FCS Express 7 Release Notes

 

Version 7.10.0007 - October 14, 2021
Enhancements

  1. Added ability to insert hyperlinks in textboxes (12604)
  2. Added Progress bar for transformations to show progress and allow cancellation (68895))
  3. Improved speed of loading Cytek data (96035)
  4. Improve automatic identification of compensation controls for BioRad files (97655)
  5. Only recreate parts of auto-comp/auto-unmixing layout that is required (98877)
  6. Stop loading/applying compensation to files that have identity matrix
  7. Created Jaccard similarity pipeline step
  8. Added Feature Selection pipeline step based on SD (100930)
  9. Added variance based parameter selection pipeline step (102358)
  10. Added ability to read large Sony files that have invalid FCS headers (102624)
  11. Improved speed of tSNE and UMAP (103270)
  12. Added feature for jumping to the datasource of a token (103347).
  13. Improved name of parameters created by feature extraction steps (104132)
  14. Fixed the order of displaying columns after merging files (99338)
  15. Finalized support for M1 CPUs (104082)
  16. Improved Python pipeline step so classification results could be used by downstream steps (103478)
  17. Improvements in config file licensing on Mac (103675)
  18. Reordered endmembers so that Autofluoresence parameters will be at the end (103284)
Bug Fixes

  1. When a Data specific gate is created by dragging a plot onto the Gate Navigator, the correct compensation is applied (82534)
  2. Fixed bug that could happen when saving layout right when navigators were collapsing (90619)
  3. Fixed bug that could lead to crash in histogram stats table (92013)
  4. Fixed bug that UTF-8 characters in keyword values were not read properly (94090)
  5. Fixed alignment when creating multi-plots (94774)
  6. Fixed a crash that could occur when dragging Data Specific Gates (96135)
  7. Fixed a problem that could cause the Multicycle and Proliferation fit overlays to be drawn in an incorrect scale after magnifying the resolution (96289)
  8. Fixed a problem with displaying Accuri plate data when options are set to remember parameters by name (96903)
  9. Sped up gates that were applied to downsampled tSNE data (97029)
  10. Prevent text boxes on plots from getting larger when the layout is loaded without data (97111)
  11. Previously, Excel reports created during batch processing were not always being opened at the end of the batch even if the checkbox for opening the file was checked (97612)
  12. Improved text for changes to layout status in audit trail log (98157)
  13. Fixed bug that data specific gates were lost if the data list was reorganized (98572)
  14. Clarified naming of "Copy FCS data to clipboard" permission (98816)
  15. Fixed bug that caused errors with markers if the layout was saved with one decimal separator and opened with another (99047)
  16. Fixed crash when trying to save layout with large amounts of embedded data (99148)
  17. Added RemoveExtension function (99422)
  18. Fixed applying Unmixing to merged Cytek data files (99457)
  19. Improve stability working with very large data files (99657)
  20. Improved speed of moving gates when Matrix Visualizer was present (99670)
  21. Gate downsampling steps did not use the correct data specific gate (99728)
  22. Fixed bug that adding many overlays to a parameter heatmap causes a big slowdown (99976)
  23. Fixed crash that could happen when deselecting parameters in Merge to Spectra pipeline step (100341)
  24. When adding histogram overlays, added "Duplicate" button, and for 2D overlays, renamed "Another" button to Duplicate (100820)
  25. Fixed bug that clicking in compensation matrix changed the coloring of the compensation cell (100839)
  26. Fixed a refresh problem in the Downsampling Algorithm step (100991)
  27. "Create KMeans Transformation" was not appearing in the security Permissions List (101004)
  28. Fixed a cutoff in the interface of the axis formatting category (101026)
  29. Fixed colors of the compensation matrix in a text box to match the colors in the compensation window grid (102015)
