Flowjo 10

BD Research Cloud is now integrated with FlowJo v10.8!BD Research Cloud is an application for communication and collaboration across a lab’s entire toolbox, including but not limited to flow cytometry and sequencing processes. Being integrated directly into the FlowJo workspace means you can access any analyses and data-sets shared with you in BD Research Cloud workflows through the click of a button. Downloading from BD Research CloudIf you haven’t yet signed up for the FlowJo Cloud, you can do so here.Clicking the Add Sample From BD Research Cloud or Open From BD Research Cloud buttons in FlowJo’s workspace will take you your BD Research Cloud account. You’ll be offered a dialog from FlowJo illustrating all of the FlowJo analyses and FCS data files shared with you through your various BD Research Cloud workflows. After you choose the files you’d like to explore, click the Add button and those artifacts will either be loaded into your current workspace (in the case of raw data files), or opened for continued analysis in the case of FlowJo analyses.Uploading Your Analysis to BD Research CloudOnce you’ve completed your work session in FlowJo, and want to move the analysis into a BD Research Cloud workflow, simply visit the File tab, within the Save As option there you’ll find the Save to BD Research Cloud selection. This will bring you back to the BD Research Cloud workflows dialog, where you can choose the appropriate directory to save your analysis. If you need any extra assistance using the BD Research Cloud Integration tool feel free to send us an email: [email protected], we’ll be glad to help!Tags: FlowJo

UpdatesImproved authentication. The HTTPS connections to FlowJo Portal for authentication/authorization purposes can be secured by either a FlowJo SSL certificates or newly by an SSL certificates installed by the end user’s corporate security or IT.Total Spread Matrix (TSM) is now available for matrices created in FlowJo. TSM is the Spillover Spreading Matrix (SSM) without normalization to the florescent intensity of the probe. Panel designers consider the brightness of a dye as well as its spread as factors impacting that ability to separate populations. These factors are combined in the SSM metric, but de-coupled in TSM so that the designer may factor in the total spread introduced into a panel apart from brightness. This new measure is available in the SSM dropdown in the Compensation Editor.Overlapping curly quad boundaries corrected.Improved support for LMD files.Improved handling of v9 files.Known IssuesAuthentication – 24-hour offline grace period (for FlowJo Site License serial number users) will not become active correctly for certain use cases, particularly if internet is available via proxy.When creating a keyword value series, and replacing numeric entries with text, the text entry box cannot be selected via mouse click. Workaround: Use the Tab key on the keyboard to move to the correct data entry box.Proliferation nodes applied to a group will not have the same functionality compared to group owned gates, i.e. proliferation nodes applied to synchronized groups will not adjust automatically when one node is altered, and the color/font-style of proliferation nodes will not match their group.Import/Export from Diva works best with BD(TM) FACSDiva version 8.5. Double-clicking on a WSP file or other FlowJo workspace file will not open that workspace in FlowJo, but will instead re-launch the software. Workaround: Drag and drop the workspace of interest into an already open FlowJo workspace.Locale settings in FlowJo preference which indicate decimal delimiters with commas will cause a range of errors. Workaround: Use US locale settings, even in other regions to keep everything working smoothly.Manual Gates set from the “Graph” tab of the Graph Window cannot be set in Windows 7.The “OK” option under Manual Gating may be hidden off-screen in some cases. Workaround: Use “Tab” key functionality to move the selection onto that button.Spectral compensation involving samples with height or width parameters is prone to generate improper matrices.PluginsR based and Java plugins may not function when files or file paths include spaces or special characters. Workaround: Remove spaces and special characters from data files and file paths.Derived parameters generated from plugins can be lost after a workspace is saved. Workaround: Export FCS file(s) on which plugins are run including all derived parameters there, and re-import the exported files for downstream analysis. Alternatively, the derived parameter .csv files can be found in the derived parameter folder created by the plugin and they can be drag and dropped onto the sample to reconnect the analysis.

FlowJo gives you the most flexibility possible with exported graphics. You can easily ungroup any graphic, and change the font attributes, line styles, etc., to make any graph look exactly the way you want in the Layout Editor.Hints on exporting graphsIn the layout editor, you can copy/paste graphsto clipboard (copy/paste)to file (save or batch-to-file)File Tab -> Exportx As Image….. pdf, svg, emf, png, jpg and gif.Exporting plots and batch reports – Send whole layouts to half a dozen file formats. Send a batch operation directly to a presentation, a PDF, even a web-ready slideshow!Copy/paste images for use in other programs – If you only want to export some layout elements, FlowJo lets you use common file formats in simple copy-paste actions.Batch analysis: The greatest strength of FlowJo is its ability to generate a batch analysis with a simple and flexible structure. Our approach lies in the grouping structure within the workspace.Create an example layout, and with a single button, produce a batch layout wherein each sample or group of samples is analyzed and displayed identically to your example. The new layout can be displayed within FlowJo, or converted into a Web page, Powerpoint slide, an instant printout, appended to an Excel file, or saved as an HTML movie. See Layout Editor exports for more information.Resize the page, not the graph: Many new users spend a lot of time individually resizing graphs to fit the desired number on a page. If you want the graphs to be the same size relative to each other, leave them at their default size, but drag the page breaks or use Scale To Page, Scale To Height, or Scale To Width commands from the Arrange Tab.If you want graphs to have different sizes relative to each other, select all of the ones to resize, double click one and set its scaling in the Graph Definition window. When you apply the changes, all of the selected graphs will resize uniformly. Posted March 3, 2013 by Seth Duncan & filed under . -->

