FlowJo is the Swiss army knife of Flow Cytometric analysis programs. It contains tools for all of the jobs you need to easily and efficiently perform any type of data analysis from start to finish. For detailed release notes through v. 5.7.1, CLICK HERE.
Index:
Version 7.6 (February 22, 2010)
Version 7.5.5 (August 03, 2009)
Version 7.5.3 (June 23, 2009)
Version 7.5 (June 1, 2009)
Version 7.2.5 (April 6, 2008)
Version 7.2.4 (February 27, 2008)
Version 7.2.2 (June 6, 2007)
Version 7.2 (February 8, 2007)
Version 7.1.3 (October 9th 2006)
Version 7.1.2 (August 3rd 2006)
Version 7.1.1 (July 5th 2006)
Version 7.1.0 (May 17th 2006)
Version 7.0.6 (April 28th 2006)
February 22nd, 2010 - 7.6 Features/Release Notes
| Component | Summary of Features Added | |
| Workspace | ||
| - | Sample properties in Workspace right-click menu | |
| - | Reagents in 'Edit Columns' listed according to parameter. | |
| - | Export WS to Excel added (from File menu) | |
| - | Save gates when deleteing group owned gates | |
| - | Editable text traits in Workspace | |
| - | Column width is based on file name and not gate names | |
| - | ACS shouldn't open own window | |
| - | Create Group From Selection added (also in Table Editor) | |
| - | Keep "FL-Reagent" pseudokeyword and "$P#S" keyword contents in synch | |
| - | Combination (Boolean) Gates - use +/- symbol instead of "~" | |
| - | Changed decimal precision to significant figures number | |
| - | Allow "duplicate gate" feature | |
| - | Allow $P#N keyword modification like in the mac version (with a warning) | |
| - | Ability to set the default workspace columns to always display certain keywords. | |
| - | Ability to highlight a group and still see group color | |
| Table Editor | ||
| - | Turn on heat maps from Menu or right click | |
| - | Pagination of tables is too wide | |
| - | Excel button to create direct CSV file | |
| - | Excel "open after save" is default | |
| - | Sig. Figs. Default | |
| - | Table headers don't transfer to LE | |
| Preferences | ||
| - | Added preference for reading 2.0 section of Coulter files | |
| - | Added preference to make points in 3D scatter larger | |
| - | Change calibration parameter | |
| Platforms | ||
| - | Population comparison - Platform added | |
| - | Population comparison - Apply All button | |
| - | Population comparison - Multiple controls | |
| - | Population comparison - Preserving viewing format sample to sample | |
| - | Population comparison - Color scheme | |
| Layout Editor | ||
| - | LE10 Contour Overlays | |
| - | Saving layouts which include external graphics retain the image''s absolute reference | |
| - | Placeholders should not print | |
| - | The iteration is set to sample by default | |
| - | Copy picture with gates to place FJML into clipboard | |
| - | New attributes for grids; "resize with chart" and "keep aspect ratio" | |
| - | Progress indicator when changing graph type in LE | |
| - | Deleting mutiple layouts at once | |
| - | Large Dots for Backgating | |
| - | LE graph gate font preferences | |
| - | Preference for filled histograms in the LE | |
| - | Changing line thickness/attributes for overlays simultaneously | |
| - | Drag multiple selections from WS to LE | |
| - | Copy plot from LE as Vector graphic (like Mac) | |
| - | Export graphics to PNG format in PPT | |
| Graph Window | ||
| - | Naming each quad gate | |
| - | Ctrl+R to reset existing graph window | |
| - | Version numbers quad gates in different fashion than the Mac | |
| - | Adjust nodes in quad gates | |
| - | Window title just shows file name | |
| - | Change fonts in statistics in GW | |
| - | Multiple duplicate graph windows (like Mac) added | |
| - | Pref to place annotation outside of gate | |
| - | Control disabled on Manual Gates | |
| - | Magnetic Gates added (like Mac) | |
| - | Click enter key to update dot plot number | |
| - | Have gate selected when opening a graph window | |
| - | Implemented Curly Quads | |
| - | Curly Quads should retain slope when background is adjusted | |
| - | Fill Histogram on Graph Window | |
| File Formats | ||
| - | Enhanced handling of ranges for Accuri, Coulter, Miltenyi files | |
| Compensation | ||
| - | Autotransform uncompensated parameters | |
| - | Added a user-defined prefix/suffix for identifying Compensated parameters | |
| - | Ability to drag matrix to a sample group. | |
| - | Apply button for 'set transform values' dialog box | |
| - | Live compensation matrix editing (keystroke combinations, like Mac) | |
| 3D Viewer | ||
| - | Add next/previous buttons to 3D viewer | |
| - | Up button to open graph window from 3d viewer | |
| - | Use more events in bubble plots | |
| - | Increase voxel slices more than 32 | |
| - | Add back scroll for assigning colors to parameters |
Component |
Summary of Bugs Fixed |
|
| Workspace |
|
|
| 7.5 has some issues opening workspaces and templates | ||
| Problem with deleting group owned gates | ||
| Dialog for quiting at startup with muliply FJ | ||
| Copy to group does not maintain sample panel selection properly. | ||
| NAN AND n/a needs to be the same | ||
| Keyword Value Series wraps around list. | ||
| WS10 Print cancel stack | ||
| Changing groups needs to clear selection in Sample tree | ||
| File/save dialog reshuffles windows | ||
| Delete a row that''s already deleted produces stack | ||
| Can''t load samples into 7.6b6 | ||
| Copy a contracted gating tree to the group, only the viewable gates will transfer to the group | ||
| Dragging group owned gates take text properties with them | ||
| Copy modified group owned gate doesn't always ask to replace | ||
| HIV Study specific NPE thrown on group change in workspace. | ||
| Workspace won't sort while keyword is being edited | ||
| No workspace indicator when scrolling through samples in GW | ||
| Mode calculated incorrectly | ||
| Ctrl - A select all in wsp not repsonding | ||
| Concatenate with new parameter | ||
| No files added error window when loading files | ||
| Sample selection arrows when scolling GW missing in WSP | ||
| Summit Concatenation | ||
| Select equivalent nodes not responding in workspace | ||
| Creating a combination/boolean gate results in an NPE | ||
| Class Cast Exception when stored values for editing a keyword eceeded the 25 limit | ||
| Frequency of ... provides 000 when great greatparent is selected | ||
| Dragged nodes from sample view to group view are offset by one when dropped. | ||
| Confirmation dialog for deleting nodes in group mis-fires | ||
| Changing groups changes sort order | ||
| Problem with "create group from sample selection macro" | ||
| Help/About FlowJo goes to a webpage, instead of a status dialog | ||
| Can't create a keyword value series in existing keyword | ||
| Edit columns bug when 2 WS opened | ||
| Right clicking on Name column and clicking on "Edit Columns" does nothing. | ||
| Edit Column Names Window does not update (after first use?) | ||
| Add Derived Parameter... - Exception | ||
| Edit coulmns display selects multiple columns names or none | ||
| Adding samples to the wsp resets the default column width. | ||
| Keyword value series text boxes no longer dynamically updated... | ||
| Keyword value series dialog search and replace broken | ||
| Workspace-to-worskpace drag problem | ||
| Couple of workspace drag-to-group problems WITH QUADS | ||
| Add fsc3.0 data induce bug | ||
| Lost ordering in Workspace | ||
| Large text sizes truncate before they need too | ||
| Close wsp still get "do you want to save table?" | ||
| NPE when trying to replace gate | ||
| Copy/Paste bugs | ||
| GetFlowJoLocale() returns wrong info | ||
| NPE when opening prefs menu from wsp | ||
| Column width of group panel incorrect until you resize them manually | ||
| group selection display is incomplete box should be blue, only showing half | ||
| Add statistic button available when group selected | ||
| Bugs when changing the name of a group-owned gate | ||
| Expand all command doesn't work | ||
| Frequency of .... srar. doesn't follow Sig. Figs. pref. | ||
| Comp data not exporting | ||
| Mac sig figs missing change display | ||
| MFI's greater than 999 lose their first digit | ||
| Statistics copied to group duplicate in main sample | ||
| Help menu hardcoded URLs | ||
| Losing sig figs after save in prefs | ||
| Undo (Rückgängig) in (Swiss)german localization gives faulty characters | ||
| items on right-hand pane of Edit Column Names are not selectable | ||
| Deleting a bifurcated gate from the wsp deletes them all | ||
| Weird item in wsp righ click menu: samplesRemoveButton | ||
| Unresponsive Menu items | ||
| Right click on columns, choose edit columns produces exception | ||
| Add Undo for Remove Samples command | ||
