Version 11 Documentation
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10.0.7 Exhaustive Release Notes

For a digest of these release notes, please see this page.  This page contains an exhaustive list of issues that have been reported and fixed, new features implemented, and known issues.

Fixed:

FlowJo 10.0.7r2:

  • Significant Improvements:
    • Compensation is now “remembered” in templates
    • Compensation population size restriction has been reduced to a warning if under 5%.
    • Manual gating will override matrix calculation and allow matrix to calculate
    • Cytek data transforms fixed
    • Miltenyi fcs3.1 concatenate files scale issue
    • 10.0.6 workspace opened in 10.0.7 could drop parameters
  • Stability,and other issues addressed:
    • Some annotation fields did not allow text entry
    • Comp Matrix Editor could stay open open with an applied Matrix when closing workspace.
    • Export FCS now includes changed keywords. (It has not in the past.)
    • Two bisector gates on population produced a 2D gate
    • Table Editor: Fixed Keywords menu to not filter based on what was already used.
    • Heat Mapping Without Values now works
    • 10.0.6 workspace data reconnection issue resolved
    • (rare) v1006 workspace wont open in v1007 – fixed
    • FCS2 Portion of Galios Data was not always visualizing correctly
  • Several cosmetic fixed including dialogs and tip text rollovers have been improved.
    • Previous Arrow icon in Preferences is backwards.
    • Gate Naming Dialogue – restored autocomplete from favorites when entering gate name
    • Contact FJ form did not not appear in all cases.
    • Text in new gate naming dialogue is not highlighted
    • Binding Node Icon created
  • Linux Version:
    • linux graph data scaling issue fixed
    • IAE in launcherDialog when exiting in Linux in VMware
  • Several broken links to docs were fixed
  • BMS Version
    • BMS version – Table exports overwrite each other
    • BMS version – The Select button for setting the output path in prefs is cutoff

FlowJo 10.0.7:

  • Annotation
    • Clicking Annotate Experiment in Plate Editor throws a stack.
    • Annotate Exp. Figures Tab: Divider between the Figure table and the preview acts strangely
    • Annotate Experiment Instrument Panel Panel & Comp. text fields don’t get along
  • Boolean Gates
    • Boolean tools all throw stacks and do not create valid gates
    • Creating Combo gates throws a stack.
    • Creating NOT gate on grandchild causes the stat of the gates to be lost
  • Cell Cycle
    • FJ is still calculating after CC is applied.
    • Cell cycle throws stack at open
    • CC File:Print… Menu throws a stack
    • CC1D platform arrows not working (throws quiet stacks)
    • delete cc Node = stack
    • Switching bivariate samples using arrow buttons can throw stack
    • switching rapidly in bivariate sometimes show quiet stack
    • CC throws stack on FACSArray file with no S Phase Marker
    • CC tutorial data is not being scaled correctly in the CC platform
    • Cell cycle Multivariate gates can’t be dragged
    • Cell Cycle Go Menu has blank entry as first menu item
    • Cell Cycle Bivariate Y Axis has no label
    • Cell Cycle Bivariate gate labels all piled up at top left of chart and non selectable or moveable
    • Cell Cycle Bivariate T buttons do nothing
    • Cell Cycle Bivariate right click menus are a mess
    • CC1D gate disappears when dragged
    • CC File:Save Graphic As… menu looks like it works but does not save
    • CC tooltip for Calculate… menu undefined.
    • CC Edie Menu options do not seem valid for CC platform?
    • CC Help Menu all have bad links…
    • Cell Cycle on non cell cycle data show warning but still opens platform
    • Copying CC node to group and switching from univariate to bivariate and back throws stack
    • CC1D mean peak stat incorrect
    • CC1D stats in TE are all “0”
    • TE formula references are all “Cell Cycle/Freq. of Parent”
    • Deleting CC node from Group doesn’t eliminate from WS
    • CC1D G2 and S phase stats overlapping on GUI
    • CC Multivariate EM Has extra widgets
    • Stringnames are shown for Copy Stats and Preferences in Edit menu.
    • CC 1D > G2 shows 0% in Platform
    • CC Next and Prev. arrows only partially update platform window
    • CC creating CC on more than one sample throws stack
    • 1D CC Re-open workspace with CC, CC node opens blank CC window
    • CC Group owned CC opens empty window and does not generate statistics
    • CC gate name and freq. of a Bivariate plot are piled up
    • CC chart stripped of analyses when applying save graphic as
    • CC in Simple Mode Bivariate & Multivariate stacks and no gates created
    • CC Changing the Bivariate gates does not trigger a recalculation of the Multivariate gates
    • CC Dragging CC node to LE makes not a pretty picture
    • CC Drag Dropped CC Node to LE = Stack & no image
    • CC First create of CC Note, Bivariate gates are bad
    • next / prev don’t update Y axis
    • Opening multiple CC platforms, the windows don’t offset like other platforms
    • cell cycle stat -100
    • Add 1d stats to workspace
    • label Bivariate & 1d stats in workspace
    • Duplicate 1D stats appear when arrowing through CC samples
    • Unable to analyze multiparameter CC data file, cutoff warning message, no parameter selection
    • All stats are zero for LMD Cell cycle data
    • Cell Cycle Stats mean peak stat incorrect
    • CC & LE… graph in LE changes with Platform
    • CC in LE changes graph type depending on Platform window
    • Cell Cycle Multivariate EM right click menus non fucntional
    • Cannot get past biomarker selection interface in CC test set 5
    • loading a saved workspace with cell cycle analyses shows -100 stat
    • CC 1D Drag into LE repositions S phase marker
    • CC1D histogram scaled differently in CC node vs LE after Transform.
    • CC1D G1, G2 (peak), S-phase stats incorrect
    • CC1D stats in TE incorrect, do not correspond to GW
    • Dragging CC node with different view in CC sets shows overlays in LE.