  30. Removed spurious error messages that were displayed after relocating files (102027)
  31. Page orientation changed after changing size control on ribbon (102084)
  32. Fixed bug where exported data had incorrect $TOT keyword following transformation (102096)
  33. Improved how visualizers work with older saved layouts (102219)
  34. Fixed crash if you had 2 graph layout methods for the same parameter in the same pipeline step (102639)
  35. Fixed bug that plots sometimes came up empty after relocating files (102763)
  36. Fixed a problem where exporting a PNG image of selected layout objects results in blank objects (102773)
  37. Fixed SSM to handle negative values more appropriately (102848)
  38. Improved tSNE Layout method pipeline step (102850)
  39. Fixed memory leak when cancelling a paste operation into a spreadsheet (102955)
  40. Gate views' expanded state were not being saved properly if they were on invisible pages (103084)
  41. Fixed bug to include error message if the "parameter to unmix" did not exist in all single stained control files (103130)
  42. Improved Error messages when cannot login to security database (103271)
  43. Fixed bug that blank parameter name suffixes on pipeline steps were not being saved (103336)
  44. Fixed bug that when adding or removing single stained controls caused plots to change (103283)
  45. Fixed bug Undo/Redo of adding item to single stained controls (103415)
  46. Fixed crash loading some layouts (103695)
  47. Fixed a problem with multiselecting plots on Macs with the M1 chip (103732)
  48. Fixed rare crash in UMAP (103863)
  49. Fixed a problem where data in a saved layout with automatic compensation could not be recompensated after loading (103998)
  50. Fixed crash that could occasionally happen with pipelines, related to multi-threading (104018)
  51. Fixed problem when multisiselcting incompatible Instrument Specific Settings (104049)
  52. Security rules were previously not enforced when using drag and drop to reorder the data list (104098)
  53. Fixed crash with Sony data (104124)
  54. Improved circular-reference checking when creating Gated Data Files to prevent the data from depending on itself, and preventing a stack overflow (104131)
  55. Changes to Step #5 in the auto-comp wizard did not automatically update the layout (104154)
  56. Updated the USB dongle drivers to make sure that FCS Express can communicate with the dongle on all computers. (104056)
  57. Fixed bug that expired internet dongle / site license config file was not being renewed properly (104250)
  58. Stop including autofluorescence controls in SSM and CSI matrices (104282)
  59. Spectral parameters created by pipeline now use biexponential as default scaling (104285)
  60. Undo did not work after changing the "recalculation matrix automatically" checkbox in the auto-compensation wizard (104319)
  61. Fixed crash that could happen when specifying a large number of color levels in a color palette (104339)
  62. Filter out all null values when getting the rows for the automatic compensations - previously some data files saved in layouts with automatic compensations could not be reloaded (104351)
  63. Fixed bug that 'User Name' and 'Reason for change' where not appearing in system audit trail reports (104380)
  64. Fixed a crash triggered by copying gates linked to markers to a new page (104484)
  65. Created specific user options for regression stats (104519)
  66. Fixed a bug where tokens inside text boxes that are put into edit mode temporarily change their values to a previous value (104589)
  67. Updated dongle drivers to remove dependency on Microsoft Visual C runtime library (104704)
  68. Fixed bug that plots would sometimes change parameters when compensation was recalculated (104800)
  69. Previously, tokens derived from gates linked to quadrants on plots from pages that had not yet been viewed after opening the layout might display ERROR or 0 (102014)
  70. Fixed crashes that could happen if the users temp folder was read-only (104947)
  71. In certain rare circumstances, dot plot image was placed in incorrect location on plot (104948)

