays at the bottom left when the window is resized

Cell Cycle Platform:

• The statistics table is properly sized when the window is first opened
• You can now delete a range that isn't being used by the constraints
• The constraints menu no longer resets its value to something incorrect on a subsequent click

Workspace:

• Relocating moved files only asks once (per directory). In addition, when FlowJo now asks you
  to locate the original file, you must select the exact file (previously, you only needed to select any file in the same directory)
• You may now choose any application to launch for statistics or graphic output, and the
  applications are properly launched

Graphs:

• When copying a histogram to Excel, the data rather than the graphic is pasted (unless this preference is turned off). Previously, Excel would pick out the graphic instead
• Graph movies of histograms showed all events in every frame; now they show the correct subset of events
• When changing to manual scaling for histograms, the min & max fields are filled in with correct values

Statistics:

• Selecting "Frequency of..." requires a population to be selected from the popup before it is added

August 18th, 2002: Version 4.1.1 released
SUMMARY OF CHANGES SINCE 4.0.2

Important Notes:

Workspaces created by FlowJo version 4.1 cannot be read by FlowJo Version 4.0 and older.
However, FlowJo version 4.1 can read workspaces created by all previous versions.

Changes since 4.02

Major:

Multiprocessing!

• FlowJo now takes advantage of the Macintoshes capability to do multiple calculations simultaneously - Symmetric MultiProcessing (SMP). This feature is most significant on Macs with more than one processor (e.g., dual-processor G4 computers), where you will see FlowJo speed along almost twice as fast while it does compensation, gating, or statistics! Even on single-processor machines, FlowJo takes advantage of SMP to compensate while it reads a file from disk--reducing the effective compensation time to zero. TreeStar is proud to be the first flow software manufacturer to take advantage of SMP to enable users to spend more time analyzing data and less time waiting for the computer!Multigraph Overlay Platform
  The multigraph overlay platform can now show contour plots (with or without outliers). This is makes large data files easy to analyze with this platform.Changed the balance between computation and monitor/refresh toward computation. This significant increases the analysis throughput (speed) of FlowJo.

General:

• Checks the version of the CarbonLib file on your computer (version 4 requires CarbonLib 1.5 or greater to run in OS9).New preference to disable SMP. Restart required to effect this change.

Workspace:

• The Workspace column editor dialog allows you to create new keywords for immediate display as columns.
• Double clicking the workspace column divider resizes the column widths by taking into account the width of the column header as well as the column values themselves.
• If files are relocated, and there are multiple files with the exact same name in the workspace, then FlowJo asks for confirmation to check if the correct file is being read.The Group create dialog - if you click below stain list it now unselects all and the outline/shadow for font no longer shown in menu.

Graphs and Gates:

• You can manually enter quadrant gate values; or create multiple gates manually.
• Histogram scaling options (manual or auto) have been added to graph window choices.
• A new preference has been added to define how many significant figures to show for the gate frequencies on graphs.
• Scientific Notation is no longer used on axes labels in a linear scale.
• Dot plots and contour plots are now always drawn with maximum pixel resolution--for better resolution when enlarged.Setting Gate color to "N" (none) restores it to the system default (i.e., the color of the gate adjusts to be maximally different from the graph background color).

Layouts and Tables:

• The interface for choosing control samples when iterating overlayed samples has been clarified.If summary statistics (mean and SD) are calculated for a table (preference is on), then summary stats are included when the table is exported to a spreadsheet program.
• Moving a gate's frequency immediately repositions the frequency on plots in the Layout Editor.
• Scale to tile is fixed in the Layout's Tiled view and scale to page automatically avoids page breaks.
• Can click (select) and press delete (or edit->Clear) to remove rows from tables (summary stats are recalculated).
• Can now put FJML into Layout Item annotation (like keyword values!)Annotation copied from annotation column of workspace iterates properly (only true for NEW workspaces.
• To make it work for old, type "<Annotation>" into the annotation box of the layout item).
• The "Show Histograms" command (under the Graph menu) now launches an overlay node showing histograms.
• You can now set the text attributes for the Annotation and Legend items (by double clicking on item or Get Info).