    • Setting region constraints
    • CC Table duplicate labels, first one should be < 2N
    • Re-Opened workspace does not show 2D & EM CC Data
    • CC 1D Change X parameter not permitted
    • CC 1D constrain ratio yields strange 4N stats.
    • Unknown stat on CC 1D GUI
    • Statistics added to cell cycle nodes disappear upon constraint application
    • CC platform is not saving its constraint state upon application
    • CC1D GUI stats incorrect (Update issue)
    • CC1D constraints checkbox drops WS stats
    • CC1D node gates incorrect
    • Reopened workspace BiVariate CC showing wrong Y param
    • CC 1D Constraining CV and Ratio drops CV constraint
    • CC Re-Open Workspace, null param warning (better STRs)
    • able to create zero width constraint gate with strange effects
    • CC & LE… graph in LE changes with Platform II – New STRs
    • CC 1D does not remember what axis param was chosen
    • CC Biomarker Selector Dialog Cancel does not cancel.
    • CC1D TE cv stats incorrect
    • CC1D 2N/4N gate snaps to same location in vertical
    • Double-click CC node changes X-axis parameter
  • Command Line: commanjo needs tooltips
  • Comp Matrix Editor
    • Clicking Edit Compensation Matrix button is throwing a stack
    • Overlay Uncompensated button in the ME is not previewing the samples and throwing a stack.
    • Overlay Uncompensated on Comp Ctrls is not on by default though checked and throws stack when unchecked.
    • There is 2 hidden unselectable options in the ME.
    • Stack when clicking the View Matrix button in Compensation and graphs are missing..
    • Matrix looks distorted when opened through the badge of a sample
    • compensation editor problem reported by helene
    • ME doesn’t fill background to edge, and scroll bar thinks height is larger than it should.
    • loading multiple compensation matrices from files
    • Compensation Calculation with 13 color data set provides no user feedback to correct gates
    • Formatting for Positive Negative control gates in overlay does not match GUI coloring
    • Updates to positive gate not reflected in overlays in CME
    • Unable to select the color palette.
  • Compensation
    • Compensation Dialog does not open and throws a stack.
    • MoFlo Data Doesn’t Show Any Parameters in the CE
    • NPE in cytek data handling
    • Comp Ctrls, Sample, Neg and Pos vibrate when mousing over them. PC Only
    • Right click menu on badge to add comp shows string name
    • Stain name is lost and Parameter name highlighting not present in a reopened WSP
    • Compensation Window Tooltips
    • Comp wizard drop-down doesn’t add population.
    • Compensation dialog menu stringname tooltip issues.
    • CE clears instead of resets it
    • Compensation Menus on Positive and Negative samples need to be cleaned up.
  • Derived Parameters
    • derived parameter window changes size when option panel selected
    • Increasing Derived parameters minimum range is throwing a stack
    • Can’t create Derived Param
    • Event# parameter not available for derived parameters
    • derived parameter node renames itself
    • Custom transform on Derived Param is not restored from workspace or Template
    • Transforms are not being applied with Derived Parameter when group applied.
  • Dialogs
    • Save & Save As will overwrite existing file with no warning
    • Changing the Sorting order is removing data in find/replace
    • Show all keywords in menus checkbox in modify group dialog not staying selected after applying
    • Stringname is shown in the Group dialog for the Any Keyword selection.
    • “You” tab of Startup License Sequence shows extraneous “Next” button
    • Open, save and non specific save as dialogs are not using ideal osx dialogs
    • Adding non demo file to demo mode brings up wrong dialog
    • AutoQuad tool tip showing string name
    • Create Cell Cycle Gates tool tip showing string name
    • Annotation dialog / Plate & Experiment text fields need to resize
    • Group Dialog tooltips largely undefined
    • Manual gate dialog has display issues
    • Next button should to be removed from the License tab.
    • The Date fields in the Annotate Experiment dialog is not fully shown.
    • no error message when os is switched to offline mode while running FJ shipping version
    • unable to add stat thru stat dialog
    • sentence cut off in proxy settings dialog
    • Don’t Show Again does not work with Rename for all on Group owned gate.
    • Don’t Ask…Delete group stops asking and stops deleting,
    • Are you sure you want to create and open X platform windows dialog controls are reversed
    • Keyword Value Series… Dialog does start with correct number of edit boxes
    • Manually Enter Gate Instructions are Editable
    • Keyword Popup Does not protect from going off the bottom of the screen (Mac only)
    • Stringname is shown for the Tooltip for Dont Show Again checkbox
    • DIVA FCS2 warning has extra buttons
    • New in VX Link in About Dialog does nothgin
    • Can’t cancel ACS open from Workspace Version dialog
  • Document – WSP
    • Transform of a Derived parameter is not saved in the workspace
    • Workspace with no Samples looses created layouts
  • Export
    • save as excel from the workspace throws NPE
    • data export issue reported by Chris Bray of Verity Software House
    • exporting from the workspace is causing FlowJo to crash
    • Group export of Sample Data locks up with Engine 406 Error
    • These Coulter Files don’t Concatenate Properly
    • Exporting CSV does not save any additions made.
    • Concatenate in Export dialog shows stringname for tooltip.
  • FCS Scan
    • FCS Scan Stacks when button pushed
    • FCS Scan fails to list FCS files from “Documents” folder
    • Help button is replaced by a text when Show Duplicates is checked.
  • File Formats
    • Miltenyi Data in MQD format not displayed correctly
    • Stack opening Template (pre-fix) with Layouts
    • vX cannot open FlowJo 9.7.1 Jo files
    • Re-open workspace Error:target population does not have the Comp…” on re-opening the workspace.
    • 9.7.1.jo file drag to open jo file does not create a new workspace
  • Graph Window
    • Opening Parent in graph window throws stack… specific case only!
