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- David DiGiusto, Ph.D.
Director of Analytical Cytometry, Beckman Research Institute of the City of Hope National Medical Center

This page allows you to download the latest release of FCS Express 6 - Research version. To upgrade to the latest IVD version please click here.

To upgrade to the last release of FCS Express 5, please click here.

To upgrade to the last release of FCS Express 4, please click here.

The current FCS Express release is 6.02.0004.

FCS Express 6 for Windows - 64 Bit

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FCS Express 6 for Windows - 32 Bit

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FCS Express 6 for Mac

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Download FCS Express 6 Plus for Mac

Release Notes

Version 6.02.0004 - March 27, 2017 (Research Use Only)

Bug Fixes

  1. Fixed a crash that occurred when creating SPADE transformations (this affected RUO only) (55638,55890)
Version 6.02.0003 - March 16, 2017

Bug Fixes

  1. Fixed a crash that occurred after copying quads from one plot to another, then linking them (53905)
  2. Double-clicking on downloaded layouts or published files will now be cause them to open in the Reader (53889)
Version 6.02.0002 - Feb 28, 2017 (Research Use Only)


  1. SPADE transformations are available (30241)
  2. Introduced Tiling Options to printing/saving to PDF/PPT during batch processing (42309)
  3. Introduced Tiling Options to saving to PPT (not during batch) (12232)
  4. Optimized database connections, and they are no longer dependent on ADO (30354)
  5. Can now drop a gate into marker endpoints, and a dialog will appear for selecting which statistic to link the endpoint to (30179)
  6. Batch Processing Runner window can now be docked (16911)
  7. In R transformation options, allow selecting how clustering results are represented (18822)
  8. In tSNE options, allow entering the number of iterations (40516)
  9. Improved the speed of working with compensation matrices (41472)
  10. Improved plotting speed with log parameters (41464)
  11. New Spreadsheet formulas available: RegressionPlotXtoY and RegressionPlotYtoX (41364)
  12. Improved speed of Spectral Plots (41218)
  13. Enabled the standard mac key combination for displaying options (Command + comma) (41165)
  14. Introduced an option for creating a File Identifier column when merging data files (41047)
  15. Improved speed when displaying the Format window for plots on Mac (40991)
  16. When dragging and dropping onto a Marker vertex, the marker vertex now becomes locked (40726)
  17. Multiple Duplicate and Next can now be created in a Custom Grid, regardless of the original position of the plots (42290)
  18. SOP Runner window can now be docked (42626)
  19. There is now a Mac-specific version of the manual (43227)