Platforms:

• Proliferation platform draws components (individual generations) by default.
• Multigraph Overlay platform now prints scaled to a single page.
• Cluster platform now prints scaled to a single page.
• Uncompensated parameters are now hidden in menus - press the option key to show all parameters.

Bug Fixes:

• Fixed exporting of files that were originally read in as FCS3.0 files.
• Fixed a bug that could cause a crash while moving a gate in the graph window.
• Fixed reading multicolor background gates from workspaces.
• If there is no printer initialized in OS9, then FlowJo asks to Choose a print driver instead of crashing.
• Clustering can now be performed on compensated parameters.
• Fixed rare crash during clustering caused by allowing uniform peak division.
• Initial drawing of the graph in the proliferation platform is now correctly drawn.
• Improved the "Set Annotation" dialog window.
• Printing workspaces and tables now functions properly.
• Gates on angled overlay histograms are now hidden to avoid distortion.
• Moving a gate's frequency on small or large graph window properly repositions the number.
• When aligning graph objects in the Layout Editor - the annotation and legend items are properly repositioned.
• Changing axes while a graphic is computing no longer generates a file reading error.
• The Layout Editor item dialog doesn't cause program to hang if tasks are executing.
• Manual gate entry now works properly if graph window is not "normal" size.Fixed: bug that can cause crash while adding statistics to a workspace (in OS9).
• Option-double clicking in the Layout Grid properly creates a text item.Cluster platform finishes clustering before closing to prevent crash.
• Overlays of graphs can be created within grids.Dashing now works as an overlayed histogram line option.
• Fixed a bug that crashed if you tried to copy ONLY an annotation or a legend item.
• Fixed a rare crash when "show history" was chosen for a graph in the Layout Editor.
• Saving graphics as PICT files to disk now saves the file in a vector rather than bitmap format (had to overcome an Apple "feature").
• When you drag cell cycle node to a group, the model is not invalidated.
• Unselected gate tinting no longer resets the gate color to system default.Page range for printing from the layout editor is now correct.
• Fixed: Show ancestry--history graphs show axis labelsFixed: Define default gate names (Preferences) doesn't cause problem in OS9
• Fixed: Print from layout editor in OS9
• Fixed: In Layout Batch View (Tiles), setting page scaling manually (Page Setup...) now works
• Fixed: Launch help browser in OS9
• Added preference for default legend position
• Fixed: Histogram gates don't show frequency if preferences is to not show frequency
• Fixed: Movie platform initializes default parameter menu and doesn't crash if no selection made
• Added in preferences field for layout/table name in printouts ("#batchname") (this is now default, but for existing users, they have to either add it or select default preferences)

Known issues that will be addressed soon:

• dashed & dotted liens don't work in offset overlayed histograms;
• Y axis should be hidden in overlaid histograms;
• all scrolling thumb controls, when released, are off by some amount; LE manually changing page size changes paper type to "other";
• plus a few other more minor things.
  

May 21, 2002: Version 4.0.2 released.
SUMMARY OF CHANGES SINCE 3.7.1

Important Note:

• Workspaces created by FlowJo version 4.0 cannot be read by FlowJo Version 3 and older.
• However, FlowJo version 4.0 can read workspaces created by previous versions. Click here for upgrade information.

Major:

• Carbonization for OSX: now you get the beautiful new Aqua interface and OSX functionality!
• Supports new Hasp USB dongle. Version 3 users will need to swap keys when upgrading to v4.

Major new platforms:

• Cluster Platform - this exciting new algorithm, developed by Dr. Mario Roederer, finds subpopulations for you.
• Multiple Graph Overlay Platform - overlays subpopulations and displays multiple views of each sample.
• Multicolor Background Gate - calculate
• Remote (FTP) Easy navigation for reading and saving Workspaces stored on a remote server. Reads data files stored remotely.Color palettes and default color choices are expanded to include 16-bit color. You can now specify the fore and back colors on graphs.