    • Delete Gate with child open throws 2 stacks
    • NPE When Opening a group gated population on comp
    • Graph Window Make Movie Stack
    • clicking y or x axis parameter menu in graph window is throwing a stack
    • Can’t create a range gate dragging left to right
    • Not loading in any data from this LSRII Data Set
    • Fast Preview no longer appearing
    • IsFloC: Custom Transform Graph bad when linear and min is close to 0 (specific sample Gain Related?)
    • Graph Window Up Arrow no longer shows parent population params with the gate
    • Spider gate Q1 is showing X/Y coordinates in GW – W7 only
    • manual gate – cannot mix percentage & intensity
    • Gridlines do not display on LE
    • Curly quads cut off upon resize
    • Gate Annotation on Graph window Snaps to right edge from too far away (Very strong magnet!)
    • Graph window Increase & Decrease Gate Size buttons don’t work on Rectangle Gates
    • Decrease size button on Graph Window does not visually show when available
    • children plots not updating when parent gate is moved
    • manual gating dialog seems to be missing action buttons
    • can open multiple graph windows
    • Control gates do not keep their value when applied to a sample
    • Continuously moving any of the Quads slows down FJ.
    • Spider gate turns into a regular quad when adjusted inside another type of gate.
    • Quads 1 & 3 change annotation on transposed axes
    • Transposed curly quad gates move operation incorrect
    • Spider gate creates an extra line when changed from Lin to Log or Biex.
    • Q1 annotation on a Transposed Spider Quad is cutoff
    • Can’t delete quad gates in Graph window
    • Opening the Child of any of the 3 Quads through the GW will view the Parent GW.
    • Deleting a Quad from the GW removes Comp Ctrls and the Badge of the sample is blank.
    • close and reopen GW resets gate annotations
    • FlowJo not displaying time parameter
    • biexp scaling on histos Y axes
    • Offset quad gates showing duplicate edges
    • spider gate legs don’t show handles
    • Off-axis gates snap back on Miltenyi FCS3.1 Data
    • Curly quads shift location in GW
    • Cytof Events on Y axis don’t show up in the gate on the edge
    • Remove sound for GW opening.
    • Positive Annotation to be shown on a 2d plot after a bisector is created on a histo.
    • right click menu showing string name
    • GW Open Child Population should be disabled with no gate selected
    • Can’t drag annotation on 1D chart
    • In Simple Mode, some Graph menus are missing all items
    • Gates can not be dragged to top of graph
    • Giant Curly Quad Gate from template and does not draw in graph
    • Spider gate with transposed axis bad things happen when moving end points
    • Transpose axis with Quad or curly quad the annotations & stats don’t update
    • Transpose Axis with Quad shows a box around Q1
    • Copy Histogram to excel copies incorrect population
    • Bisector gates open with unfilled histograms (when pref is set to filled histos)
    • Miltenyi Transform tooltip shows stringname.
    • Quad gates are not drawing vertical bar when asymmetrical
    • Range gate won’t deselect if in same graph as Bisector Gate
    • Bisector gate’s population opens in psudocolor instead of Histo.
    • Stain name parameter requires click-refresh in WS before application to GW
    • ec800 X and Y scales are not being read?
    • Graph window of child opens stretched if any options panel is open in the parent
    • FJDotPlot indexing inconsistency
    • Quad gates are deleted without confirmation dialog
    • Breadcrumb trail in graph win goes bad when adjusting cc gates
    • Annotation in the GW can be cutoff only on the rightside.
    • Editing Range gates in 2D plots doesn’t constrain movement
  • Graphics
    • Exit Icon needs revision
    • Export icon improvement needed
    • Experiment needs new icon
    • Populations icon needs work
    • Edit comp matrix icon work…
    • Check Sample Quality icon still needs check mark moved left to be clearer.
    • Keywords icon needs work
    • We need a Chart Properties icon
    • Properties.. icon needs changes
    • Launcher window needs re-design
    • Plate Preference Panel needs icon
    • Panel Wizard icon in Prefs needs improvement.
    • Preference dialog Previous and Next buttons should have arrows and not dots.
    • Icons for disclosable panels
    • PE Icon changes…read from workspace, move wells to workspace
    • File Save Icon using wrong artwork
    • Icon for plate “deselect all” action
    • Transform Axis Window is using old arrow art for next & prev arrows
    • derive parameters Icon could use a revision
  • Grids
    • Stack is thrown in the LE when making an overlay in a grid
    • Ability to open Graph Def and edit a graph that is in a grid
    • Too easy to move charts out of a grid
    • Shadow changes the number of cells seen in a grid
    • Right click menu functions on Grids need tooltips.
    • Tooltip shows stringname for Enable Iteration and Scale Figs on Cell Resize.
  • Kinetics
    • Smoothing options do not work
    • most settings do not change graph
    • Closed options panel show missing string(s)
  • Launch: Opening a saved WSP by double clicking on it opens two and one is blank
  • Layout Cell Cycle
    • Y Axis of CC changes when added to the LE.
    • Cell cycle batched label goes blinky
  • Layout Charts
    • Cannot change graph type in LE
    • Stack is thrown when selecting All Parameters by Y from the right click menu in the LE.
    • Dropping a Stats Table LE tool into a Grid throws a stack.
    • All Layout tools overlap the ruler when a Histogram Stagger Offset plot is selected.
    • Adding columns to legends does not work on multiple plots
    • Ability to change x/y annotation on multiple plots in the LE
    • Ancestry is still shown after unchecked in the Graph Definition.
    • Batched Table does not reflect the Fill and Gradient until it is clicked on.
    • Out of Memory adjusting Zoom on a Batched NxN plot.
    • Disabling the Enable Iteration does not work on Grids.
    • Backgating is still shown after unchecked in the Graph Definition.