| Undoing stat drag to group undoes one by one | ||
| Collapsing a group opens modify group dialog on first click | ||
| Text selection display trouble | ||
| Population comparison | ||
| Export bug | ||
| Workspace statistics disappear when selected | ||
| Groups losing colors | ||
| Drag to anywhere unresponsive | ||
| Apply value to group missing | ||
| Sample names not showing in workspace when selected | ||
| Right click menu in wsp unresponsive | ||
| Print Preview Step size is 1 inch, not 1/8 | ||
| Export/concat message repeats | ||
| Export overwrite policy pref does not make unique name | ||
| Alt-Drag to group doesn't propagate subpopulations | ||
| Group tree shows the number of samples for the subpopulations | ||
| Workspace disclosure arrows get stuck when open/close | ||
| Prefs not showing in prefs box | ||
| Create groups by Keyword Value menu item throws NPE | ||
| Windows only Java engine out of date: Can't shift click top to bottom | ||
| SetGroup Value has reappeared in Groups menu of workspace. | ||
| Export/concatenate truncates file name (FCS3 and CSV export options) | ||
| Can't Ctrl+window click to select certain samples | ||
| Selecting "Copy Value to Group" from groups menu throws exception | ||
| Edit columns | ||
| Right click menu in wsp unresponsive | ||
| Changing font from 10 or 12 to 24 or 30 in wsp breaks wsp disclosures | ||
| Deleting combination gates gives NPE | ||
| Can't deselect after you shift-click all samples in the wsp | ||
| Options in Tools menu of wsp that should gray out, but don't. | ||
| Right click column header in wsp, remove column not working | ||
| Keyword value series doesn't repeat | ||
| First drag doesn't add samples Mac | ||
| Can't drag 3D node to group | ||
| Hierarchy not retained when allocating deleted group gate to first sample. | ||
| Magnetic gates applied to group won't overwrite existing gates (of same name/population) | ||
| Workspace Edit Columns doesn't undo | ||
| Workspaces seem to be empty when opened | ||
| Copy Gate to Group does not obey gating hierarchy | ||
| Group disclosure triangles unrepsonsive | ||
| Unable to select Frequency of Total File from Workspace menu | ||
| Can drag and copy individual quadrants of quad gates | ||
| Copy Value to Group never grayed out. Mulitple clicks on/off required to copy to group | ||
| Dragging a proliferation node to the group is unresponsive | ||
| Broken Font Preferences | ||
| Can't drag to group | ||
| Shift click to select anything in the workspace is unrepsonsive | ||
| Make Not Gate always available and icon doesn't change in wsp | ||
| Deleting combination gates created from quads deletes both the combo gates and the quad gates | ||
| Adding Keyword value series freezes FJ | ||
| Can't drag Cell Cycle node to group | ||
| Child deleted when allocating to first sample | ||
| Dragging off by one in group pane | ||
| Http links points to old webpage | ||
| Single click on multiple selections no longer selects target | ||
| Erroneous "plot could not be constructed" notification | ||
| Resize columns button busted in b41 | ||
| Drag to group pointer becomes missaligned if group panel scrolled | ||
| Group owned gate deletion - allocate to first sample, doesn't work. | ||
| Cut make an NPE | ||
| Statistic menu choice disappears | ||
| It's possible to create mutliple groups with the same name | ||
| Sort order disbanded when loading folders | ||
| NPE from "About Flowjo" window | ||
| About dongles needs redirect | ||
| Saved workspace with JPG in LE won't open | ||
| Width of culumns in Propertie table can not be changed | ||
| Opening a saved template produces NPE | ||
| Edit group selection does not come ungrayed when group is selected | ||
| Unable to change order of columns in the workspace | ||
| Unable to "x" out of edit columns | ||
| AppleEvent handlers not installed | ||
| Two blank workspaces opened when starting up FlowJo | ||
| Apply Button in Edit Font dialog is not visible until window resize | ||
| Create group window: long keywords hide entry box | ||
| Make a change in a group induce group name to change | ||
| Open create group window repeatily and it renders smaller and smaller | ||
| Workspace not refreshing | ||
| Oversized workspace window - out of eclipse | ||
| Default contour levels don't change when set in prefs | ||
| Absolute scale of histograms used whatever preference is set to. | ||
| Autogate color not applied | ||
| Graph window annotation position is not set by preference | ||
| Deleting Group Owned Gate - not keeping hierachy PC only | ||
| Overwrite preference | ||
| Group Properties Dialog - asks to apply changes even if no changes made | ||
| Save as Excel defaults to saving over workspace | ||
| Export to FCS3 twice with same file deletes both files | ||
| FlowJo will open same workspace in multiple windows. | ||
| Drag samples text overlap in workspace | ||
| >100% stats in 7.5.5 workspace into 7.6 | ||
| Show frequncy of gate is off by default | ||
| Dragging samples in wsp produces ghost image that gets stuck - PC only | ||
| Icon displaced while dragging items in Wsp - PC only | ||
| Make AND gate shortcut unresponsive - PC only | ||
| Table Editor |
|
|
| TE03 in table output, the second row samples is scrollable | ||
| Adding a column in TE makes the column a formula | ||
| Correlation plots uses wrong data | ||
| Column headings move, but the numbers don''t | ||
| Table editor column information window is not taking column heading text edits to change column headings | ||
| Still get the confirmation: do you want to save this table with saved table | ||
| Clear in the Edit Menu | ||
| TE table node deletion confirmation reshuffles windows. | ||
| TE07 Generate Group from Table Selection places Group Name dialog wrong | ||
| Generate Group from Table Selection places Group Name dialog wrong | ||
| Batch in TE not responding and producing stack | ||
| Output "To File" in TE not responding. | ||
| Recalucating gates in TE freezes TE table | ||
| Statistic calculation in the TE wrong | ||
| Correlation-line plot shows mean and std points | ||
| Cancel Export to excel still makes sound likes it's exporting | ||
| Output Menu in TE non responsive | ||
| Add TE to LE makes you lose the first sample stat | ||
| Not saving table still opens save dialog box | ||
| columns out of sync in TE | ||
| Adding stats adds double stats to sample | ||
| Regression line in correlation plots unresponsive | ||
| Numerous items in TE causes names to be replaced with generics | ||
| Help on tables in a generated table leads to todo.com | ||
| Column header default name duplicates itself | ||
| changing the file type in file panel does not change the extension of the file name | ||
| If you don't edit column heading you get median for formulas | ||
| Table generation unresponsive | ||
| Print preview for TE is blank | ||
| Generated table shows 000% for ungated population | ||
| Can't create multiple tables | ||
| TE "Save As..." unresponsive | ||
| Edit column in the TE opens column information even though no column to edit is selected. | ||
| NPE in TE and LE when attempting to iterate by keyword | ||
| Broken TE menu items | ||
| Conditional formatting (color) in TE not obeyed if heatmaps are used | ||
| Create group from selection in TE generated table allows groups to have same name | ||
| Table columns headers don't come out when added to LE or saved as CSV | ||
| TE Median, mean, ect. stats don't have the gating info | ||
| Setting Table iteration from Preferences is unrepsonsive | ||
| Header and Footer don't appear in tables | ||
| Table Column header not displaying the population cell and name cell | ||
| Table batch to CSV are missing table column names, spacing off, and quotes are present | ||
| Commas showing in TE headers | ||
| Custom column names 'cruft' | ||
| When choosing a custom name for a sample in the TE, the name will always say "ungated" | ||
| XML open document in TE throwing stack | ||
| TE not printing all data | ||
| Switch columns in a table then saving to excel doesn't show changes. | ||
| issues with correlation plot and n/a stats | ||
| Correlation plot missing x axis | ||
| Table editor cell does not take +, -, *, / sign | ||
| Add Table to Layout lose the table lines of column and row (Mac only ) | ||
| Uable to make line chart with correlation plot | ||
| Iiteration by keyword gives wrong output | ||
| Heat Map in Table - not toggleable on/off | ||
| Custom named columns appear on different header row depending on node being gate or stat | ||
| Not prompted to overwrite Excel file | ||
| Reording columns in the TE with drag/drop, row ends up two high when dragging upward | ||
| Can't see drags into the TE | ||