Bug Fixes

  1. Previously, if combination gates were used for coloring dots on more than one plot, then depending on the order in which the plots were drawn by FCS Express, the plots may not have been drawn to include all gate colors (42105)
  2. Data parameter tokens that are derived from a plot now correctly reflect the compensation on that plot (43474)
  3. Fixed a crash that could happen when there are specific kinds of tokens on the layout (eg “Current Username” token), and FCS Express’ connection to a database or internet dongle was disconnected (40684)
  4. On Mac, made sure that the “More Colors” selection in the color drop-down list displays a dialog (30390)
  5. Fixed a crash that occurred after adding an overlay to a heat map with a transformation (30327)
  6. Behavior for clicking with modifiers (Command key, Ctrl, Shift) on Mac was standardized (30127)
  7. Displaying contour plot outliers was made more reliable (41226, 30124)
  8. Fixed a crash that occurred after loading a layout, then replacing the data on a plot with a data file that has fewer parameters (30120)
  9. Prevented an error message that could be displayed while loading .ci files: “cumulativeData.txt has duplicate entries” (30070)
  10. Improved scaling of the Data Header window on high-DPI displays
  11. Fixed applying object insertion permissions when pasting an entire page (390)
  12. Fixed a crash that occurred after adding an overlay to plots with no visible overlays (40666)
  13. Improved stability of loading layouts with SRAW files (40624)
  14. Fixed a crash that could occur when dragging multiple gates inside the Gate View to a new parent gate (40711)
  15. Fixed a crash that occurred when inserting a token with an invalid cell value into a spreadsheet (41506)
  16. Prevented deleting from the transformations window when no items were present (41451)
  17. Fixed a crash when editing tokens inside the Options window, in the Plot Title options (41432)
  18. Improved display of text in Excel (Column Mode) action on Mac and high-DPI displays (41395)
  19. Improved display of the Multiple Duplicate and Next dialog on Mac and high-DPI displays (41369)
  20. Made sure that checkboxes appear on the popup menu for stat grids on Mac (41368)
  21. Fixed a crash that could occur during batch processing if the layout is showing more than one page at a time (41361)
  22. Enabled support for log in Spectrum plots (41316)
  23. Improved display in Batch Processing Runner window on Mac and high-DPI displays (41277)
  24. Fixed wording in error messages during R transformations (41265)
  25. Previously, gate text boxes could disappear after dragging a gate into a spreadsheet if 2 pages were displayed (41224)
  26. When editing existing transformations, if you change the template file, previously, the parameter list didn’t update (41214)
  27. Tokens inside spreadsheet cells derived directly from data files can now changes files in Next/Previous/Batch operations (41206, 42711)
  28. Previously, on Mac, Excel worksheets created during batch processing would not automatically open even if the checkbox was checked (41190)
  29. Prevented error message “Could not find parameter number; either the data is nil or the method is invalid” in cases when parameters are remembered by Name, and switching to a data file with fewer parameters (41089)
  30. Previously, when undoing replacing a histogram overlay, the wrong compensation might have been applied (40960)
  31. Fixed unlinking gates via the Gate Properties window (40930)
  32. Fixed a bug in tokens in the formula for Allow Editing gates, where the tokens would not track which plot they were on (17597)
  33. Improved spacing when rotating labels on the Y axis of plots (17735)
  34. Fixed crash report generation on Mac (40794)
  35. Previously, clicking in the top-left of a spreadsheet to select all cells cause FCS Express to hang (40823)
  36. Applying and un-applying transformations, that trigger the plots to change parameters, now including the parameter change when performing undoing (40845)
  37. Improved the way plots handle invalid parameters (40849)
  38. In certain cases, the Multiple Duplicate and Next dialog would previously not detect any available iterations (41371)
  39. Improved display in Axis options window on Mac (41394)
  40. Improved display of Histogram Specific options window on Mac (42131)
  41. Fixed a crash that occurred when showing the startup window after closing all layouts and logging out (42054)
  42. Improved speed when working in layouts with many nested snapshots (42060)
  43. Changed the keyboard shortcuts for Next/Previous data on Mac to be Alt+Left/Right instead of Command (42152)
  44. Fixed a crash that could occur after deleting markers in the format window, also led to markers being displayed in the wrong order and not being displayed on preview (42227, 18577, 42890)
  45. Previously, FCS Express could hang while importing certain ci files (42236)
  46. Improved display of axis labels on angles (42285)
  47. Fixed a crash when pasting tokens into the Title options (42307)
  48. Reduced the size of program dlls (42382)
  49. Previously, if you changed the Title options for several plots at the same time, and some were histograms and some 2d plots, and inserted a Current Gate token, the value would not be displayed on one of the types of plots (42409)
  50. Enabled a new report for the number of unique users logged in during a time period (42446)
  51. Fixed a crash that occurred after linking marker endpoints in a circular way (42473, 42548)
  52. Fixed a crash caused by editing parameter math items after reloading a layout (42477)
  53. Fixed the behavior of gates created on parameters that are no longer valid - previously, in some cases, all cells were being allowed (42478)
  54. Reenabled changing the order of files in the data list by dragging and dropping (42547)
  55. Previously, when gates were removed from TSNE plots, color dot plots continued to display their colors (42629)
  56. Fixed a crash when renaming a gate, if a heat map plot was open but not showing (42717)
  57. Previously, PDFs were automatically opened at the end of batch processing even if the checkbox for opening was turned off (42756)
  58. Compensation for new ci file formats is now being handled correctly (42807)
  59. Fixed a scenario where markers with linked endpoints were not always updated when the tokens updated, if there were more than one marker on the plot (42816)
  60. Previously, markers were sometimes shrunk to the axis after changing the legend options to always display solid boxes (42951)
  61. Improved the display of text in the Configuration wizard on Mac (43085)
  62. Previously, quad text boxes did not always update in real time when moving the quad centerpoint (43095)
  63. Improved the way data-specific gates and iterations interact with each other (43111)
  64. Previously, data-specific gates were lost when changing relatively location of data files on loading a layout (43114)
  65. Fixed a bug where extrakeywords.csv was not being read in correctly due Windows treating the csv delimiter differently in different locales (43126)
  66. Fixed a crash that could occur when dragging and dropping a plot into a spreadsheet cell to create a token, then selecting the overlay # as the statistic (43128)
  67. Fixed a crash on Mac that happened when editing the smoothing setting for multiple histogram overlays (43137)
  68. Improved the error message text when a purchase has not been approved (43162)
  69. Fixed a crash caused by applying Absolute to the color level selection when formatting a density plot (43207)
  70. Fixed the ImageJ Excel worksheet to work correctly on Mac (43326)
  71. Fixed a crash when viewing Cytoflex data files that have no events (43421)
  72. Improved stability on Mac (43625, 43634)
Version 6.01.0010 - December 8, 2016 (Research Use Only)