    • bg/fg colors not recognized in layout editor charts
    • “no line” setting on a graph in the layout still shows a faint line
    • adjunct histograms overextend selection handles when batched
    • Change the wording for Remove Cells From Grid.
    • LE graph def parameter list error
    • runaway x axis tick
    • All figs, FG and BG color lost after apply and OK
    • grid gets painted past chart in the LE
    • Colors in overlay legend are not showing
    • Ancestry & Backgating on Overlay should not be options
    • Ancestry/Backgating shows label far to the right of the chart for Bisector gates
    • Bisector Gate in Graph in LE missing 2nd Stat Label
    • Mismatched Iteration warning in LE not appearing for Overlays
    • Draw Rectangle Gate in 1D graph
    • wide data crashes NxN
  • Layout Editor
    • Plate Tool on LE – gone when re-opening the WSP
    • Batching with statistics in the LE is throwing errors
    • Re-Open Workspace Layout Editor has phantom layout
    • Curly Backgating doesn’t work
    • Lock Content in the LE does not work on Text ribbon functions.
    • Graph Definition changes only affect one of multiple selected samples.
    • LE Text Box Insert Keyword Menu malformed
    • Cannot rename the X and Y axis labels through the Graph Definition.
    • Plate Tool on LE rollover text is incorrect
    • LE Properties Panel has inverted icons for show & hide
    • sporadic CME in complex layouts rebinding samples
    • LEBatch Band : The Across vs Down radio group always reverts to Down after creating the batch.
    • Stringnames are shown for the Tooltips under the Annotation tab in the Graph Definition
    • LE after dragging a Guide line, the cursor does not change when hovering over the guide until the selection changes
    • Can’t grab the page break control in the LE if a fig is on top of it.
    • Move Figure Presets from Ribbon to Properties:Info in LE
    •  easy way to NPE in LECHartController
    •  layout editor window resizes when closed an reopened
    • Graph Definition window not adding/deleting populations
    • unable to paste image into le
    • save figure as in the le is not working
    • Batch to pdf in layout
    • Clicking the Add New Layout button in the LE does not select the New Layout.
    • Bisector Histogram annotations not added to LE
    • LE Batched Table: Set Cell Padding Does not grow table to min size until you try to resize it
    • LE Grids: Remove X and Remove Y Axis menus incorrectly enabled
    • LE Dragging object to combine them work only under certain conditions based on creation order
    • Multigraph Overlay issue with 2D graphs
    • Tooltip shows stringname for Edit in right click menu.
    • Histogram Overlay Y Axis Modes Not Applying
    • Statistics Dragged Into LE Not Displaying Properly
    •  Layout’s line tool keeps line horizontal during creation
    • Line tool resize moves other point
    • LE Paste should past into the visible part of the window
    • Applying Fig preset does not update the Properties Band
    • LE Grid Right Click Menu using wrong popup
    • Iterating Layouts with Page Up/Dn doesn’t refresh Iteration band
    • pagination not stored in layouts
    • If the copied figs are too close to the edge of the LE, the paste piles them up in the corner
    • CDF scale changes in LE
    • Group Boundaries in LE Too Large
    • Icons missing in the LE & PE Lists
    • Multiple instances of the Layout band fails in the LE
    • No scrollbar after undo in LE
  • Layout Iteration
    • Iterate by Sample selection in LE is throwing a stack with CC data loaded
    • Stack is thrown upon Panel Iteration selection
    • Multigraph All Params causes bad layout with comp populations
    • workspace and sample iteration naming conflict
    • can’t deselect after batching
    • Iteration Off contains Value drop down list when Batch to Printer is cancelled.
    • Iteration Values are reset to default setting after batching.
  • Layout Outputs
    • Save Button & Cmd S throw NPE Stack
    • Stack is thrown when overwriting an opened batched PDF from the LE
    • Ability for graphs/object to have transparency when outputted to PPT
    • Batching to web page shows density plot very pixalated
    • Show Outliers function doesnt show when Batched to PDF
    • Batched Layout no longer saving the isBatch flag in xml file
    • append to powerpoint fails when batching
    • Create Batch never finishes if specified path no longer exists
    • in Header or Footer not available when printing
    • Disable append to PowerPoint for now
    • ‘Save Image As.. pdf From LE is not including headers/footers in produced report
  • Layout Overlays
    • creating an overlay causes the rainbow wheel of death
    • Plot retains wrong color in LE Remove Layer
    • Line style should show in the legend
    • Legend is blank on an Overlay.
    • Staggered Histograms only display transform lines for linear params
    • change all layers of the histogram overlay at once
    • Legend color box doesn’t fill on Histogram Overlays
  • Layout Plates
    • Selecting Cut on a Plate Tool throws a stack.
    • Dragging Plate Tool throws a stack.
    • Stack adding plate data to template with Plate in LE
    • Plate tool in LE is not populated when loading template
    • LE save image as… plate tool cuts off annotation and left labels
    • Rich tool tip for LE Plate Tool has incorrect description
    • NPE When deleting a non group owned gate if a Plate is open in the LE
    • Cant edit well id (was: Plate Tool missing “D3” well info)
    • LE Plate tool is using Plate Editor Prefs and it should not be.
    • Layout Plates Missing Annotation
  • Links
    • Web doc naming scheme out of synch with FJ’s
    • Help button on Window when no workspaces are open leads to 404
    • kinetics help web link broken
    • proliferation help web link broken
    • redundant links in ws help band
    • MIFlowCyt help web links not working
    • keyword value series help web link
    • iterate by keyword dialog help web link broken
    • web link in le iterate by keyword diag broken
    • no help web links in the pe
    • PE All help links= 404 Errors
    • Kinetics Define Threshold Value dialog help 404 error
  • Other
    • Keyword Popup with search no longer searching
    • FlowJo window has transparency issues.