| Iterating in the TE by cells and tube is creating an error | ||
| Platforms |
|
|
| Next button in kinetics closes window | ||
| Platform node nav buttons do not light up when node is dragged to group | ||
| Copy histogram with curves give black background. | ||
| Batch CC in LE gives wrong y axis scaling | ||
| proliferation won't open | ||
| NOT gate freezes FlowJo | ||
| Population comparison pull down menus are intert | ||
| Population comparison - File name display | ||
| Plate editor close than cancel closes anyways | ||
| 2D cell cycle is not available | ||
| Dragging kinetics node to group resets parameter selection | ||
| Cell cycle: draw compent box fail to response | ||
| Cell cycle overlay is mostly broken | ||
| Proliferation buttons don't scroll through samples | ||
| 2d cell cycle window doesn't obey parameter selection | ||
| Clicking in DP preview window gives npe | ||
| Apply to Group in DP window unresponsive | ||
| Pop Comparison Table blank | ||
| Cycling samples in Pop Comparison throws NPE | ||
| Printing Pop comparison does not obey landscape feature | ||
| Printing a graph from the Cell Cycle Platform is off center | ||
| Opening Kinetics platform is throwing this exception | ||
| Printing a graph from the Kinetics Platform is off center | ||
| Printing a graph from the Proliferation Platform is off center | ||
| Printing a graph from the 2D Cell Cycle Platform is off center | ||
| First kinetics nodes blank in the LE after draging to group | ||
| Cell cycle is missing its x axis | ||
| Manual scaling in Kinetics does not work | ||
| Cell Cycle in TE | ||
| CC error while creating table | ||
| Range gate in CC platform is not updating live | ||
| Kinetics range markers can not be deleted. | ||
| Multiple range creation in Kinetics fails to accept user inputs | ||
| CC mean in constraints should be blank when using min and max | ||
| Menus are centered instead of left justified | ||
| Preference window not opening from Kinetics window | ||
| Next and Previous sample not functioning in Kinetics | ||
| Plate dimenstion doesn't allow > 9 entered for rows or columns | ||
| Show overlay unresponsive in Proliferation platform | ||
| Proliferation preference settings not maintained in prefs | ||
| Inconsistent formatting in Kinetics tool | ||
| Proliferation "Copy Histo w/curves" gives error dialoge "Plot can't be constructed" | ||
| Table doesn't update proliferation changes in changed sample | ||
| Plate Editor |
|
|
| Plate editor has wrong icon | ||
| Dragging in a stat to the Plate editor | ||
| Acquisition button does not open | ||
| Multiple bugs in Plate Editor | ||
| Layout Outputs |
|
|
| Copy To clipboard clips top number in Y axis. | ||
| Clipping bug in batching to webpage | ||
| Graphics don''t respond to landscape feature in print | ||
| Batch to PPT axis offset | ||
| Layout Editor |
|
|
| X axis label shifts depending on lin/log scaling (or scientific notation) | ||
| Deleting nodes in Wsp, doesn't delete in LE | ||
| Custom graph names LE batching | ||
| Cannot change custom X/Y axes in layout for multiple plots | ||
| Annotation Preference, show full path | ||
| Quicktime wiki | ||
| Setting control in LE grays out frequency | ||
| Keywords in annotations do not batch | ||
| Biexponential plots have "0" lined up with exponents on Y axis | ||
| Locked control at sample level does not work | ||
| Gate font and color are incorrectly initiated/extracted | ||
| 3D Viewer UnResponsive | ||
| Cancel Batch to Printer Dialog | ||
| Adjunct histograms batching | ||
| Annotation dialog box throws null exception | ||
| Cursor/% sign disappears when moving statistics in graph window | ||
| Dragging a Sample to the LE changes the graph type. | ||
| Losing cursor in LE with staggering Histograms | ||
| Right click menu on graph in LE not responding | ||
| Can't not save the graph setting from the graph defination window to other graphs | ||
| Autobatch option not working | ||
| NPE in 3d viewer | ||
| NPE after clicking undo in the LE | ||
| Can't delete a graph in the LE | ||
| Undo Bug List | ||
| Delete not working in LE | ||
| Resized charts in LE become unrecognizable | ||
| < and ">" chars truncate textboxes in LE | ||
| Saving layouts with disk icon shows dialog twice and disables page breaks | ||
| Histogram doesn't update with color change in LE | ||
| Mouse over on table editor and layout editor are incorrect | ||
| Change y-axis scaling to auto and apply, the label turns to count, but there are no ticks or numbers. | ||
| Every action in layout button bar is duplicated | ||
| Save state to prefs crashes FJ | ||
| Batching to Webpage cuts off the very top of the 4 on the Y axis | ||
| Dragging a stat or a graph to the grid in LE throws NPE | ||
| Extra row in table when added to LE | ||
| Sample names not showing in LE | ||
| Samples that are dragged to the LE no long show the Sample name/pop. name/ count. | ||
| Text in grids get borders | ||
| Align shortcuts in layout editor don't work | ||
| Templates do not relink charts if "panel" iteration is used | ||
| FJML not parsed in LE | ||
| Headers and Footers do not appear in LE batch output | ||
| Printing a page of the LE cuts all the graphics | ||
| Saving as .emf and putting into Microsoft office suite includes scroll bars in image. | ||
| Histogram filled in black | ||
| Overlay histogram turns black can't tell samples apart | ||
| Dragging stats to LE show code and not stat | ||
| Annotation text properties grayed out in LE | ||
| Kinetics charts in LE allow changing Y axis: label changes but plot does not | ||
| Group owned gates showing "no Population" in LE | ||
| File "Save" default location is program files | ||
| Drag statistic to the LE cannot drop on graph. | ||
| Statistics text properties box in LE - apply/ok grayed out. | ||
| Right click on menu in LE throws NPE | ||
| Freq of total is zero in the TE | ||
| SVG saving fails | ||
| Manipulating annotation contents throws exception | ||
| OK and Apply buttons are grayed out when trying to put some content in text tool | ||
| Annotation/Legend button in annotation tab unresponsive | ||
| Numbers Only... but can input letter | ||
| Changing from graph to histogram in LE loses y axis | ||
| Histogram coloring, line style and line weight not working 7.6 b 28 | ||
| Turning on Simpler UI freezes FJ | ||
| Graph definitions -save doesnt seem to work | ||
| Modified group owned gates do not turn their bold font off. | ||
| Freq. of Parent showing 0.00 when dragged to LE | ||
| Insert Picture is missing from File menu in the LE | ||
| Batch to printer ignores landscape option in print preview | ||
| Insert picture option in LE is non responsive | ||
| Object properties broken in LE | ||
| Contours are red when dragged to LE | ||
| Exception when opening LE | ||
| No tick marks on x-axis in LE | ||
| Checkbox on Scale percentage in Graph Def window doesn't do anything | ||
| PPT button gives Exception with Adjunct histograms | ||
| Batching to PPT removes some graphics | ||
| Tint Sample/control in Pop Compare Removes original histogram line | ||
| LE Legend Incorrect Size | ||
| Object properties for Grid in LE throws NPE | ||
| Open Original Graph always available in LE Object menu | ||
| Layout Editor menu items that have the same keystroke shortcut | ||
| Proliferation/CC has background histogram filled when in the LE | ||
| Changing graph to histo in LE throug graph definitions window fills in histo | ||
| Annotation left behind when aligning in LE | ||
| Changing histogram scaling fills histogram in black | ||
| PPT click should produce a slide per page | ||
| PPT temp file not deleting | ||
| Change graphic output to landscape for PPT slide | ||
| Labels on axis in LE cannot be changed | ||
| justify box in text creator in LE | ||
| MGOs are duplicating | ||
| Changes to legend from graph def window aren't holding | ||
| Exception when overlaying two nodes in the LE | ||
| LE Overly layer color selection doesn't undo | ||
| LE Overlay add legend column doesn't undo | ||
| LE Overlay remove layer doesn't undo | ||
| Layout editor batch generates duplicate plots | ||
| Deleting a layout brings wsp window forward | ||
| Axis names not maintained when graph is moved. | ||
| Save as PDF cuts off plot | ||
| LE: Redo Adding a layer to overlay doesn't work | ||
| Batch dialog doesn't update to reflect change of group focus in workspace after 1st batch | ||
| ungrouping multigraphs from batched tile causes multigraph to jump to wrong position | ||
| plot cannot be constructed when dragging equiv nodes to layout | ||
| duplication of grouped objects does not fully duplicate | ||
| Fit in Window goes to 50% every time | ||
| Can't drag firs sub pop into LE from any samples | ||
