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.
- 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
- 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 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 <Reset This Parameter> 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.
- 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
- 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
- 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
- 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.
- 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
- <DocumentName/> 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
- 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
- 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
- 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
- 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
- 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
- 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 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
- 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
- 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.
- 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 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.
- 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
- Cell Cycle (New Platform)
- CSV Export added parameter annotation
- Export dialog defaults the output format to FCS3
- Exporting compensated parameters into new FCS files (new checkbox)
- 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.
- 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
- 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
- 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
- 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
- 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.
- 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
- 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!)