FlowJo for Macintosh V8 - New Features
Major New Features:
• A new Compensation Wizard makes setting up compensation matrices fast, easy, and rigorous!
• A new AutoCompensation Scripting Platform allows you to define a script that will automatically find compensation tubes, analyze them, generate the compensation matrix, and apply it to the appropriate samples. For Templates, this is particularly powerful, as the script is applied whenever new data is loaded into a workspace. This can fully automate the compensation process!
• The Table Editor has been revised extensively. It is much faster, there are new custom-formatting options for output tables, you can create formula columns, you can output attributes such as gate coordinates or compensation matrices, and you can set iteration like the LayoutEditor to have the maximum flexibility in how textual output is created.
• Table and Layout definitions can be dragged (or copied)from one workspace to another to easily replicate.
• You can now choose Page Setup to define custom printed page sizes associated with the program and/or each individual Layout.
• There is a new Polyvariate graph tool that lets you display and gate on more than 2 parameters at a time.
• A new interface is available to help you create compensation matrices quickly and rigorously! Launch the platform by selecting “Compensation Wizard” from the Compensation menu. If you select the compensation tubes (or a Group of compensation tubes) in theWorkspace, they will be automatically loaded into the Wizard. Let it guide you through the process! (There are a number of short cuts that you can take to speed the process—specifically, creating a gate on each compensation tube to identify lymphocytes or singlet beads; and, if necessary, to create positive and negative gates for compensation tubes with mixed populations).
• There is a new method to tell FlowJo how to automatically find compensation samples, gate them, create the compensation matrix, and apply the matrix to experimental tubes. You can define multiple such scripts so that different matrices can be generated for different tubes. The script is automatically executed whenever new data files are added to the workspace (or template). This script can completely automate the compensation process. For a full description of the AutoCompensation Scripts, please request the documentation from Tree Star.
• Because of the significant new features and capabilities, the Table Editor has a different User Interface that provides access to these features. As well, there is a new “Table” menu that is specific for Tables, like the “Layout” menu is for Layouts.
• Tables now iterate like Layouts: you can specify an iteration attribute (default is to Iterate by Nth, n = 1) and discrimination attributes. This lets you build Tables where each row in the output table might take values from different tubes. (This becomes particularly powerful when combined with the formula editor, which then lets you compute values across samples, for example, averages, ratios, minima, maxima, etc.).
• You can now drag Tables from one Table Editor to another (click on the Table name, and drag to the new Editor). Alternatively, you can copy/paste entire tables between workspaces.
• Significant performance enhancements make building large tables considerably faster.
• You can double-click on the Table name to open the Information dialog for the table.
• You can double-click on a column definition in the Table to edit the custom formatting for values in that column, including the ability to hide a column in the output.
• You can create formula columns that are arbitrary mathematical (or string) operations performed on other columns in the table.
• You can add “attributes” of gates to the Table editor: for example, the gate coordinates, the magnetic gate offset, the compensation matrix, etc. A new menu in the Table Editor defines what is added to the table when you drag a gate into theTable Editor.
• You can now drag Layouts from one Layout Editor to another (click on the Layout name, and drag to the new Editor). Alternatively, you can copy/paste entire layouts between workspaces.
• You can double-click on the Layout name to open the Information dialog for the layout.
• The Information dialog lets you select a workspace Group to be used for Iteration for that layout.
• Layout Tables can display gate coordinates and magnetic gate offset vectors.
• Cmd-E (Graph menu -> Transpose Axes) can be used on graphs in the Layout Editor.
• Moving the mouse over and around Overlay Legends now provides much better feedback and responsiveness.
• You can choose “Select Equivalent Objects” under the Edit menu—this will automatically select all objects in the layout of the same type(s) as the currently selected object(s).
• In the “MultiItem Editor Dialog” (select multiple objects and double click):
1. You can select “Make Uniform”. This makes all overlays that are selected have the same color and line styles as the top-most, left-most overlay that is selected.
2. You can add keyword values to the annotations of all selected graphs.
• Newly-created Textboxes are automatically sized to the text that was entered.
• When editing the annotation for a graph item, you can enter carriage returns to space information better.
• FlowJo will not let you create a new batched layout that is too large for display or printing. When your batched output is this large, you should consider directing the output directly to printers or to the Preview function.
General:
• There are numerous performance enhancements, particularly for batch generation and for using workspaces with large numbers of samples.
• There is a new “Table” menu, that is similar to the“Layout” menu. Both Table and Layout menus have changed to reflect new capabilities and are better organized.
• Keyword selection dialogs now show sample keyword values for any selected sample, assisting in determine which keywords you wanted to choose.