| Clicking on the save icon in the LE erases page breaks | ||
| Exception when selecting the clipboard in the LE | ||
| LE not updating for GW gate label | ||
| plot disappears in LE | ||
| Annotation Preference bugs | ||
| Show Graph Tittle in the prefs breaks annotation | ||
| Broken Layouts Preferences | ||
| LE Redo is always available. Throws NPE if hit before there has been an Undo action. | ||
| Simple UI creates blank batches | ||
| Unable to batch by panel and getting NPE when switching iteration from keyword to panel | ||
| Legend disappears when making any changes from Graph Def window | ||
| LE data/scale mismatch | ||
| Any changes made from the Graph Definition window if accessed from a grid, deletes the grid. | ||
| PPT single slides broken | ||
| PPT batches broken | ||
| Batching pop comparison...all plots are identical. | ||
| Child populations can't be shift selected in the workspace | ||
| rename error dialog missing: "Can not rename stat node" from workspace | ||
| Stat nodes in the LE on first drag are always placed 128 pixels too far up and left | ||
| Previous defined graph comes out blank in LE regardless of iteratioin set when saved | ||
| Append to PPT fails if a non PPTX file is selected | ||
| Append to PPT fails on PPTX file with more than one image per slide | ||
| append to ppt fails if file does not exist | ||
| Append to PPT fails on previous made powerpoint file | ||
| Batching of statistics in LE editor malfunctioning | ||
| Keywords "Sample", "Panel" and "Off" do not allow to iterate by discriminator | ||
| When dragging multiple samples in the LE they are dropped on top of each other | ||
| Batch to PDF using headers/footers - file is damage and cannot be opened | ||
| Adding statitics to legend on kinetics nodes causes exception | ||
| Multigraph not showing when checked in LE | ||
| Help button does nothing on Object properties box | ||
| Stack thrown when trying to close gw after duplicating it | ||
| deleteing samples or populations leads to inconsistent layout editor state | ||
| Batching in LE with JPG background created exception in Eclipse | ||
| click on batch in TE or LE give an error sound | ||
| lost the graph overlay after batch | ||
| Copy axis in LE and then delete plot leaves plot in LE | ||
| N don't apply for grid attributes | ||
| wrong axis name in LE when graph type changed | ||
| show legend, show multigraph, show annotation set on multiple plots in LE only changes one | ||
| LE histogram offset | ||
| Change multiple fonts in the LE, move graph and the labels disappear | ||
| LE with JPG in won't batch | ||
| Graph in LE from template do not repopulate | ||
| Layout Graph Font Style not updating. | ||
| Set Control from graph legend does not set control | ||
| selecting a different group affect the graph displayed in the LE | ||
| Histogram don't scale correctly in the LE | ||
| Batches in the LE do not take custom name instead use generic name Layout-Batch | ||
| PPT doesn't open when "open after creation" is selected | ||
| Append to PPT no longer works | ||
| Show Ancestry horizontally does not respond | ||
| Show Ancestry horizontally does not respond | ||
| Option boxes are ignored in batches | ||
| Change of grid size loses data already in grid | ||
| Undo after editing properties dialog of grid removes grid | ||
| Stats in LE are not updating with samples | ||
| Multigraph options not displaying as expected in LE | ||
| Can't undo placement of stat in LE | ||
| gate change don't update completely on a layout batch | ||
| Change mutliple items in LE | ||
| Batching with multi graph to a movie removes multi graph top line | ||
| Quicktime batch ignores "open" checkbox - PC only | ||
| NPE on undo in LE after setting page breaks | ||
| Movies on Mac - checkbox open after creation, never opens movie | ||
| Double Translation: Copy a graph in the LE and move it - annotation moves twice as much | ||
| Can't undo overlay | ||
| Duplicated graphs in the LE place MGO's in above graph - should be lower right hand corner | ||
| Properties grayed out in LE for adjunct historgrams - PC only | ||
| Cells number in grid in LE can't go above 9 | ||
| Check mark missing on menus | ||
| Position of Ancestry is absolute, not relative to graph | ||
| Reopening panel iteration throws le out of sync | ||
| Annotation shows as little box when cleared in prefs | ||
| layout editor charts and pulldown menu inconsistent | ||
| Proliferation node histogram changes axis when moved to LE | ||
| wrong display after batch of kinetic graph | ||
| batch turns off when draging a graph in the LE | ||
| out of memory after batch to PDF | ||
| Axes disappear in LE | ||
| Layout Editor - iterate by panel | ||
| Shift - resize grid throws top of grid off screen | ||
| draggin mutliple child gates to the LE places them out of order | ||
| graph display settting does not carry over to layout | ||
| Sample Mismatch Policy Dialog coming up erroneously in Layout Editor | ||
| Overlaying two overlays deletes samples | ||
| LE grid pasting graphs randomly truncated until refresh | ||
| Arrow keys to move items causes all graph clones to be selected. | ||
| Successive changes within the graphs definitions in the LE do not apply to all graphs | ||
| MGO empty when added to graph in LE | ||
| Batching acts like Simple UI is stuck on for Batch. -PC Only | ||
| NPE in LE from Table imported from TE | ||
| Layout Charts |
|
|
| Right click autobatch-on does not work | ||
| Drag txt to layout, double click, ok, loses line feeds | ||
| Show axis in grids does not maintain grid spacing | ||
| Ungroup not grayed out when not a group | ||
| Fonts in LE are unreadable when resized | ||
| Deleting LE brings workspace window forward. | ||
| Wrong axis name in the LE | ||
| Graph Window |
|
|
| GW02 Y axis selection changes to Auto | ||
| GW05 refresh bug for %max | ||
| Arrows not working with gates in GW | ||
| Multiply gates toggle | ||
| Initial draw of a GW shows just the outline with no update until file is read in | ||
| Ctrl-A: 'Select all Gates' | ||
| Range gate not working with arrow keys | ||
| Save state to Pref not responding in GW | ||
| Histogram smoothing more like MAC on small population | ||
| Scrambled contour in GW | ||
| Next / prev buttons not working in 7.6 | ||
| % missing from GW when moving gate annotation | ||
| Manual Gate Entry Dialog fails to recognize it should be on a histogram. | ||
| Manually entered gates are messed up on 32 bit data | ||
| Control check box should be enabled by default | ||
| Graphs not maintaining spec | ||
| Can't move the statistic away from the gate in the GW | ||
| Gate Frequency if locked in place | ||
| Duplicate box in graph window | ||
| Error message when bifurcated gate | ||
| Manuel gating percentile quad naming issue and gates unresponsive | ||
| Double click gates in GW doesn't open new gw | ||
| Quad gates don't allow moving stat. boxes | ||
| Make movie from GW throws NPE | ||
| Right Click function bugs | ||
| Histogram export unresponsive | ||
| arrowing a non-control manually created 1D range gate, grows it | ||
| Graph window preferences does not link from graph window | ||
| Make movie from GW unresponsive | ||
| Gate events inside in GW | ||
| Graph Window -> Save As throws ClassCastException | ||
| Graph Window -> Print throws ClassCastException | ||
| GW changing back to original after changed to histogram | ||
| Spider gates in graph window do not gate what is picked | ||
| Histogram gates reset to middle | ||
| Losing "save state to prefs" | ||
| Manual entered gates for percentile aren't created properly | ||
| Check boxes under Active Gates in the GW unresponsive | ||
| Curly quads don't drag to group | ||
| Curly quads not well defined on biex plots | ||
| Exception in gw after dragging to group. | ||
| Curly Quads give 0 count | ||
| Gate creation in GW also adds a no op gate move to undo stack. | ||
| Curly quads don't refresh | ||
| GW active gate stat out of sync not showing percent of cells | ||
| Long names in gw for active gate do not show even if window is expanded | ||
| Contour graphs filled in black | ||
| Edit>copy picture in GW cannot be pasted to LE or PP | ||
| Synchronize gates does not work with curly quads | ||
| Time parameter is incorrect for 32bit BCI files | ||
| Bisector gate for histogram shows quadrant gate before gating | ||
| Unsmoothed dots are offset by 1 pixel relative to smoothed + outlier dots | ||
| Quad gates in layout , and GW, have extra lines | ||
| Graph window in back | ||
| Histogram Y axis doesn't update when expected | ||
| Making quads gives bisector feedback | ||
| Seting gate color is unresponsive | ||
| Graph window menu items that have the same keystroke shortcut | ||