General:

• Save graphs and reports in new file formats like Photoshop and PNG (use the Preferences to change the default file format).
• Clip2Gif is no longer needed to export graphics in non-PICT file formats.
• New USB dongles work in OSX (click here for more information about dongle compatibility, exchange, and installation).
• Network dongles will not be supported with Version 4 (contact us for other licensing options).
• Command-key binding changed dramatically
• A new menu item under the "FlowJo" menu opens serial number dialog (request trial SN, register SN or enter SN)
• In OS9, memory info shows memory remaining; in OSX, the memory allocated to FlowJo is displayed.
• New option to automatically save Workspaces as different versions (invoke with the Preferences); this option is not available for remote Workspaces.
• When naming a gate you can add the name to a permanent list (that you can choose from in future sessions); otherwise, each name is saved in the pulldown menu only for this session (until you quit FlowJo).
• FlowJo remembers a previously typed gate name and fills in (predicts) that name the next time you type in the first letters!
  

Preferences:

• New preference creates a New Workspace upon launching FlowJo (the default = yes).
• Changed the default Preference to show table summary stats (mean and standard deviation calculation for each statistic).
• A new preferences file (FlowJo v4 Preferences) is created upon the first launch of v4, set all your preferences!
• New preference added to determine the % of physical RAM to use in OSX.
• Now you can define the content of the footer that appears at the bottom of printed reports from the Layout Editor.
• Selecting "Default" preferences resets the workspace view to default as well.
• Added the ability to choose the colors for overlays in the Layout Editor.
• Removed the #colors preference for JPEG/GIF/TIFF output options.
• Graph window size preference changed (resizeable replaced by "large"). All graph windows show the same information and are resizeable.
• Added new "Text" panel to Preferences (you can change all the text attributes at once!).
• Adding "event number" parameter is now a Preference (when set, will add to subsequently opened samples).
  New Preference gives the choice of adding a stats table to the graphic when a platform node is dragged to the Layout Editor.
• Can now create new samples names from the concatenation of other keyword names (in Preferences).
• A new Preference allows the use of the System Keychain if desired for remote operations.
• Has "Default" button (works the same as menu operation).
• Can define default fore and background and axis colors for graphs and layouts.

Workspace:

• Remote samples: keywords created for URL, server, and path (#File_URL, #File_RemoteServer, #File_RemotePath)
• Create group: fixed comparison of keyword values when non-numeric (i.e., >, <, etc)
• Dragging within the workspace is far more efficient.
• Double click column separator bar (vertical bar) to resize column; option-double click to change all columns.
• Create Value Series has been made even more powerful: Now starts from the currently-edited value (rather than the first in the group)
• Can specify how many values to fill.
• Can specify a replication count.
• Shows the first several values in the series as you edit.
• No longer shows free memory monitor.
• When adding files to workspace, live groups operate in alphabetical order (previously, no defined order).
• Can select multiple files (or folder of files) to add from the "Add Samples" dialog.

Remote file operation (FTP):

• Can navigate FTP (NT) server to add data files.
• Can open/save workspace to FTP server (NOTE: multiple copies of same Workspace could be open!)

• Renaming a parameter stain (via edit) now updates window popup menu list immediately.
• Better navigation while editing keyword fields.
• Fixed a problem where creating a new gate on population that comes from a group would set that population no longer to be owned by the group
• Fixed: Edit->Select Every nth now properly selects every nth sample in the current group rather than every nth sample in the workspace

Statistics:

• Added % of any ancestor statistic (no more grandparents!)

Compensation:

• Matrix file is now saved as SimpleText file.
• Option for background gating information storage (read documentation carefully).

Movies:

• Graph movies can show gates and gate frequencies frame-by-frame.

Groups:

• Group create dialog remembers previous state (disclosure triangles).

Table Editor:

• Bug fix: Populations with commas in their name led to bad table column titles.When editing column names, hitting return/enter goes down to next one (shift- goes up)
• Table report asks if you want to save before closing (if output was not saved).
• Table output: double clicking on a column bar in the title autoresizes column (option-double-click to resize all columns)
• Now confirms before deleting a table.