• The Statistics Dialog window will not show “channel” based statistics unless the “option” key is depressed when the dialog is called up (via the “sigma” button). Channel-based statistics are rarely needed.
• Any graph (graph window or Layout graph) can now be turned into a PolyVariate Plot. This platform allows you to display information from any number of parameters, by offsetting events in a typical 2D plot along a diagonal of your choice by the amount of fluorescence on a third, fourth, etc. parameter. To edit the PolyVariate attributes, click on the clock icon that appears in the graphwindow, or select PolyVariate Plot from the Graph menu.
• You can now search for and replace keyword values (like a text editor’s search/replace function); this can be automated to perform a number of search/replace operations. This is useful for batch editing keyword values that need to be made uniform or corrected across many workspaces.
• A new menu item (Compensation->Import…) lets you import compensation matrices from other (open) workspaces. This makes copying compensation matrices from one workspace to another simple!
• When you select “Sort” from the workspace, the current sort order is shown so that you can make modifications.
• The menu item “Create Group From Keyword Value” can always be selected; if you are not editing a keyword value at the time, the dialog will ask you wish keyword you wish to use to create new groups from.
• You can show the gate coordinates and magnetic gate offset vector in the workspace as new columns.
• The indentation of statistics nodes has been increased slightly to improve visualization of the workspace list.
Workspace Groups:
• You can now choose to rename gates at the Group level—the renaming is propagated to every sample in that group.
• Stain name mismatching is no longer an option; samples with mismatched stain names will now always receive the group’s gates.
• New preferences:
1. Obey “PnDISPLAY” keyword. DiVa-exported data files have a keyword that tells FlowJo whether you would like a parameter viewed as Log or Linear scaling. When this preference is checked, then the value of that keyword over-rides any other preferences you may have set.
2. Custom larger sizes for dots in dot displays. When you select “low resolution” for displays that generate dots (dot plots, outlier plots, unsmoothed density plots), you can now have FlowJo generate even larger dots than before—custom size. This is particularly useful for displays in publications that are shrunk dramatically.
3. Default timeout on Notification/Confirmation dialogs. You can set a number of seconds that FlowJo will wait for a response when it asks for confirmation on an action—if there is no response within the specified time, FlowJo selects the default response and continues. (If the Preferences is set to zero [default], then FlowJo will wait indefinitely as before). This is useful to ensure that massive batch operations can run to completion unattended.• Preferences removed:
1. The preference controlling “Stain name mismatching” has been removed. Stain name mismatching is now always allowed.
2. The preference to turn off “Symmetric Multiprocessing” on multiprocessor machines has been removed; FlowJo will always take advantage of every processor on the computer.
• The menu item for transformation has been renamed to “Define BiExponential Plot”.
• The dialog for specifying transformations has a disclosure triangle to hide the parameters unless needed.
• If you change the advanced options for transformations, the new values are saved in the Preferences and are used for future transformations.
• Previously, when you created Boolean Gates, the gates referred to were “absolute” references. Therefore, if you copied that Boolean gate to another subset in the same sample, it still referred to the original gates. You now have the option of referring to gates in “relative” terms – i.e., as a subset of the current gate. Therefore, you could create a Boolean gate that is “IL2 or TNF” on the CD4 gate, and copy that to the CD8 gate in the same sample. These will now refer to the IL2 and TNF gates created for the CD8 subset. The Boolean gate definition window has two different menus that let you select which subsets you want to choose; in general, you will probably want to use the new, “relative” gate references. Boolean Combination Gates - automatically create a series of Boolean gates that represent all combinations (plus and minus) of a set of gates.
Bug fixes.
• Biexponential Transformations computed on hardware-compensated data will only be applied to other datafiles with identical matrices.
• You can delete multiple time slices in the Kinetics platform simultaneously.
• The workspace will show icons to the left of each gate name even if the name column is too narrow to display the name.
• Editing text entries in the SciBook is properly saved.
• Saving workspaces in XML format will save the graph options regarding hiding or showing axis ticks, numbers, and labels.
• If you change the specification of a group’s criteria for sample inclusion, those changes are implemented immediately rather than only for new samples.
• The color palette preferences for Layout overlays is correctly saved and read.
• Deleting the first level of an overlay in the Layout Editor no longer causes a crash.
• Copy output tables in transposed format (hold down the option key while clicking on copy) correctly formats the summary statistics (mean & sd).
• The cell cycle, proliferation, and kinetics windows are correctly repositioned on the monitor when closed and re-opened.
• Dragging multiple FCS files from the Finder onto the FlowJo icon will now create only one new workspace (rather than one for each data file).
• Duplicating a Layout now preserves the pagination information (scale size, landscape/portrait).
• There is no longer a limitation of 16 time slices that received color coding in the Kinetics platform.