| Transpose Axes does not transpose data in GW | ||
| Exception closing gw | ||
| Choosing Quad from Graph menu of gw allows additional quads to be created | ||
| Area of gate type keeps increasing when switching between rect/poly/ellipse | ||
| Changing contour levels from right click unresponsive | ||
| Preferences by level in graph window doesn't hold | ||
| Changing contour levels through right-click is not reflected by option panel combo box | ||
| Changing contour levels is not undoable | ||
| Unable to cycle through child samples with parent gw open | ||
| Quad node retains group owned status after being allocated back to samples | ||
| Default sample names missing spacing when creating manual gates in gw | ||
| Gates allocated to first sample disappear from first sample's graph window | ||
| Gate disappears first time when using T Button to change between lin and log (for non-32 bit parameters) | ||
| Curly quads disappear after click around | ||
| Can't undo line thickness in the gw | ||
| First undo in gw is always undo contour levels should just be undo | ||
| Printing a graph from the gw is off center in the print preview screen | ||
| Converting an ellipse gate to a poly gate throws NPE | ||
| Ellipse gates showing 0.0% | ||
| Autogating not working | ||
| Manual paramteter range speciification not working... | ||
| Edit menu items in GW that are always available | ||
| Show Event Parameter Preference doesn't work | ||
| Use Exponents in Log Axis Labels preference doesn't work | ||
| Remove transforms fails for uncompensated parameters | ||
| Statistics: (return of doublelog?) | ||
| After adding a statistic in the gw the statistic box close automatically | ||
| Autotransform of moflo xdp data gives incomplete tick marks on axis | ||
| Bisector gate alt drags to spider quad | ||
| Copy histograms as text copies incorrect numbers | ||
| Quads don't show up in cloned graph windows upon creation | ||
| Quad gates stuck when dragged off of graph window | ||
| Quad turns into spider | ||
| Undo on quad gate removes entire gate | ||
| Quad gate throws NPE on Mac | ||
| Quad gate turns into spider unexpectedly | ||
| Moving a rect gate adds a "Set Fig's Line Thickness" to the undo list. | ||
| Quad gates duplicating and disappearing | ||
| Gates not copying to LE | ||
| First undo in GW is undo gate moved | ||
| Movie from Graph window shows odd number | ||
| 3D button in GW not working consistently | ||
| Oversized graph window | ||
| Graph window Edit menu "Copy statistics" fail to function | ||
| Accuri Data Remember | ||
| Display range window grays buttons and doesn't allow saves | ||
| Transform button available for CDF | ||
| CDF does not reach 100% | ||
| Show grid in GW changes axis values on histograms and CDF | ||
| Wrong shorcut key in GW | ||
| GW long parameter names don't get truncated appropriately, and X axis decades is lost | ||
| Horizontal spacing between graph window tool buttons | ||
| Biexponential transforms are showing on the Y-axis when they shouldn't | ||
| Parameter Range change in GW gives blank graph | ||
| Pref for tinting does not work | ||
| Frequency displays on gates whether this preference is checked or not | ||
| Population name shown on gate whether this preference is checked or not | ||
| Gate median is off no matter how preference is set | ||
| Gate change apply to wrong sample | ||
| No tools tips for icons in the gw for 3D and duplicate buttons | ||
| Change display range is giving warnig that ranges were change when they were not. | ||
| Engine |
|
|
| Concatenate Spigot Influx Files | ||
| 7.5.4 Release Download | ||
| Draggin multiple statistics only drags one | ||
| Dragging statistics into LE only drags name and not statistic | ||
| Meta Bug: File reading. | ||
| Exporting Multiple Subsets | ||
| Frequency of (blank) provides 000 when parent is selected | ||
| *New* Concatenation Issue with Summit files in v7.5.5 | ||
| Copy to group timer keeps spinning | ||
| Apostrophe in file name | ||
| The time parameter in v7.6 does not display the approriate range. | ||
| Missing files dialog box | ||
| On Mac Flowjo 7.6 changes Hardware Address depending on Network settings | ||
| About Flowjo shows incorrect OS Ver, Java Ver, Build num | ||
| Auto-transform unchecked by default in prefs. | ||
| Accuri data file reading. | ||
| Galios FCS3 linear parameters read/binned incorrectly | ||
| 7.6 needs to work with newest dongles | ||
| Accuri Rebin issue | ||
| Can't save wsp or wspt to USB device on mac only | ||
| Locating files is complicated | ||
| Dongle works with Beta Versions | ||
| Query Error and FlowJo crashing with de-identified SIV FCS file | ||
| Compensation |
|
|
| Comp. not responding to group selection | ||
| Compensation wizard chooses SSC-W incorrectly | ||
| Export/cont loading blank fcs files | ||
| Summit Transform | ||
| Exception in Comp editor with no samples | ||
| Show Uncompensated parameter preference | ||
| Localization screws up extracts from CompEditor | ||
| Compensation editor has no response | ||
| Compensation editor window won't open | ||
| Comp editor: to apply positive and negative population from two tubes to one parameter | ||
| Compensation window | ||
| Add samples to comp editor | ||
| Compensation - add matrix to current group | ||
| Comp editor: show compoments should be check if showing | ||
| Compensation Wizard Aggressively Rounding Spillover Values | ||
| Compensation wizard gates no longer have 'cw' prefix | ||
| Compensation Wizard Gate Creation | ||
| Compensation Recalculation Freezes FlowJo | ||
| Apply button in Comp Editor freezes FJ | ||
| Compensation window with user defined auto gate | ||
| Comp Editor Menu items that appear broken | ||
| Saving prefs always turns off 'show comp matrix' in comp editor. | ||
| Transform settings in comp editor keep minimizing when added | ||
| Drag matrix from comp. to samples becomes a huge square that covers samples | ||
| NPE when Show/Hide Compensation Scripts | ||
| NPE when adjusting wizard gates | ||
| Comp names above matrix are off center | ||
| Getting Java error in comp. editor | ||
| Remove Compensation Menu Item - failing | ||
| Comp Editor problems - 5 | ||
| Compensation matrices change | ||
| Java errors when editing matrix in Comp. editor | ||
| Acquisition defined matrix does not take name change in the workspace. | ||
| Remove transforms and then reaaply changes decades in gw | ||
| Comp matrix modifiers buggy | ||
| Assigned samples don't disappear after clicking on 'finish' | ||
| Authentication | l
|
|
| Flowjo wont initially open on mac without active internet | ||
| FJ not checking for new version or beta | ||
| 3D Viewer |
|
|
| Manual setup in 3D not saved | ||
| Stack dump- 3D voxel plot | ||
| Opening 3D viewer produces Stack | ||
| 3d Viewer Bug list | ||
| 3D viewer give NPE | ||
| 3d platform in OSX does not finish making movie | ||
| 3D toggles (for next sample) do not update when 3D node dragged to group. | ||
| Cycling samples in 3D, window loses data display, shifts display controls to center of window | ||
| 3D perspective rotation sliders not working | ||
| maximizing the 3d platform full screen screws up layout of the window | ||
| 3D platform has lost indication of origin, axes labels in wrong place. | ||
| please limit number of displayed events if (point cloud) && (size) | ||
| Pref for dot size in 3d broken | ||
| Setting number of events limit in 3D is unresponsive | ||
| Cancel button freezes in 3D viewer | ||
| 3d Viewer tries to create 9,999,999 frames | ||
| Upon open a sample in 3d, size is set to very small, have to reajust to see sample | ||
| 3D viewer help needs adjusted link | ||
| Window adjusts incorrectly in 3D viewer | ||
| 3D preferences | ||
| Dot size grays out when changing pref in 3D | ||
| Cube color doesn't change in 3D as defined in prefs | ||
| 3D z-axis not showing correct parameter | ||
| 3D slider off window (on mac only) | ||
| 3D plot - bubble plots default to very small bubbles. |
August 03, 2009 - 7.5.5 Features/Release Notes
- fix problems moving gates above proliferation nodes while prolif is in LE but platform window not open
- fix: GW01 Retested 6-1-09 EH
on an histogram, make a bifurcated gate. Then make a range gate. Select the range gate only, and try to move it with the arrows: it moves the bifurcated gate instead of the range gate.7.5b137 LN - CytoCGControlPanel - update axis labels when focus is lost (used to require return key)
- fixing gate annotation drawing in correct color
- LEChartController, GraphSpec - for 7.5.2: texttrait name is "Gates" not "Gate" or "Graph"
- Warn user that FlowJo could not be started because another program is using it's listening port.