Version 7.08.0018 - July 27, 2021

Enhancements

Transformations / Pipelines

  1. Added FlowCut algorithm (94486)
  2. Added "Batch SOM" algorithm (97420)
  3. Added Python integration pipeline step (97073)
  4. Added ability to use tSNE or UMAP to graph clusters (99164)
  5. Store Transformation Results within the layout when saving (40474)
  6. Added ability to filter parameters in pipeline steps (93339)
  7. Created KNN Pipeline Step (96033)
  8. Added LowTimeDensity downsampling (96074)
  9. Added ability to add suffix to tSNE parameter so you can have multiple tSNE in the same pipeline (96451)
  10. New MST graph layout (96649)
  11. Created pipeline steps to allow to fill a parameter with monotonically increasing values (96643)
  12. Adding pipeline steps that can generate random numbers in various distributions (96937)
  13. Added ability to apply scaling to all or checked parameters in non-pipeline transformations (97508)
  14. Add Gate Downsampling Pipeline Step (97724)
  15. Add Meta clustering as new parameter is now the default for SOM (97122)
  16. Root pipeline step has all parameters selected by default (98679)
  17. Changed FlowSOM to use the faster SOM algorithm (98537)

 

Compensation and Unmixing

  1. Compensation / Unmixing matrix automatically updates when gates/data changes (97551)
  2. SSM and CSI matrices automatically created via auto-comp and auto-unmixing (72061)
  3. Unmixing Matrix Visualizer is built automatically when the matrix is built (96800)
  4. Changing auto-comp/unmixing settings will only update layout items that have changed (92068)
  5. Build auto-comp/auto-unmixing layout automatically as setup changes (97914)

 

Speed and Performance

  1. Improved speed when adding tokens into spreadsheets (99948)
  2. Improved efficiency of loading layouts (98343)
  3. Improved performance with 384 well plates (88257)
  4. Implemented multi-threading for consensus clustering using Hierarchical Clustering (98509)
  5. Improved Speed of Radio Graph Layout method (96533)
  6. Changed code to use hyperthreaded cores (101539)

 

Spreadsheets and Charts

  1. Added Violin and Beeswarm plots (93626)
  2. Added Levey Jennings Plots (95948)
  3. Added UNIQUE function to spreadsheet (94089)
  4. Added condition number formula to spreadsheet (95793)
  5. Added ability to batch process to Internal Spreadsheet (95891)
  6. Added ability to hide all cell borders, column and row headers in spreadsheets (42790)
  7. Introduced Tukey Statistics into spreadsheet (88638)
  8. Fixed multi-line parameter labels on spreadsheets to use all leading lines with text (97802)
  9. Stopped showing minor tick marks on bar plots (98821)
  10. Implemented addition PDF and CDF functions in Spreadsheets (98826)
  11. Implemented PROB, PERCENTRANK.EXC, PERCENTRANK.INC, PERMUTATIONA functions in spreadsheet (98827)
  12. Implemented Frequency, Harmean, Kurt, TrimMean functions in spreadsheets (98828)

 

Security and Audit Trails

  1. Added ability to add rules to control permissions for signing/unsigning specific signatures (97994)

 

Miscellaneous

  1. Removed the dialog for finding and loading user profile files from previous versions (19557)
  2. Improved ability for gates created on one FCS file to be applied to data files with a different range of data (40892)
  3. Added ability to set background color for image columns in data grid (56908)
  4. Added option to control the "off page" color (67958)
  5. Allowed users to provide a custom denominator to calculate a percentage of an arbitrary gate (89219)
  6. Added User Option to specify the maximum font size for multiplots (93430)
  7. Created a new version 7 plot theme (93431)
  8. Improved parameter selection dialog that appears when inserting multi-plots (93219)
  9. Optionally display a dialog when creating markers to allow the user to name the markers (93711)
  10. Added ability to enter wavelength ranges for spectral merge via detector name instead of number (93836)
  11. Tokens will now be displayed in regular text instead of labels (94192)
  12. Improved the size of the layout messages dialog on high DPI systems (94932)
  13. Slightly modified channel calibration curve fitting (96672)
  14. Plots now display the parameter label even when not showing data, and the parameter can be changed (96826)
  15. Added ability to have well gates all use the same color (97198)
  16. Added ability to add Gated Data to Data List to facilitate batch processing across gates (97462)
  17. Improved gates so they are not cut off based on the plot they were originally drawn on (97670)
  18. Added tokens to return whether files in the data list are empty (98364)
  19. Stop showing decimals on the X axis of spectral plots (99502)
  20. Properly handle time parameter in FCS files exported from the Helios (95852)
  21. Introduced a new property to allow controlling which sides of text boxes are anchored to the sides of the plots (93812)
Bug Fixes