    • FlowJo Finder version is 1.0 on osX
    • Popups do not dismiss when FlowJo loses focus.
  • Panel Wizard: Opening the panel wizard in offline mode is throwing a stack
  • Plate Editor
    • Plate editor & LE Plate Tool is not using Pref for Well ID
    • Stack when opening Plate Editor with no data
    • Clicking Cancel for Set Plate Dimensions throws a stack.
    • Clicking Read From Workspace throws a stack when data is in the WS.
    • PE: Select Group Stack
    • Clicking the Add Keyword/Value button throws a stack.
    • Opening workspace > 96 well plate, shows stack when trying to open PE
    • Stack is thrown when importing BAD CSV into PE or through drag and drop.
    • importing a csv is causing a stack
    • Plate editor import throws stacks on import
    • PE Wells should not be allowed to contain multiple instances of the same keyword
    • PE Remove Staging Well does nothing
    • PE Open… Does not open a files saved with Save
    • Plate Meta Fields are not cleared(or restored) with multiple plates
    • PE Paste is not pasting into the selected cell
    • PE Filter Drop Down is hard coded and should be dynamic from data
    • PE – Well display does not update when using arrow keys to move selected well
    • PE Keyword Filter changes
    • PE Changes to Staging Wells
    • PE Well Display Area changes
    • PE Modify name and function of Read from Workspace
    • PE Move Wells to Workspace needs to change name and function
    • PE Use the Circle drawn on a well to indicate an associated file in the workspace
    • PE: Heat maps showing only BLACK Wells
    • Plates show contents of some wells and not others
    • staging well right click duplicate not duplicating
    • Copy and past in PE changed WELL IDs
    • Plate Editor, when wsp reopened loses plate name, attributes and user annotations…
    • Plate Tool title is “…Under Construction…”
    • In Plate Editor, new plated do not have a default name
    • Plate Editor “Add” button does not look like a button
    • Plate Editor Pencil button has bad rollover text
    • Plate Editor continuous spew of data to the console
    • PE Plates do not close when the associated workspace closes
    • reopened workspace Saved Plate is missing data and strange
    • PE: Selecting different plate in plate list does not update the well information panel
    • Ignore duplicate keywords in drags to wells
    • Plate Editor needs WindowPosition persistance
    • Plate name edits in sidebar revert when switching plates away and back
    • Plate editor staging well drag throws stack
    • Make Group makes a group with only one file in it despite well selection
    • Opening a saved plate XML file in plate editor
    • PE Annotate Experiment Dialog opens too small
    • Plate Editor Read from WS not populating all wells
    • set plate dimensions
    • bug uncovered at high plate size
    • Not everytime will a keyword drag and drop to a cell and Staging Well in PE. PC Only
    • PE: Plate is sized wrong row & col count reversed
    • Set Plate Dimensions does not work.
    • PE Make Group Help Button no-op
    • PE Cut, Copy Paste not working
    • PE Creating keywords automatically adds the keyword to the selected cell
    • PE: Show Attributes button highlight is reversed
    • PE Clear Selected Wells does not clear wells loaded from workspace
    • PE Show heat maps button is highlighted reversed
    • PE Read from workspace multiple times duplicates keywords
    • PE Bottom Panel (staging wells etc) is too easy to separate from the Plate window when resizing the plate window
    • PE add Clear Selection button
    • PE Import Tool tip needs additional information
    • PE: Color Borders of categorical keys button does nothing
    • PE Use Thicker Borders does nothing (as far as I can tell)
    • PE:Don’t allow user to add empty keyword/value pairs
    • Rename staging well, dialog should default to current name selected
    • Selecting a named group does not clear selected staging well
    • PE: no way to remove a named selection of wells
    • Dragging Staging wells onto another staging well
    • PE should not use samples from workspace until user tells it to
    • Editing Fields at top of plate cuts off font
    • PE Keyword field should not be editable.. just the value field
    • Remove the ADD button from the PE Keywords Band
    • PE: Wells should not associate with samples until the user chooses to do so
    • Plate Editor not using Well ID Plate Pref for Import csv file
    • Apply Plate Keywords to Group not working.
    • Keyboard commands for cut, copy & paste don’t work with plate editor wells
    • PE disable Make Group button if wells are not associated with samples
    • Change value of a keyword in a well should ONLY change the selected well
    • Copy multiple Wells and Paste in PE = Stack
    • Remove staging well button still active even when no staging wells are selected
    • New plate in PE needs new color and default name “-copy”
    • PE Dragging lots of Keywords to a Staging Well breaks the UI
    • PE The horizontal layout of the draggable bottom panel looks terrible in vertical mode
    • PE Saving a workspace with a plate, upon re-opening, always has an extra plate in the list
    • Dragging staging well to well, row or column shows stack
    • Plate Editor Set Plate Dimensions… dialog need beautification
  • Plots
    • Time series values ordered by workspace sort, not Time
    • Time Plot of 5 Stats = Stack
    • Histogram plots in the LE should keep the default color to match the GW plot.
    • Y axis label in time plots should adjust when window is rescaled like the x axis
  • Population Comparison: Population Comparison Batching in TE problems
  • Preferences
    • stack thrown at keyword/value pair deletion
    • Adding Comp Pref Keyword that does not exist in fcs = STACKS
    • Stacks when opening overlay settings menu
    • the panel wizard icon coloring is inconsistent in prefs window
    • Default Plate Size pref is not affected by the Reset button.