- fix compensation problems for users with exotic locales
- NPE caught when canceling print from workspace
- StatisticSelectionPanel - fixed Population button enabling to work with 1 dependent
- gatingML: fix non standard emitted xml, allow our gatingML files to be read by new R parser
- ExportDialog - Qianjun's request to label the "select" button accordingly.
- don't ask to save if user quits from LicenseInfoDialog
- ScatterPlot - move up Y axis
- FigGroup - make group with extra MARGIN (line 102) to offset for axis clipping
- GWO2 histogram resets to Auto
- when adding samples to a template, change it to a workspace
- New authorization code to plug hole in offline log file. When offline log file created, timestamp is written to prefs file. At startup, if serial number is FLS and network is down, and timestamp attribute is present, but offline log file does NOT exist, then user must reconnect to network to reauthorize.
- Aaron's BIGGUN! Statistics on 2nd level gates don't update when a synchronized group owned gate above it is moved. This can be seen in the basic tutorial. Ly>Fl1+>MFI, synchronize and move LY.
- Jill's loss of child gates when group-owned dragged to All Samples
- save and restore the print layout info in the Layout
- removed Save button from print dialog
DialogFooter is reformatting and typed collections (optional backpatch) - Fixed an NPE in createQueries
- Fixed Hide Column in Table Editor (removed redundant flag)
improved testValidity to warn user if info is incomplete - FPolygonGate reading of ellipses weren't omitted correct xml
- change quad order
- platforms: have platforms be updated by their parents when gates are moved
- Fix: export a file, CSV is selected by default. Change to FCS file and the extension maintains a csv extension.
- FIXED READING ELLIPSE GATES
June 23, 2009 - 7.5.3 Features/Release Notes
Fixed
- fixed bug in formula test validity
- fixed indexing bug stopping last formula from being calculated
- fixed gate annotation drawing in correct color
- fix problems moving gates above proliferation nodes while prolif is in LE but platform window not open
- histogram range gate moving bifurcated gate instead of the range gate when both are present
- LE text trait name changed to "Gates" not "Gate" or "Graph"
- compensation problems for users with exotic locales
- non standard emitted xml, allow our gatingML files to be read by new R parser
- histogram resets to Auto
- loss of child gates when group-owned dragged to All Samples
- Hide Column in Table Editor (removed redundant flag)
- right-click layouts, you can "autobatch-on"
- save in print does not save in current
- NPE caught when canceling print from workspace
- adding samples to a template, change it to a workspace
- fix mouse tracker display
- fix kinetics node parent when dragged to group
- export of a file, CSV is selected by default changed to FCS file and the extension maintains a csv extension
- pref lookup in wrong element
- Hide column in TE, not responding
- warn user that FlowJo could not be started because another program is using it's listening port
- save and restore the print layout info in the Layout
- NPE in createQueries
- fixed Population button enabling to work with 1 dependent
- DialogFooter is reformatting and typed collections
- fixed statistics on 2nd level gates not updating when a synchronized group owned gate above it is moved
- have platforms be updated by their parents when gates are moved
- offset for axis clipping
Changed
- changed logic in TableData to not put header info in row 0
- Excel, CVS, Tab, HTML tables all have new header row generated
- removed Save button from print dialog
- repositioned the popup to come up under the field
- don't ask to save if user quits from LicenseInfoDialog
- improved testValidity to warn user if info is incomplete
- better selection of population names in table editor statistic addition
- new authorization code to plug hole in offline log file
June 1, 2009 - 7.5 Features/Release Notes
Version 7.5 contains large structural improvements.
It employs substantially more of the Java frameworks, conforms to gating ML, and delivers higher performance for desktop data analysis with the support of multicore processors and secure data administration. (The backend details we hope will remain uninteresting to the biologist.)
- Improved reporting and printing, increased options for formatting reports, PowerPoint button
- More capabilities to save and replay reports, increasing the ability to automate analysis
- Two-click multigraph overlay options
- Simplified offset histogram options
- Improved batch/iteration interface
- Improved backgating display
- Improved value series interface
- Export/Concatenate now allows creation of new parameters in the Concatenation dialogue.
- Support for Accuri and CXP data files
- Save gate info into FCS files
- 3D data view
- T- button allows lin/log changes
- Scale changes can be copied to all parameters
- Direct export options
- Heatmapping of table values
- Correlation plots
- Derived Params
-Allows selective range for axis zooming
-Improved user interface - Cell Cycle
- Improved fitting
- 2D model analysis allows for better isolation of the phases - Proliferation
- Improved fitting - Preferences:
Full preference settings for all areas of FlowJo: text, layouts, graphs, workspace and more - Acquisition:
Cytek acquisition module, called Cypod
April 6th 2008, Version 7.2.5 release
- "out of memory" errors were addressed by better defaults
- authorization fixes for consistent hardware addresses (Nortel adapters)
- bug fix for printing contents of workspace
- authorization fix when multiple USB thumbdrives are attached
- One version now runs on Win2000/XP/Vista
- Compatible with new and old black dongles
Known Issues:
- calibration from V5 and early V7 workspaces should be recalculated
- the "custom label" visible in table editor when nodes are dragged into the table editor should not be used in creating formulae. Instead, type over them with your own (ergo, custom) labels and use those.
- windows 64 bit does not work with serial numbers yet.
- file export ignores custom keywords
Fixed since 7.2.1:
Authorization:
- proxy support for site license holders has been fixed (sorry for the delay!)
- full S/N or dongle, About FJ displayed DEMO mode.. fixed
- added Vista support (dongles, serial numbers, FLS, proxy)
- added partial win xp 64 bit support (see Known Issues..)
GW:
- rect gate is offset by 10 pixels when first created).
- bug where output to pdf/svg did not work in graph window and layout editor.
- Open saved WS with a GW(s) will indicate it's been edited.
- conceptual problem with implementation of bisector gate
- Invalid Not Gate - would make a gate higher than 100 %
- toggling gate 'events inside' changed the gate coordinates.
- X or Y axis is changing after graph type is changed.
- Ellipse gates from older workspaces would not calculate the right frequencies.
Table Editor:
- Formula for Quad gates not adding up to 100 percent
- error message popped up sometimes on table selection
- fixed error where -1 would show as a stat for empty gates
- some stats will now be shown as "N/A" vs. 0 where appropriate
- fixed table sorting
FCS spec:
- Fixed logic in Sample.createBeckmanCoulterCompMatrix.
- Allow compensation on SSC-W parameter when it's index is greater than 3, to support old cellquest machines where ssc-w was used as a fluorescent channel.
Layout:
- keyword/discriminator iteration did not work for templates.
- Batching to PDF would not iterate annotation for some of the charts
- error messages pop up in old layouts
- grid behavior improved on re-opening saved WS's
- After batched to PDF page brake returned to default setting. fixed.
- There was a problem with overlay in V 7.2.1, fixed.
- Edit menu Edit Chart fails to de-select the chart option
- stat nodes in LE need "gating path" option
- new: adjunct histograms. Drag a chart to LE, right click, add adjunct histo's.
Workspace:
- Files would not load after Reset to Defaults in Prefer. using a S/N
- added a need a global preferences reset button
- Renaming samples was no longer possible
- added 'Alt Preferences' option
- Stat node "Freq of Parent" was not the same as gate node
- Stat "Freq of Parent" failed to track/update with gate node after quad gate was moved
- DiVa sample stain name didn't carry forward to new parameter
- combination boolean gates are now calculating right cell counts
- fixed compatibility of 5.7.2 workspace
- new private pref: private_writeAbsoluteFilePath, when set to ="1" in your flowjo7.prefs file, will create absolute paths (ex. c:\user\data\file.fcs)
Platforms:
- fixed ability to make manual timeslices in kinetics
- calibration works!
- e-added support for kinetics node overlays
- compensation and calibration parameters will be auto-added to group upon their creation
- V7 on OSX:
- quicktime movies broken if V7 runs on mac
Authorization:
- FLS lookup should be much more rapid now
- different demo serial numbers will be issued starting 7.2 release
- serial number fields will show the "paste" menu when clicked
- fixed the problem with multiple hardware addresses, licensing via serial number should be easier.
Buttons and menus:
- "quit" button would ignore changes in FJ License Info dialog. Fixed.
Compensation:
- added compensation scripting. Explained here.
Diva:
- diva data from 3.1, 4.0, or 4.0.1 will be compensated properly
- we're no longer transforming linearly scaled diva parameters.