  1. Improved text in audit trail when a new gate is applied to an overlay on a plot (97828)
  2. Improved the wording of text boxes in logs, to include their context (97878)
  3. Fixed bug that ""overlay to show"" on spectral plots did not work properly when multiple plots (98089)
  4. Fixed a crash caused by referencing the same parameter twice in a parameter math formula (98165)
  5. Fixed crash when loading layouts under particular circumstances (98322)
  6. Appended compensation parameters will now use the maximum resolution value of the original parameters (98331)
  7. When plots axis options are set to use parameter label sets, the plots will now use the default options if the given parameter is not included in the label set (98334)
  8. Fixed crash that occurred when loading layouts with data files that has keywords of the form Px (98451)
  9. Fixed crash when resizing nodes on parameter and gate heatmaps (98587)
  10. Fixed bug that data specific gates were lost when loading a new iteration into the data list (98595)
  11. Fixed bug where files from FacsAria were incorrectly treated as if they were index sort files (98612)
  12. Fixed a regression that prevented importing Diva experiments (99046)
  13. Fixed a crash that could occur when changing a histogram to a Multicycle plot (99050)
  14. Fixed bug that DSG were sometimes lost on relocated data (99065)
  15. Scaling pipeline step did not remember "automatic" setting upon reloading the layout (99112)
  16. Fixed bug when applying thresholding pipeline step to spectral data (99130)
  17. Fixed a crash that could occur when remembering scaling by data parameter with histograms (99259)
  18. Fixed bug that legend on visualizer scatter plot would change when the layout was re-loaded (99265)
  19. Fixed bug that unmixing spreadsheet shows all error if there is a column with an error (99266)
  20. Fixed crash that could happen with consensus clustering (99340)
  21. Fixed an error dialog that could appear after upgrading a network installation (99356)
  22. Fixed intermittent crash when right clicking on navigator frames (99360)
  23. Added detailed logging for changes to transformation properties (99409)
  24. Fixed crash when dragging and dropping across pages (99506)
  25. Fixed Crash when Deleting a gate from the gate Navigator (99507)
  26. Fixed bug that compensation matrices became all zero after data was relocated (99515)
  27. Improved Undo in pipelines (99637)
  28. Fixed crash in pipelines when there are no pages on the layout (99652)
  29. Fixed a crash that could be triggered by using Parameter Scaling Associations with manual access scalings (99961)
  30. Fixed bug where parameter heatmaps were sometimes blank after reloading (100007)
  31. Fixed bug when inserting compensation tokens when matrix was not defined (100098)
  32. Fixed updating empty heatmaps after loading a plate (100114)
  33. Fixed a crash that could occur when loading a layout with plots using a compensation that no longer exists (100201)
  34. Fixed a crash that could be triggered by dropping a non-parameter-specific statistic for multiple gates into a spreadsheet (100375)
  35. Improved speed of saving layouts when there were transformations in the layout (100421)
  36. Fixed bug with selecting parameters after transformation drag and drop (100461)
  37. Marker creation form now starts with the OK button enabled (100597)
  38. Fixed a crash that occurred when loading a BD FacsDiva experiment file into a compensation, when the options are set to not allow them (100718)
  39. Relocation dialog for Multi file fcs reader was not appearing when one of the individual fcs files was missing (100850)
  40. Fixed crash in UMAP when number of neighbours is high (100889)
  41. Removed ability to add parameters in compensation matrix editor (101010)
  42. Merged FCS files with different PnB would give strange results (101077)
  43. Prevent a crash that could occur when loading large data files (102093)
  44. Improved memory usage in tSNE algorithm (102132)
  45. Fixed a crash that could occur after opening a saved layout with the formatter open, then subsequently inserting a spreadsheet (102323)
  46. Fixed a potential crash when switching categories in the formatter or switching selected plots (102526)
  47. Fixed Crash with UMAP when there were too many events (102587)
  48. Improved high-resolution display of pipeline steps settings (102813) not released yet
  49. SSM CSI and visualized matrix show up as blank if you don't first open the compensation navigator (103167) not released yet
  50. Fixed a bug about parameters being lost in unmixing wizard after reopening layout (96247)
  51. Fixed a bug where having different legend text on multiple overlays could cause the values to be cleared when multi-selecting the overlays in the formatter (96443)
  52. Fixed bug that scatter parameters in the auto-compensation wizard would revert to the incorrect parameters when changing controls (96453)