Bug Fixes

  1. Previously, when the Windows CHM help file was open beside a layout, searching in the CHM would sometimes lead to a crash
  2. Fixed a crash that occurred while sorting the Data List
  3. Fixed a crash that could occur on the Mac when selecting a file from the "Recent Places" list
  4. Fixed a crash that occurred when loading a layout saved with Data-Specific gates, if the original data files were missing and the data files were replaced during loading
  5. Fixed a problem that was introduced in 6.01.0009 that caused log-based color levels in density and contour plots to be displayed as linearly scaled if there were no negative numbers in the values
  6. Prevented a crash that occurred when editing compensation manually, if a blank was entered into the compensation value field
  7. Prevented a crash that could occur when using bar plots to plot spreadsheet data, if there was an invalid formula in the spreadsheet
  8. In version 6.01.0009, if you were updating from the previous version, the DNSEABridge executable was not replaced with the newer version - this has been fixed
Version 6.01.0009 - November 21, 2016 (Research Use Only)


  1. The BD Accuri importer can now import from .CI files as well as .C6
  2. Dragging a marker from one plot to another now creates a linked marker on the second plot
  3. Added a button for explicitly executing R scripts
  4. Parameter Math sequences from version 4 and 5 layouts are now imported into a new Parameter Math transformation.
  5. Improved storing transformation template files so they can be saved with relative paths
  6. Reduced the sensitivity of the mouse scroll wheel for MacOS
  7. Formatting quadrant text boxes now starts on the Contents category
  8. Improved handling of defaults for batch items in reports with field labels, where the field label has not been explicitly set
  9. Signing electronic signatures now requires entering the user name as well as password the first time in a session (subsequent signings only require the password)
  10. Errors the occur while performing R scripts and other transformations are now added to the layout's log (accessible on the status bar of the layout)
  11. Added an option for displaying histogram overlays in the legend using a box instead of a line
  12. The option for dithering colors on color dot plots has been changed to default to false
  13. Added coloring in compensation matrix tables in text boxes
  14. Dragging a marker onto an empty part of the page now inserts a text box and token, like it already did for gates
  15. Dragging data files onto a spreadsheet cell now pops up a dialog for selecting a stat or keyword token
  16. Added the ability to click on gate or quad vertices in a plot and select them even if they are "underneath" another gate
  17. Improved the usability of the crash dialog
  18. Improved the spacing between the labels and titles on vertical axes on plots