Population Comparison:

• Feedback display during chi T cutoff selection improved (flicker, value jumps removed).
• Fixed: If new control node is set, then layout statistics automatically update.
• Fixed: If shown in Layout, automatically updates as graph window is modified.
• "Bug": When switching multivariate/univariate view: stats are not automatically recomputed. Layout editor view will be wrong (if switching to multivariate; LE can't show multivariate)

Graph Window:

• Histograms and CDFs plots are drawn as polygons (no longer ungroup to elements).
• Graph tools floating window removed (tools now on Graph windows).
• Inverted graph option removed (choose the background and foreground colors yourself!).
• Can change foreground/background colors (if changed, prefs don't affect anymore for that graph).
• Note that tinting of gates is optimized for black or white backgrounds.
• "Grayscale" Density and Zebra plots are now drawn according to foreground/background colors (can be weird!).
• Fixed occasional random crash when redoing a polygon gate.
• Complete change of graph window: Tools, etc are now onboard.
• Ellipse gates are now free-rotating (click & drag, then resize).
• Calculating graphs are dimmed.
• Gate annotation shows % of parent rather than % of total (consistent with number in graph).
• Bug Fix: first gated event would not be drawn in a dot plot (but would in all other types).
• Option-sample select from graph window (popup menu) changes all open graph window to that sample.
• Always resizeable (zoom button switches between 4 good sizes).
• First quad gate on a population does not request a prefix.

Magnetic gate fixes:

• If magnetic gate was created on sample level and had no events within the gate, would not move.
• Create new magnetic gate: would move, but % displayed on graph would not immediately update.

Layout Editor:

• Fixed: When iterating an overlay histogram with multiple samples, discriminator now works.
• Keystrokes to align (L = Left, R = Right, H = Horizontal Center, B = Bottom, V = Vertical Center, S = Horizontal Distribute, D = Vertical Distribute)
• When creating a batched layout using a special iterator, the new layout's discriminator becomes that iterator.
• Can define footer contents in Preferences.
• Now confirms before deleting a layout.
• Preference for # of colors in JPEG etc. output removed (is always 16 bit).
• Can undo alignment operation.
• Selecting a tool changes the cursor to appropriate tool icon.
• Selecting "next" or "previous" sample will rotate to the beginning or end of list.

Graphs:

• Editable graph labels.
• Can separately hide ticks, numbers, or labels.
• "Apply" buttons in info dialogs (can set your changes without closing!).
• Can change foreground/background colors (if changed, prefs don't affect anymore for that graph).
• Inverted graph option removed (choose the background and foreground colors yourself!).
• Resizing graphs moves annotation and legend cleverly (to maintain relative position).
• Horizontal history is now default for "get history" option.

Overlays:

• Rotated histograms ("3D") (set angle to zero to get old style overlays).
• Overlays use colors as you define them in the Preferences.

• Live resizing of text boxes (easier to get desired result).
• Kinetics displays are much more efficient.
• Avoid cutting off graphs option implemented in layout view.
• When multiple graphs are dragged to Layout view, they are spread out better.

Cell Cycle:

• New window design.
• Can overlay in Layout Editor (without models drawn).

Kinetics:

• TimeTicks keyword is used to properly display time parameter (if present).
• Fixed range colors (for copy etc).

Proliferation:

• Fixed: "Copy Table" button works

Other Fixes:

• Supports non-standard time parameter generated by Summit (MoFlo)
• Fixes bug in launching Help page from the Help menu
• Fixes bug which created a file called "Leaks.log" whenever program was run
• Changed dialog for requesting serial number to include more options
• Improved appearance of path name in Graph Window (if you like purple text :)
• If locating a moved file fails, then layout editor turns on placeholders
• Fixes crash when drawing graphs in layout editor if an error occurred while opening the file
• Adjusted alignment of graphs by axis, so that they overlap exactly