  53. Fixed bug where startup scrips did not remember selected parameters when going backwards in the wizard (96454)
  54. Changed extension for user exportable/importable preferences files (96492)
  55. Added support for MSOLEDBSQL and TLS1.2 (96525)
  56. bars were not appearing on bar plots after dragging token onto empty bar plot (96751) wrong number
  57. fixed crash when copying/pasting markers from auto-comp plots (96694)
  58. Fixed bug that not all heat maps used parameter names from "parameter labels" (96803)
  59. Improved the way FCS Express calculates the biex values in certain data distributions (97246)
  60. Fixed bug that column headers from dropped tokens did not always reflect the correct parameter names (97316)
  61. Fixed a crash that could occur when linking quads to gates (97318)
  62. fixed bug that conditional batch processing actions did not save results properly if they were not active in the last iteration of the batch (97504)
  63. Fixed crash after moving a gate that was created on a log-log plot when displaying on a linear plot and moving it to a region below zero (97526)
  64. Fixed a bug that could lead custom tokens to not be deletable in the custom token list (97730)
  65. Increased the delay to make it easier to enter information in spin edits (97761)
  66. Improved speed of batch processing to PowerPoint (97809)
  67. Newly introduced stats were not appearing properly in the menu of old layouts (95838)
  68. Added Display name suffix for Normalization and 0-1 Scaling steps. (94858)
  69. Prompting for filename when inserting spectral plot, even if top most data had spectral parameter (94869)
  70. Previously, when creating files during batch processing, if the file couldn't be overwritten and had to be saved as a different name, then after batch processing the incorrect file was opened (95055)
  71. Fixed bug that some properties of the Flow Rate Check pipeline step were not being saved when saving a layout (95551)
  72. Fixed captions on report frames (95687)
  73. Fixed rare crash that could occur on Mac when requesting password (95774)
  74. No gate will be at the top of the list of gates in drop-down combo boxes (95790)
  75. Corrected typo in "Fluidigm" (94229)
  76. Fixed bug when copying a plot to the clipboard when there were a lot of plots on the layout (94336)
  77. Bar plot labels will now apply the decimal formatting from spreadsheets (93916)
  78. Fixed some cases where text boxes with tokens in them did not properly resize when the token changed (93721)
  79. Fixed bug that a Version 6 layout would crash when opening in Version 7 (93699)
  80. fixed text on descriptions in spreadsheet formatting frames (93301)
  81. Improved speed opening compensation window for loaded layouts (93473)
  82. Improved the way ticks are displayed on spectrum plots (93516, 81760)
  83. Fixed the way percentile ranges are applied when loading data through instrument-specific settings (93523)
  84. Improved error handling in the case where performing transformations on data files that are missing parameters selected in the template (93557)
  85. Fixed a problem that could cause text boxes to temporarily not update after they have been added to a batch processing export (92395)
  86. Fixed bug where you could sometimes not drag and drop after opening a plot (92729)
  87. Fixed bug that you could not delete the default user if it was not the first user in the user list (92806)
  88. Fixed bug that undoing a parameter change forced a transformation to recalculate even if auto-update was off (93153)
  89. Fixed pasting into transformation options window (89475)
  90. The default for new plots will be for gates that are at the edge of the plot's resolution range is changing to not include events that are out of range of the data (91343)
  91. Fixed bug that you can link markers to existing non-marker gates (91682)
  92. Improved logging text (83801)
  93. Improved the Divide Axis Labels option (71394)
  94. Fixed bug that certain actions were still allowed on Data Specific gates even if the user did not have allow gate edit permission (75372)
  95. Improved speed of dragging/dropping tokens into a spreadsheet (76036)
  96. Fixed bug where Data specific gates did not disappear from plots if you replaced the gated with a replacement that had different parameters (78921)
  97. When selecting stats from multiple gates to drag in spreadsheet, do not duplicate non gate related stats (80364)
  98. Fixed crash when selecting all columns in a spreadsheet and pressing delete (82020)
  99. Prevented a rare crash that could have occurred after reloading a layout saved in an inconsistent state (82282)
  100. Fixed a problem that could cause a gate to move after it's been dragged out of a plot to create a new plot (83532)
  101. Fixed a crash that could occur when pasting multiple plots off a page (95897)
  102. Fixed a bug that caused titles to be doubled on heatmaps (95877)
Version 7.06.0015 - January 27, 2021 (View Recorded Webinar)
Enhancements