- DiVa prefs are now embedded into workspace files, and will over-ride local prefs if different.
- fixed problem with opening large diva files (tested up to 2.5M events)
Graph Window:
- gate freq. positioning and color inconsistent - fixed.
- dragging gates around would sometimes put some vertices off-screen. fixed.
- implemented polygon gate editing - alt+click = delete ctrl+alt = duplicate
- added keyboard shortcut ctrl+shift+r - resets all graph window sizes to one size.
- fixed the bug which made some windows oblong and warped.
- stats area now has scrollbars
- added ability to control fill setting in the histogram thru right-click menu
- added ability to copy histogram data as scale or channel values.
- preferences window painted in the wrong layer. Could lead to GUI block. Fixed.
- gating tools have keyboard shortcuts: (q)uad, (s)elect, (e)lipse, (r)ectangle, (p)olygon. In histogram mode, Q- bisecotor and I- range gate.
- double click gating tools to make them "stick" (draw other gates)
- fixed ellipse gates
- no more PINK gates. default changed to BLACK.
Kinetics
- KI fixed all kinds of kinetics bugs (FCS3 and FCS2 files, scaling, plotting, stats vs. mac)
Layout Editor
- dotting and dashing quality for overlay plots, lines, arrows, etc..
- overlay UI enhancements in the legend of overlays in layouts
- last layout is not deletable
- erratic change of sample selection in the layout
- sometimes gates would become extra-highlighted for no reason.. fixed.
- layouts with iteration errors would sometimes display a blank box without explaining.. fixed.
- chart duplication resulted in dragging chart without annotation. fixed.
- fixed series of bugs with multi-graph overlays. Added kb shortcut ctrl+shift+M to add graph.
- re-opened workspaces with batched layout would show the same stats or keywords.. fixed.
- saving to PDF fixed from layouts. PDF's will now use layout's pagination.
- batch dialog now remembers settings for each output when you switch output options
- printing dotplots with frequency floaters would make floaters unreadable.. fixed
- creating an oval gate in LE would put FlowJo in a weird state. fixed.
- improved gate editing UI - reduced number of mouse clicks in gate editing to 1
- fixed unit distribution axis lables to be independent of sigFigs setting
- fixed overlay line attribute bug
- legend-set controls are more consistent
- legend widths are now dynamically updated to fit content
- X axis label will now properly move closer if "hide numbers" checked in Graph Def'n dialog.
- saving textbox commits contents to become default annotation for graphs.. fixed.
- added rightclick menu which makes certain menu items easier to access (ie. paste)
- moving a gate in LE would snap the gate back.. fixed.
- added "set control" to right-click legend menu
- rightclick on chart shows parameters with current parameter grayed out.
- layout would not allow overlaying the same gate over itself, fixed.
- enabled gating to work properly in "graph sets"
- new zoom tool - left to the old one - allows drawing a rect-selection of what to zoom in on
- fixed header/footer
- implemented autobatching of layouts
Plate Editor
- fixed file menu items
Preferences
- disabled changing $FIL by renaming sample
- added pref for linear FL channel scaling for DiVa parameters
- added ability to save prefs for legend styling: line thickness, columns, colors..
- if flowjo diva scaling options are in effect, they will now take priority over $PNdisplay kw
- FlowJo's got a new private preference, private_showStainInStatisticsDialog. Set it to ="1" or "0" to toggle display of prefs with/out stain names (ex. fitc-a vs. fitc-a CD3)
- deleting a gate from favorites would corrupt remaining gates into a single-string.. fixed
- added right-click "paste" operation to serial number fields ;)
- added 32 bit (DIVA etc.) prefs link under Edit menu
Table Editor
- TE added shortcut to graph window (double-click on a row)
- can now move columns (drag column header to re-arrange output)
- added "copy raw" and "html" flavors to the clipboard
- can now set "clipboard" as an output option for generating tables
- can now "hide" output columns (double-click on an item in editor to enable attribute)
Workspace
- boolean gate's children nodes would sometimes calculate wrong %, fixed.
- boolean gates would misbehave when parent gates renamed
- nested boolean gates and their NOT gates would misbehave.. fixed
- group owned gates are no longer rename-able (have to detach it from group, then rename it)
- added support for the coulter CXP FCS3 format ($DFC...) - this needs verification
- closing workspace while adding samples would cause an error. Fixed.
- entering a "/" character into file name during save operation would nullify the save, fixed.
- deleting a compmatrix now properly un-compensates files in WS view.
- changing group name resets gate styling.. fixed
- can add multiple keywords in one shot
- added support for relative URI's if workspace is in parent folder relative to data.
- when editing keywords, users can now go across (tab) or down (enter)
- FCS and CSV data export as well as FCS concatenation have been fixed.
- ability to copy spreadsheets into flowjo to label keyword values has been added.
- ability to export csv files with gate inclusion/exclusion per event info added.
- can now drag files from one workspace window to another. gates, too.
- calibrated parameters did not work before. They work now.
- October
9th 2006, Version 7.1.3 released
- Better error message when dropping control populations in the drop boxes of the compensation editor.
- Better retention of drop boxes in the compensation editor when performing editing operations.
- FlowJo now recognizes SPILL keyword if the parameter has a '/' in the name.
- Cell cycle platform now shows displays better warnings and the mouse tracker matches the axes values.
- New operations were added to allow user to specify gate color and line thickness, to apply these to other gates, and to save as a preference.
- Ellipse gates no longer shift slightly when using the arrow keys to move then, due to rounding errors.
- Can now display large dots for pseudo-color graphs.
- Much improved output of pdf, svg, gif in the layout editor.
- Can now delete the legend in the layout editor by selecting it and hitting the delete key.
- New y-axis option for histogram overlays: Unit Distribution, which normalizes the area under the curves to 1.
- Correct display of histogram overlays with a postive offset (angled view).
- Correct clipping of histogram overlays when copying them to the clipboard.
- Can now save the position and properties of legends and annotations as a preference for the layout editor.
- And/Or gates correctly determine their parentage when copied to another location.
- Export gated subpopulation to new FCS files.
- Concatenate samples or other populations to new FCS files.
- Added scrollbars to popup menu in graph window to choose sibling populations.
- Added menu operation to apply modifications to group-owned gates.
- Added new functionality to auto-batch multiple layouts in one operation.
- Improved memory deallocation when a workspace is closed.
- Added experiment ID support.
- Added support for black dongles when running v7 on Mac.
- Added crash protection for engine requests (i.e. no more hard crashes.)
- Added XML validation prior to save.
- August
3rd 2006, Version 7.1.2 released
- Workspaces with many gates should experience large performance improvements.
- Multiple bugs in DiVa and non-DiVa transformation have been fixed.
- Default global transform settings are now more reasonable.
- DiVa linear parameters and scaling now more closesly match DiVa software.
- Manual editing of cell cycling and proliferation platforms have been improved.
- Several bugs in proliferation have been fixed.
- Kinetics and proliferation graphs now dynamically update in the layout editor.
- Calibration works correctly again.
- All layout editor iteration options now work correctly for workspaces and templates.
- Batching to separate pages has been fixed.
- Printing has had several fixes, especially for headers and footers.
- Exporting layout graphics to other applications now has correct scaling and better naming.
- Version 8 (Macintosh) compensation matrices should now all be read correctly.
- A number of bugs where preferences were not being remembered correctly have been fixed.
- Combination gates have had several important bug fixes.
- The table editor and its formulas have had several bugs fixed.
- Very large statistical and tabular values sometimes have their highest digits truncated. This has been fixed.
- New menu item, 'Recalculate Gates and Statistics', is now available.
- Quad gates not adding up to 100% should now all be fixed. Use the recalculate menu item if necessary on older workspaces.
- Quad annotations may now be kept in the corners using a preference.
- New predefined values, 'Graph Spec' and 'Gate Coordinates', may now be added as workspace columns.
- Parameters named with forward slashes could cause problems when gating. This has been fixed.
- A bug in ratio derived parameter was fixed.
- Lines drawn in the layout editor now are at right angles when shift is held.
- Multiple acquisition related enchancements have been added.
- Users of older dongles may now force the upgrade process to happen by holding shift and control and clicking 'About Dongles' in the license information window.
- If a user is in demo mode, this is displayed on the about window.
- Release notes are now visible through the workspace help menu.
- Many help links have been corrected.
- Several additional, miscellaneous bugs have been fixed.