    • Plate preferences switched
    • CC Prefs – General
    • Workspace Sort Order Pref not in effect for future workspaces NEW STRs
    • Incorrect Sentence Checkbox Tip
    • fav gate names session-transient (not stored in prefs)
    • Reset Prefs should not reset License state
    • default value change in Number of Local Engines pref
    • Splash Graphic Preference Not Persisting
    • Prefs dialog needs to be made modal to the Application
    • Header & Footer Table Prefs not working
    • TE Pref remove the Close Tables without saving checkbox
    • Layouts Pref ‘Fill Histogram Overlays’ Not Working
    • Annotation Prefs- Can check ‘backgating’ when ‘ancestry’ isn’t checked
    • Annotation Prefs – Backgating Not Working
    • Missing string but it’s in the dictionaries
    • Plate ID in Plate prefs is showing a stringname.
    • Entering decimal numbers with Country language pref set to Germany
    • Compensation Prefs Remove Button no-op
    • compensation preferences text is cutoff
    • Matrix Editor section shifts down and disappears from clicking the Add button.
    • Editing Comp Prefs Keywords adds bad criteria to comp group
    • Plates Prefs – Intended Feature Doesn’t Exist
    • Unable to choose what to delete. Each row should have a delete
    • Layouts Prefs – Panel is cut off
  • Printing
    • Cannot scale Table to one page for printing
    • Footer Treestar Icon disspaears when changing between Paper styles in Landscape Orientation – pc only
    • Padding in Print dialog needs a limit.
    • Print preview through the GW splits a single sample into 2 previews.
    • Printing a histo plot from graph window is missing the color fill.
    • Global Print dialog – Reset does not affect Rows and Columns digits.
    • layout page breaks are not used in the print dialog
    • Header/Footer Treestar info is missing in Print.
    • Avoid page breaks moves graphs all over the place
  • Refresh Issues
    • Y axis scaling changes when graph defs are accessed – refresh issue
    • Heatmapping doesn’t apply to stats table – refresh issue
    • Use placeholders is not working in the LE
  • Ribbons
    • Dragging off a ribbon on collapsed tab mode throws a stack.
    • file tab; document ribbon save as… should be Save As Workspace…(
    • Save As Workspace… Brings up dialog looking for ws.save.workspace
    • context “freq. of” actions from the Statistics band in Workspace tab – no worky
    • Ribbon sub-menu’s extend out of visible range
    • Figure Presets ribbon only works in the farthest right tab when used in multiple tabs.
    • Figure Presets Apply & Plus button should be disabled if there is no figure selected
    • Ribbon bands don’t go away when popped up
    • Removing a collapsed Biology band closes FJ but is still running. PC only
  • Sample Quality: Sample Quality Check throws stack if a group is deleted.
  • Script Editor: script editor throwing stack upon running script
  • Shortcut Keys
    • The Enter key becomes the Undo shortcut key on a Curly and Spider Quad.
    • By default the FJ icon and the FlowJo tab have the same ALT shortcut.
  • Statistics:
    • Statistics Ribbon- Validation Stack when adding Median or CV from icons
    • Dragging stat to the group, dups stat and contains n/a copy.
    • Frequency of Statistic for Booleans not copying correctly to Workspace.
    • When adding a ‘Freq of’ stat, the name is repeated twice
    • Adding freq. of stats from stat interface
    • Stats not calculating in workspace
    • Percentile Statistic dragged to group does not work
  • Table Editor
    • Stack is thrown refreshing from the WS with a Batched Table in the LE
    • Error appears and a Stack is thrown when Batching to Printer
    • Heatmap tables does not output to the LE
    • Additional info on Y-axis in formula time series graph
    • Table Editor needs a scroll bar for stats
    • table column sorting error
    • batch to table, sort table, double-click – GW has wrong sample
    • Remove Column header name or show full name.
    • Table Editor selected statistic does not appear in references
    • Statistic field in TE takes on the edited name from Name field.
    • copy -> paste as html is broken
    • match table editor renaming action to table file destination
    • TE > Batch to Figure does not work with Table with Keywords or Formulas
    • TE batch to figure should play Success sound like the other batch functions
    • Batched Table with Expected Range Hides the currently selected row
    • TE Formula name dropped replaced with pre-current stat name in edit mode
    • Batched Table is cutoff after selecting Resize Columns.
    • Dont Show Again checkbox does not work from Batched Table to Add to Layout.
    • Line Plot near 0 ticks missing
  • Templates
    • Template with Iteration set to Sample, Panel or keyword throws stack
    • changes to log scale or miltenyi transform dont save to template
    • on template generated workspace, changing graph type in LE looses population of graph
    • First Time Opening Template with LE chart, chart is empty
    • Group-applied gating not being applied with gating on comped parameters in templates
    • Error Opening Template w/’Use Gating-ML Conventions’ Pref Enabled
    • Error Opening Template w/’Show Ancestry’ Pref Enabled
  • Text/Stat Box
    • When adding FJML keywords, can’t separate then with return characters
    • Fontsize in LE dropdown not adjusting correctly, displays wrong font size
    • Figure Presets can’t add enter new name
    • Text boxes are in edit mode when drawn but still can’t type text
  • Transforms
    • Miltenyi Template loses transform from wsp to wspt
    • Graph in axis transform dialog not fully reset after cancel
    • Manual transformation adjustment should be disallowed for default arcsinh tranform of CyTOF data
    • Transform Window can draw range gates on graph
    • Transform Editor – Next/Previous Sample Buttons Broken
    • Y axis is missing the zero when showing transformed data
  • UI Beautification
    • slider starts at end point of scroll
    • All Samples group not locked at top
    • ToolTips do not dismiss when another app gains focus.
  • Undefined
    • engine requests when resizing window
    • Staggered and Offset Histograms do not label X Axis on Overlays
    • Influx data is causing analysis to freeze
    • Background of gate annotation doesn’t change with fill
    • contours look different in LE than GW
    • Secondary graph windows don’t update when gate deleted
    • PageUp and PageDown don’t work in inspect properties dialog
    • overlay fill (via legend) menu shows “40%” option twice
    • performance exponentially worsens as curly quads moved
    • Editing keywords uses font too big for the space
    • Create a Series of Values window transition
    • can’t adjust gates when range is small
    • ACS File Opens a Blank Workspace
    • Zip containing fcs files not loaded
    • column values are lost
    • batch to web clips charts
    • Gates on derived parameter fails in reopened workspace
    • Arcsinh Transform Edits not Restored on Workspace reload
    • Axes names not good for partec files
  • Undo/Redo
    • Undo does not change the Graph type back to original.