  1. Ability to create pipelines to analyze high-dimensional cytometry data (View Recorded Webinar)
  2. Ability to add pre-defined algorithms to the pipeline
  3. Ability to add Downsampling steps to the pipeline
  4. Ability to add Dimensionality Reduction steps to the pipeline
  5. Ability to add Clustering steps to the pipeline
  6. Ability to add Visualization steps to the pipeline
  7. Ability to add Mathematical steps to the pipeline
  8. Ability to add Quality Control steps to the pipeline
  9. Ability to group pipeline steps into folder
  10. Ability to perform Unmixing as a step in the pipeline
  11. Ability to remove unwanted parameter from a dataset (Parameter Removal pipeline step)
  12. Ability to create virtual bandpass filter on spectral data
  13. Added ability to create virtual spectra with non-spectral data (View Recorded Webinar)
  14. Axis scaling can now be associated with data parameters across all plots in a layout (91471)
  15. Compensation default order in the User Options has been changed to "Compensation Default, then FCS file" (93427)
  16. Provide an option to allow to append compensated parameters (both as User Option and as Layout Option) (97620)
  17. Added ability to plot date/time data and have dates along the axes (70663)
  18. Added ability to plot classification data directly on 2D plots (92974)
  19. Added the ability to create multiple well/classification gates from a heat map (74677)
  20. Added ability to export a file with classifications (either merged file or file with clustering) into separate files based on the classification (90289)
  21. Improved speed of startup on the network version (94990)
  22. Added ability to reload (Refresh) all open data files (92832)
  23. Added ability to rename endmembers in Unmixing matrix (93643)
  24. Added color palette designed to hide outliers (91897)
  25. Ability to plot Normalized Spectral with the Umixing Matrix Visualizer
  26. Allow dragging and dropping quads to a spreadsheet to insert quad statistics (91150)
  27. Added ability to drop quads onto batch action reports (71988)
  28. Plot legend can now be displayed in the statistics window for that plot (92964)
  29. Added option for adjusting the size of nodes in Spade and cluster plots (82181)
  30. Spreadsheet options now default to use the first row as column titles (93426)
  31. Improved hint system for adding spreadsheet formulas (93030)
  32. Sped up CSV export (93452)
  33. Enhanced Security System to log all events in UTC (93736)
  34. Added ability to specify a max value for scaling in instrument specific settings (90947)
  35. Parameters on plots will no longer be automatically updated when the new number of parameters is different from the previous (93825)
  36. New default for histogram smoothing is now 10, except for fit plot (93425)
  37. Added ability to append a custom suffix to the end of the axis title when channel calibration is applied (73196)
  38. Improved interpretation of non-standard $VOL keyword from Cytek instruments (93690)
  39. Added ability to read incorrect $VOL keyword in ZE5 files (97398)
  40. Added ability in Startup Script to change the template file for a transformation (90934)
  41. Added delays to editing the Multicycle formatting fields (91062)
  42. Added right click to parameter selection menu in transformation steps (91476)
  43. Fixed drop-down buttons on Data List to add files by default (91676)
  44. Improve compression for saved layouts (91691)
  45. Made spectral plots generated by unmixing layout builder wider (92840)
  46. Removed Low Bound and High Bound from the default set of visible stats on histograms (93428)
  47. Enhanced image loading to support 32-bit floating point grayscale images (93505)
  48. Improved the layout of plot legends (96010)
  49. Added ability to read Amnis version 6.3 files (96034)
  50. Improved speed of Arch graph layout method (96281)
  51. Improved Insert Function dialog on the spreadsheet (93752)
  52. Better handling of failed pings to the internet dongle servers (97578)
  53.  System Level Audit Trails
Bug Fixes