July 5th 2006, Version 7.1.1 released
- Considerable optimizations have been made to the internals of FlowJo to provide much better performance when analyzing large, complex data sets.
- Numerous bugs with resizing charts and other figs in the layout editor have been fixed.
- Batching direct to printer no longer has an arbitrary limit to the number of tiles per page.
- Percentile statistics in table outputs were sometimes incorrectly displaying zeros. This has been fixed.
- There is a new 'Report Bug' menu item under the 'Help' menu that presents the new bug reporting web page at http://umpqua.treestar.com/ bugs/ .
- When creating new gates, the stain name (if available) is now used for the default name instead of the parameter name.
- Compensation matrices that differ by only 0.01 (settable as a preference) or less are now treated as the same matrix.
- It is now possible to edit the properties of multiple charts in the layout editor at once. This is done by selecting all the charts to edit and then displaying the properties of one of them. Changes are then propagated to all the selected charts.
- Although functionally correct, transform vectors being calculated did not distribute the events across the negative range similarly to the Mac version. This has been changed to match the Mac version's behavior which produces better transformations with more optimal clustering.
- Quad gate annotations in older templates and workspaces sometimes would return to their original positions even after being repositioned when the quad gate was moved. Enabling the 'private_quadAnnotationsInCorner' preference now keeps quad gate annotations in the corner.
- Quad gates are no longer separable.
- A 'pause' button has been added to the gate editing tool bar in the layout editor. When pressed, the pause button delays applying editing changes (e.g. moving a gate) to other parts of the program.
- Parent graphs displayed by showing ancestry in the layout editor now only show the gate that applies to the child graph.
- When using text boxes in the layout editor which were opened from a template, problems could arise where the FJML tags (such as a keyword of the current sample) would not display incorrectly. These problems have been fixed.
- Compensation matrices in Summit 4.2 and 4.3 are now being read correctly. Due to changes between Summit versions, there were problems previously.
- 'FS Lin', 'SS Lin', 'FS Log' and 'SS Log' are now correctly treated as non-fluorescent parameters.
- Global DiVA settings were overriding template's transform settings. This has been fixed. Additionally, the global DiVa settings dialog has been enabled again.
- In the case where a sample file could not be read correctly (e.g. disk error), an endless loop was occurring which would cause an exception. This has now been fixed.
- Generated tables weren't using the formatting criteria correctly. This has been fixed.
- Some groups weren't being saved in templates. This has been fixed.
- Notification for when a new version has been improved so beta versions do not erroneously display 'New Version Available' messages.
- Several optimizations to performance have been added.
May 17th 2006, Version 7.1.0 released
- Show Backgating command in the Layout editor now displays a legend identifying parameters on each graph.
- When creating histogram overlays in the Layout Editor, right click for a new option to normalize the area under the curves.
- Histograms in the layout editor can be smoothed incrementally by right clicking and selecting Smooth.
- Change graph type and other options on multiple graphs in the layout editor by right clicking and selecting the desired options.
- Derived Parameters have their own dialog box. Reach it by right clicking on the sample in the workspace or select Derived Parameters from the Tools menu.
- Save the current state of a tool set-up by selecting Save State to Preferences in the EDIT menu. This is now available in the Workspace, Graph Window, Sayout Editor and when batching.
- OR gates and AND gates now reload correctly from saved workspaces.
- You can no longer overlay populations with different transformation settings.
- Quad Gates displaying frequency and gate names now retain their labels properly.
- Quad gates can now be nudged using the arrow keys.
April 28th 2006, Version 7.0.6 released
- New Autogating tool implemented in Graphs and Layout.
- Transformation panel adds global manipulation for Transformation settings and their application to tubes and groups. View, create, edit and remove settings, specify automatic or manual calculation for extra negative decades.
- Batch Layout to PowerPoint and PDF.
- Greatly improved batch performance.
- Improved global text trait controls.
- Faster printing.
- Supports password protected proxy servers.
- Large dots available on graphs in Graph Window and Layout Editor.
- Numerous bug fixes.
Web Start. Allows us to deploy improvements in small chunks. When you start FlowJo it will check for updates and download them. You will always have the most current version. Get it from the Download Page.
Experiment Annotator Clinical sites and high throughput research labs need to improve levels of automation to significantly decrease repetitive tasks, and enable large scale tests. FlowJo’s Experiment Annotator is a 96 well plate editor for describing staining setup using attribute - value pairs. The Experiment Annotator enables creation and editing of samples prior to collection. It is also a means to editing sample descriptions after collection.
Graph Windows Resizable graph windows are available in 7.0 for your personal dimensioning preference. Gate calculation has been optimized, and statistics may be added to all parameters. The gate creation window has the capability to retrieve gate names by way of an editable favorites list accessible during gate creation.
Layout Editor It is possible now to save/load graph setups from Multigraph overlay to graphs in the layout editor. Percentile gating is also available: a percentile gate may be applied to another population, the absolute position of the gate may differ, but the percentage of events within the gate matches that originally defined.
Preferences Templates and workspaces are now delivered with preferences set. A workspace may contain a preference element, or any subset of the elements and attributes supported in FlowJo. The setting and saving of preferences is primarily accomplished locally to each menu. On exit, workspace, templates and layouts carry their font information with them.
Workspace Group analysis gate calculations are now activated on-demand resulting in an overall performance optimization. Group functionality has been enhanced for gate creation and renaming. Synchronized groups enable the automation of application of gates across a selection of samples. Become a 7.0 beta tester, and let us work with you on your personal wish list. Have a go at the 7.0 workspace, there are various other enhancements with respect to your statistical analyses: concatenate and export FCS files to extend your raw data file selection; quickly access your 10 most recent workspaces; ongoing 32 bit data analysis capability; display a numerical series with a click of a keyword value… and more.
Table Editor The Table Editor has had many improvements expanding its functionality and integration within an organization. Advanced batching capability has been added, allowing you to create tables that intelligently combine multiple samples into single table rows. A powerful new formula engine is now available to programmatically produce columns providing a wide range of statistical, mathematical and textual operations. Flexible formatting settings have been added to give your tables a customized look and you can drag and drop these formatted tables directly into Microsoft Word, Excel and other programs. New export formats have been added: Native Excel, Excel XML, Open Document XML, CSV, HTML and RTF. You can also export into an SQL-92 script, providing a direct path for putting your tables into most databases. All exports can be done directly to an FTP site as well as to a local file. And, all of these new features may be combined into templates with one-click table creation and output.
Compensation/Transformation A new streamlined user interface enables ease of compensation and transformation analyses, as well as computations using derived parameters. The new, more intuitive approach to compensation features single step creation of the compensation matrix.
Performance A more finely tuned FlowJo engine has introduced a new level of efficiency in batching sizable analyses. Next time you run a batch from the layout, we hope you will take the opportunity to give us your feedback.
Multigraph Overlay Multigraph Overlay is now available through the Layout Editor. It is now possible to transform a graph in the Layout Editor to a Multigraph overlay, add a graph to the Multigraph overlay, and revert back to separate graphs, batch the overlay, save and reload.
Backgating Analysis Validating gate positions is one of the most important aspects of multiparameter Flow Cytometry. FlowJo now provides you with a tool to view the effect of every gate on your final gated population! In the Layout Editor, for any graph of a subset that is gated more than once, you can right-click and select Show Backgating from the pop-up menu. FlowJo displays a series of graphs where each level in the gating hierarchy is displayed, with the final gated population overlaid at each level. This overlay shows what the final gated population would look like within the context of the larger population. Therefore, you can quickly scan to see if any one of your gates is positioned incorrectly. The backgating display can be printed and copied.
Boolean Gates You can now create a gate which is a Boolean combination of any existing gates (i.e., "and", "or", and "not" combinations). Boolean gates are "live", meaning that they will reflect any changes to the gates on which they depend, with a double- click to the gate in the workspace. FlowJo can also automatically create a series of Boolean gates that represent all combinations (plus and minus) of a set of gates. For example, if you have a sample which was stained on different parameters for IL2, TNF, and IFNg, you can create a positive gate for each of the three cytokines (for example, a histogram gate). To create or edit Boolean gates, choose the parent subset(s) and select the type of gate you need from the Workspace menu. To view the whole Boolean series, select Create combination gates...
Data Movies You may now observe your samples as a QuickTime movie. This enables analyses to be viewed in a real-time as an animation or by stepping through frames one at a time for a more careful examination of samples. Access this feature from any Graph Window’s “Graph” pull down menu.