    • Redo does all 3 overlays and skips the 2nd action overlay in the LE.
    • Font size/style in Fonts dialog box does not reflect Undo update and get stack
    • Undoing a staggered offset overlay in the LE is causing graph to show no pop
    • Undo removes 2 separate Group apply’s and the Grandchild node in the WS changes to Sample level.
    • Clicking Undo on an Overlay in the LE still shows the plots in the graph.
    • Undo not implemented on Transform changes
    • Undo delete legend in LE does not return legend
    • Samples added should not be undoable when part of a wsp load
    • All Quad gate movements aren’t Undone using Undo, the gates are just removed.
  • Workspace
    • Stats with no params do not update value when added to group
    • Group applying 2 levels deep gates does not group apply the 2nd level gate and throws a stack.
    • Stack is thrown when clicking on a group.
    • Stack is thrown dragging and dropping a sample on another sample.
    • Workspace thinks its connected to sample but is not.
    • copy paste from excel does not work
    • Lists disappear when scrolled – W7 java7 only
    • Repositioning workspace column is causing column data to be duplicated
    • Making a group with a staining selection shows up empty upon completion.
    • There is a (-) replacing the Reagent Keywords in the Group dialog.
    • Cannot add a gate onto a parent of the same name
    • Quitting FlowJo with unsaved workspace asks twice to save the workspace when cancelling
    • group inclusion is live but gate inheritance is not
    • Save as ACS does not open finder
    • Cant rename group via right click menu (sometimes)
    • Right Click in Group Window is ignored if Group Col. is not leftmost
    • FJ workspace icon tool tip seems to be outdated
    • Loading Samples via Drag and Drop Adds to All groups
    • FJ workspace icon Print functions are missing.
    • group-inclusion-triggered inheritance of gates can yield frequencies greater than 100%
    • Freq. of… quick stats
    • Demo Mode warns about non demo files but DOES add them to the workspace. (They have no data)
    • beta notification was not working
    • Copy/Paste gates in WS doesn’t copy correct hierarchy if different node
    • Dragging samples from desktop to group does not add to manual group
    • Dragging samples from desktop to Group Analysis switches to All Samples
    • Edit Group Properties shows a stringname.
    • Keyword Value Series… Dialog does not update Keyword entry boxes when updating params below
    • Event # parameter not copying to Group
    • Reopen Graph Windows … not working right, remove for 10.0.7
    • Creating NOT gate the stat of the original gate is lost
    • Dragging gates between workspaces creates child gate rather than replacing same-named gate
    • Identical Gate sample is using wrong icon
    • Change “Autoquads” to “BifurGate”
    • Cut, Copy, Paste of fcs files does not work
    • Tooltip shows stringname and should be greyed out on 2nd level etc.
    • Non-native group copied nodes are retained in WS but do not update when first shown or calculate without forcing
    • Help icon in workspace doesn’t have tooltip
    • Selection in the workspace with shift key only works when shift clicking on an object ABOVE the selection
    • Dragging gates from workspace onto another one replaces existing Gate, but shows as group owned still
    • No warning when opening lots of Inspect windows
    • Grouped tethered gates do not delete from group
    • statistic and cell count in the workspace are wrong/missing
    • Groups cannot be collapsed in Group pane
    • too many gates dropped from one wsp to another
    • Comp Badge shows red on re-opened workspace
    • Can’t drag samples, gates, or stats between workspaces
    • Disclosure Triangle Hit detection fails as you move many levels deep
    • tethered gates not applying correctly to group
    • Disclosure Triangle does not work when not the leftmost column

 

New Features:

  • Cell Cycle (New Platform)
  • Export
    • CSV Export added parameter annotation
    • Export dialog defaults the output format to FCS3
    • Exporting compensated parameters into new FCS files (new checkbox)
  • Plates
    • Added a heat map setting for an entire table, not just per column for Plates
    • NEW: Plate drawing tool for the Layout Editor
  • Layout Iteration: Removed the white box around the up and down buttons from the Iteration Value.
  • Layout Plates: Added Legend for Plate Editor Heatmaps
  •  Look & Feel: Fixed Text color tone on FJ STart up icon (was too dark).
  • Plate Editor (New Platform)
    • Plate Editor Moved Both Icons from the Export Ribbon to the Document Ribbon, remove the Export Ribbon
    • Drag and drop set of keywords from Staging well to individual wells, rows, and columns
    • Ability to export Plate editor annotation as a .csv or .xls file
    • Additional Selection capability in Plate Editor
    • Plate Editor Create group button
    • Added selecting wells in plate editor from group
    • Double clicking on a value cell will make it editable.
    • Right Click options on a wells
    • Put name groups under staging wells
    • Add a Load Samples from Group button
    • Well Highlight for Keyword/Value pair feature change
    • Add labels to lists on Plate Editor
    • Plate Editor Well Copy Paste works when filtered on Keyword.
  • Preferences
    • Prefs for printing in the Layout Editor and rulers to update to the prefs set
    • Add preferences for Default Histogram Style.
    • Feature: Accuri data FSC & SSC should have different defaults
    • Default scaling for Sony SP6800 data
    • Don’t Show Again Prefs – reset now, reset on exit session. Also made them more granular, each dialog has it’s own setting.
    • Added Plate Prefs
    • Mirrored Layout Prefs & options in Layout Editor batch band
    • Cytometers preferences scrollbar added.