FlowJo software is complex, and analysis can often be accelerated by adopting the use of keyboard shortcuts. Many actions in FlowJo have been assigned shortcuts. Through using modifier keys like shift/ctrl, alt (option on macs), and cmd (for macs), as well as the right-click menu, you can often find shortcuts to context-specific functionality to aid your workflow. For more information on the Workspace click here.Component and Action Shortcut KeyMacintosh VersionWorkspaceGeneralClose WorkspaceCommand + WExitCommand + QUndoCommand + ZCustomize RibbonsCommand + ( ] )FlowJo TabNew WorkspaceCommand + NAdd SamplesCommand + Semicolon (;)New GroupCommand + GOpen Layout EditorCommand + LOpen Table EditorCommand + TPreferencesCommand + YPanel WizardCommand + Shift + PFile tabOpen WorkspaceCommand + NumPad + (/)PrintCommand + PSaveCommand + SExport / ConcantenateCommand +ESave AsCommand + Shift + SFindCommand + FFCS ScanCommand + Shift + FEdit TabCutCommand + XPasteCommand + VClearCommand + DeleteSelect AllCommand + ASelect Equivalent NodesCommand + Shift + ECollapse AllCommand + Shift + UExpand AllCommand + UWorkspace TabCreate GroupCtrl + GCopy Gate to GroupCommand + Shift + GOpen Graph WindowCommand + EnterInspectCommand + IRenameCommand + RAdd StatisticCommand + BAdd KeywordCommand + Shift + ICreate Group from Keyword ValueCommand + JCreate Keyword Value SeriesCommand + 6Tools TabCompensationCommand + MMatrix EditorCommand + Shift + MCheck Samples QualityCommand + Shift + VDerived ParametersCommand + Shift + DCreate Combination GatesCommand + Comma (,)Make Or GateCommand + Shift + OMake And GateCommand + Shift + AMake Not GateCommand + Shift + NMake Identical GatesCommand + Equals (=)Plate EditorCommand + 9Show in 3DCommand + 3Settings TabEdit ColumnsCommand + Shift + KHide/Show Statistics”)Command + Shift + B Show/Hide Comp NodesCommand + Shift + CLayout EditorLayout TabAdd A New LayoutCommand + NDuplicate LayoutCommand + Equals (=)Delete LayoutCommand + Minus (-)File TabPrintCommand + PSave Image AsCommand + SView WorkspaceCommand + 0 (zero)Open Original GraphCommand + OPropertiesCommand + IEdit TabUndoCommand + ZCutCommand + XPasteCommand + VSelect AllCommand + AObject TabFigure Presets (Apply)Command + (+)Arrange TabBring ForwardCommand + FBring to FrontCommand + Shift + FSend BackwardCommand + BSend to BackCommand + Shift + BGroupCommand + GUngroupCommand + UTopsCommand + TBottomsCommand + (Backslash)Vertical CenterCommand + Page DownVertical SpacingCommand + KLeftCommand + LRightCommand + RHorizontal CenterCommand + HHorizontal SpacingCommand + JTable EditorTables TabNew TableCommand + NDuplicate TableCommand + Equals (=)Remove TableCommand + Minus (-)For DisplayCommand + DBatch to LayoutCommand + LBatch to ClipboardCommand + KBatch to PrinterCommand + PTo FileCommand + FEdit MenuSelect AllCommand + AClearCommand + DeleteColumns MenuAdd ColumnCommand + Shift + NEdit ColumnCommand + EGraph WindowGeneral ShortcutsShow the Uncompensated parameters in the Parameters drop down listHold down Alt + Select the Axis Parameter in the Graph WindowFile MenuClose WindowCommand + WClose All Graph WindowsCommand + Shift + WSave Graphic asCommand + SPrintCommand + PEdit MenuUndoCommand + ZClearCommand + DeleteCopy Image with

You’ll notice some major improvements in this 10.0.8 release, from the very start of the application through the interface to new platforms. In terms of user feedback, features, quality, and performance, this represents a major release and we are grateful for the many conversations with loyal users and work with beginning users whose feedback help us guide this redesign. You will notice a significantly streamlined user experience to ease the ‘flow’ through FlowJo, improved performance on workspace opening, and a brand new signed installer package for Mac.New Features & Major Revisions:User Interface: Major overhaul and modernization of the user interface in every part of the application, prioritizing frequently used functions and improving analysis workflow.Cell Cycle: Watson Pragmatic and Dean-Jett-Fox univariate cell cycle models are back, with full featured constraints and display options.Export/Concatenate: Export/Concatenate has all the features you loved in v9, as well as advanced keyword-based naming and batch concatenate features.Kinetics: The Kinetics Platform is back, with better time parameter handling for data from any cytometer.Workspace:Apply Template to Workspace. You may now apply a template and see its templated analysis and reports ‘live’ in the active workspace.Cmd/Ctl S will now always save the active workspace, no matter what platform or window you have open.We also re-organized the workspace right-click menu.OS X version Our application for Mac is now digitally signed, and no longer requires changes to Security Preferences to run. Installation is one drag-and-drop away. (n.b. on Some older OS X machines, the alias file may not work on the installer dmg. To work around this, please drag FlowJo to your Applications folder.)Opening Workspaces: The time it takes to open Workspaces that have complex layouts has been significantly optimized and layouts will only be loaded when accessed..jo file opening: Improvements to .jo file opening.Transforms: We have added ArcSinh, Hyperlog, Logicle, and Miltenyi transform types which are also modifiable using the T-button (transform window) for much improved data display. Also, we have added increased stability with handling older data types (FCS 2.0).Plugin Architecture: You may now use FlowJo as a platform on which to run any external algorithms for population discovery

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