Bug Fixes

  1. Previously, when setting up quadrant authorizations, checking was not performed to prevent circular references
  2. Shortcuts on Mac now correctly use the Command key
  3. Fixed functionality for the printer icon on the quick access toolbar, and made sure that the print dialog was initialized correctly
  4. Prevented crash when performing parameter math using templates specifying non-existent files
  5. Fixed a crash triggered by data-specific gates when loaded in a layout where the data files could not be found
  6. Fixed a crash that occurred on heat maps when a gate had points with negative values
  7. Fixed copying and pasting of cells between spreadsheets on the layout
  8. Prevented a crash when attempted to calculate PCA using a gated subset that has no events
  9. Previously, permission rule formulas that included certain tokens did not always display correctly when the layout was reloaded
  10. Fixed a crash that occurred when adding a new compensation while the previous compensation matrix was being edited
  11. Changed the default folder for the auto-recovery file on MacOS to be in a standard folder
  12. Removed the incorrect % sign from density plot legends
  13. Fixed reordering items in the SOP list using drag and drop - previously the drop would put the item in an incorrect position in the list
  14. Fixed a crash that could occur in the Gate Navigator when the option to show plot nodes was turned off
  15. Improved the stability and error handling of the external application bridge
  16. Kinetics stats items now handle their gates being deleted gracefully without crashing
  17. Improved the way FCS Express interacts with MacOS in handling messages from the operating system
  18. Improved stability on MacOS
  19. Previously, spreadsheets changed their selected cell after zooming
  20. Disabled exporting data from spreadsheets using the ribbon Export button
  21. Eliminated an unnecessary Paste Special dialog when dragging cells from a data grid onto the page
  22. More UI fixes for high-resolution displays
  23. Spreadsheets no longer appear in the data list
  24. Prevented adding inappropriate statistic tokens for pie charts
  25. Improved Undo/Redo for changes inside a spreadsheet
  26. Simplified the behavior when dragging batch actions to reorder them
  27. Previously, FCS Express was unable to reopen layouts files referring to ICE data if the data had been moved on disk
  28. Removed transformations from the list of data that can be selected in the Export Data dialog - the transformations can be chosen separately in that dialog
  29. Made sure that compensation matrix tables in text boxes are displayed correctly even when the layout is set to remember parameters by name rather than number
  30. Simplified dragging vertices from one marker to another for creating links
  31. In the previous release, on MacOS a folder could not be selected after setting the data file type to FCS Plate Folder
  32. Fixed a crash that could occur when editing spreadsheet cells after merging cells
  33. Prevented changing plot types on plots that have no data loaded in order to avoid a crash
  34. Prevented sizing from being doubly applied when resizing pictures using the format window after using the Preview button
  35. Fixed a crash that could occur when dropping down the list of items in a token drop-down list
  36. Prevented spreadsheets from changing to a data file when using the Change on All buttons on the ribbon
  37. Ensured the pie charts update correctly if they are displaying spreadsheet data and the spreadsheet is on a page that's not currently visible
  38. Fixed a crash that could occur after renaming an SOP step without pressing Enter
  39. Previously, copying and pasting text with bullet items from PowerPoint into FCS Express caused a crash
  40. Fixed a crash that could occur in tSNE transformations if a parameter had no values
  41. Previously, using the configuration wizard with a network version to select a configuration file that was already saved on disk led to an error message
  42. Made tSNE calculations more robust
  43. Previously, on MacOS, selecting parameters on a plot in a list box that required horizontal scrolling was difficult to perform
  44. Fixed a crash that occurred in layouts showing Nexcelom data after opening an empty template and loading data into it
  45. Improved performance when opening the System tab in the Ribbon Backstage
  46. Fixed the usage of the default folders specified in the Options (previous it was sometimes using the most recent folder instead of the default)
  47. Previously, when plotting data from spreadsheets on dot plots, gates on those plots would include 100% of the data regardless of their position
  48. On MacOS, maximizing FCS Express now leaves room for the Dock
  49. After opening modal dialogs from the Ribbon Backstage, the title bar on the main window of the layout is now redrawn again properly
Version 6.00.0053 - September 24th, 2016 (Research Use Only)

Initial release of FCS Express 6