  • Ribbons: added ability to get to help on a ribbon when it is collapsed
  • Table Editor
    • Moved Keyword icon from Format/Keywords band to Edit/Columns band
    • TE batched report Menu Re-design
    • TE Batched Report Menus: added a “Hide/Show Summary Stats ” menu item
  • Transforms: Change default scaling for Cytof data d/t data compression at zero
  • Workspace
    • added ability for keywords to move to the top of the list once used
    • Clicking on a compensation node opens comp editor
    • Change name of “Instrumentation” band to “Cytometry” (workspace tab)
    • File Missing Icon is now easier to see

Known issues:

  • 3D Viewer
    • Axis are malformed when opened on comp parameters
    • 3D viewer does not update live with gate moves in the GW
    • Group applying a 3D node changes the parameters and the default color of the 3D plot.
    • terrain plot monochromatic, missing 3rd axis label.
    • Points Plotted at 0% on TE 3D Plot
  • Annotation: Annotate Exp. Figures Tab: Preview of the fig should be scaled to fit
  • Boolean Gates
    • Combinations of NOT Gates with AND or OR gates has problems
    • Identical Gates are not Clone gates
  • Multidimensional Cell Cycle is still under construction.
  • Compensation Matrix Editor
    • Cannot undo Matrix application
    • Group-applied size gates in compensation persist after deletion after compensation has been calculated
  • Compensation
    • Round assignment buttons do not accommodate long sample names
    • Setting the wrong size gate with some Accuri data with AutoComp (Manual gate works fine)
    • Strange scatter gates for S3 comp files
    • S3 comp gate snaps to original position after unrelated axis transform
  • ACS: No progress indication when opening ACS file
  • Export: PDF export error when legend breaks pages
  • File Formats
    • Non-ascii char in fcs file may be stripped from file display in workspace
    • 9.7.1 jo files: Bisector gate is converted to two range gates.
    • 9.7.1 jo files: Quad gates converted to 4 rect gates.
  • Graph Window
    • “Save Graphic” as SVG doesn’t produce re-scalable vector object
    • When pasting from GW to LE, Median (Black Cross) is gone
    • Changing Oval Gate midpoint is reset when changing it’s endpoint
    • Can’t select/delete quad gates in Graph window if other gates coexist.
  • Kinetics is under construction
  • Launch: Java network connections dialog flashes at startup after
  • Layout Charts: Cannot turn legend ON and add keywords at the same time.
  • Layout Editor
    • Batching NxN too many times FJ will run out of memory or throw a stack.
    • Batch to PPT w/tint, tint is solid
    • Layout presets do not change anything but object settings on figures (as designed)
    • Avoid Page Breaks – annotations moved incorrectly (or not moved at all) sometimes
    • unable to paste image with transparency into the le
    • Batched tables in LE do NOT live update
    • Show gate median not appearing in LE
    • graph bleed-thru in the LE when changing layers of overlapping graphs
    • Dragged oval into grid object does not appear until grid resize
    • batch to PDF ignores page orientation
    • Copied Text Box retains wrong font size info
    • layout editor window is collapsed upon editor opening (for some)
    • FJML Blocks overlap slightly after copy and paste Text object.
  • Layout Outputs: Clipping bug – SVG displaying gate outside graph area
  • Layout Overlays
    • Multi Graph Overlays size – lost when batching (reset to default size.)
    • Renaming populations can break overlays / legends in the LE
  • Panel Wizard: Panel Wizard has problems when it loses network connection.
  • Population Comparison: Drag Compare Population Node to LE has lots of errors in console, most of chart is has no values
  • Preferences: duplicate Cytometer preferences not being resolved
  • Printing: The LE shows the data from the GW Print Dialog and disregards anything else currently in the LE.
  • Shortcut Keys: When closing a GW through shortcut key Ctrl+W it’s also closing the WS (this is due to the key auto-repeat firing off the same events, this can be adjusted in the preferences, Diagnostics->Action Delay)
  • Statistics: adding stats to wide samples is very slow and can crash FJ (Example file had 83 parameters)
  • Table Editor
    • TE resizing columns leaves unused space on right side of window
    • TE: Formatting band does not work outside of the Visualize Tab
    • Hide Column Checkbox removed from Edit Column Dialog
    • Batched Table XML Excel does not show Column headers as seen on a regular Batched Excel
    • table column headers change when saved as .wsp then opened in new workspace when to column title provided
  • Text/Stat Box: copy paste in LE text box not working well
  • Transforms
    • Calculating indicator is missing when transform are applied
    • S3 GW and Transform window parameters do not match up
  • Platform Specific…
    • We do not support Java 7. Windows versions include Java 6, and Java 6 can be installed with OSx along with Java 7 so FlowJo can use Java 6
    • Retina displays not supported at high resolution.
    • Directories with identically named data (ie plates, panels) confuse FJ grouping
    • SampleID scale incorrect – concatenated files
    • Derived Parameter window cancel doesn’t cancel… it applies.
    • Creating a Formula with a Control Population withut supplying a name for the column may generate incorrect stats.
    • We canot handle exporting separate files from barcode files with multiple populations in them.
  • Undo/Redo
    • Note: Undo and Redo may have unexpected results. We hope this is better in a future release. If you have specific cases where undo or redo is failing, please let us know.
    • Undo Removes extra gate in WS
    • Undo Brings back a deleted gate from unrelated operation
  • Workspace
    • Insufficient progress when opening large WSP files…
    • User not provided feedback that workspace is still calculating on long calculations
    • Double clicking on left side of group in Group pane does not open group. (Click further right)
    • Cmd – W (Alt -W) Should close the frontmost window (and does not always close it)
    • Spacing in the rows and columns of the WS changes when Preference dialog is opened then closed.
    • Gate annotations don’t update w/synchronized option (but the gates do!)

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