  1. Fixed category name of Axis category to Axes (55527)
  2. fixed bug that sometimes a plot would not update if it was based on a gated transform and the gate moved (78897)
  3. Hid parameter name in gate heat map when parameter independent stats are displayed (81211)
  4. Fixed bug that sometimes when opening V6 layouts in V7, quad tokens display ERROR (81588, 95703)
  5. Resolved problem with copying and pasting from spreadsheet when comma is the the decimal separator (82056)
  6. Fixed bug that modified FCS files did not always prompt to save when closing the layout (82209)
  7. Speed improvements for gate heat maps (82672)
  8. Previously, undoing then redoing inserting tokens from data files in custom token formulas resulted in not being able to display the result (84361)
  9. Fixed bug in loading quads with biexponential scaling from certain V4 layouts (90059)
  10. Fixed crash when double clicking in array formula area in spreadsheet (90434)
  11. Fixed bug where spreadsheets that contained non-standard excel formula could not be imported by Excel (90435)
  12. Fixed bug where files added using the "All FCS File" and "Regular FCS file" were not being recognized as the same file (90445)
  13. Sped up drawing of spectral plots (90528)
  14. Fixed bugs undoing gate changes for gates that were auto-created in auto-comp when undoing auto-comp changes for gates created by the auto comp (90608)
  15. Stacked Y-axis overlays can now use a common axis title instead of each having their own (90804)
  16. Previously, attempted to invoke a feature that the license was not permitted for could result in an error message dialog that made it impossible to close the program (90805)
  17. Improved crash when clicking quickly in the data list (90840)
  18. Fixed a crash that could occur after dragging a regression plot onto a non-regression plot (90993)
  19. Contour plots will now be able to color events based on parameter values (91042)
  20. Fixed bug where layouts with a lot of plots and textboxes loaded slowly and consumed a lot of memory (91081)
  21. Updated axis tick label drawing to make sure that labels are shown (91084)
  22. Fixed High res display issue for instrument specific settings (91136)
  23. Fixed a crash that could occur when copying and pasting multiple tokens in a spreadsheet (91154)
  24. Fix how multiple overlay contour plots display their legend (91155)
  25. Added ability to enter decimal points in resolution max/min (91223)
  26. Made sure that data-specific gates can get created when using the shift key while dragging a gate (91270)
  27. Fixed crash when drawing gate that has NAN vertices (91316)
  28. Percentage stats on cluster heat maps will now be calculated as a percent of the entire population, not just of the particular cluster (91336)
  29. Fixed "next" text cut off in Overlays formatting dialog (91345)
  30. fixed cut-off label in the User Options -<Miscellaneous Options (91347)
  31. Improved error message when trying to connect to security database with sufficient database permissions (91371)
  32. Fixed crash when you start resizing something on the layout and releasing the mouse above a navigator (91372)
  33. Fixed bug that loading layouts with electronic signatures applied in non-secure version would crash (91388)
  34. Fixed bug that certain errors in the Multicycle fit would get recurring popup messages (91390)
  35. Fixed a crash that could occur when loading a layout where a plot had markers with undefined endpoints (91399)
  36. Improved automatic marker positioning for auto-compensation and unmixing (91401)
  37. Improved how unmixing token table defaulted their normalization type (91405)
  38. Fixed a problem with appending to PowerPoint presentations when an invalid filename was specified (91464)
  39. Fixed a bug where removing columns in a spreadsheet could cause the wrong columns to be removed, if the columns had previously been reordered (91474)
  40. crash when dragging text box on custom token editor when no custom token is selected (91477)
  41. Fixed bug that export split combo box on data export was coming up blank if there was no classification parameter in the data file (91492)
  42. fixed cut off text in the Export dialog (91493)
  43. Columns heatmap tables now properly reflect file names for merged fcs files (91504)
  44. Fixed bug in Kernel Density downsampling that would cause a crash in certain circumstances (91511)
  45. Fixed a crash that could occur if a spreadsheet cell is being edited while another plot gets inserted on the page (91525)
  46. Fixed bug where compensation sliders did not work on compensation matrices imported from FlowJo (91562)
  47. Fixed bug where expanding the compensation/unmixing matrix windows could be slow (91578)
  48. Fixed a problem that could cause a crash if the batch runner window was open when the layout was closed.
  49. Fixed bug that updating config file from server was not downloaded if the local confirm file expired (91651)
  50. Fixed bug where unmixing parameters could not be selected in stats token editor (91679)
  51. Fixed bugs that unmixed parameters were not available for selection when adding parameter overlays (91680)
  52. Fixed a memory leak in loading data files (91802)
  53. Fixed a memory leak in retrieving a file list via SFTP (91803)
  54. Fixed crash that could happen when trying to load corrupted preferences file (91918)
  55. Fixed bug that Time parameter was sometimes shown on log scale for cytek data (92156)
  56. If a data grid was gated on a gate, and the gate was deleted, the data grid would appear empty (92157)
  57. Fixes to handling published layouts resaved in FCS Express Reader (92168)
  58. Removed unnecessary warning message when saving a published layout in Reader (92198)
  59. Fixed bug that data grid highlighting was not consistent when "defer iteration changes" was on (92241)
  60. Fixed bug when multi-selecting gates and moving them in gate hierarchy could cause a crash (92303)
  61. Fixed crash when doing Tsne with 2 parameters selected (92368)
  62. Fixed crash inserting Parameter Heat map table if parameters were missing in some of the overlays (92446)
  63. Fixed crash when you types into the first column of the compensation/unmixing matrix (92741)
  64. Fixed bug in drag and drop system that could break under 64 bit (92748)
  65. Fixed a crash when dragging multiple data files to create tokens in a spreadsheet
  66. Improved matching of unstained controls in mixing matrix to their correct samples (92883)
  67. Fixed bug that you could not reload layouts that had unmixing tokens in a spreadsheet (92963)
  68. Previously, text boxes did not always resize to accommodate enlarged tokens after the value of those tokens was modified elsewhere in the program (93035)
  69. Fixed crash when building unmixing layout where some files had different parameter orders (93175)
  70. Fixed a crash that could occur soon after loading in old layouts (93447, 98058)
  71. Fixed crash when trying to insert tokens into array formula regions (93503)
  72. Fixed bug where manually applying unmixing to stat token sometimes gave wrong results (93571)
  73. Fixed bug where Inserting/Deleting Columns and Rows in Array Formulas Crash FCS Express (93639)
  74. Fixed the link displayed in potential error messages in the C6 importer (93684)
  75. Fixed bug where deleting a gate that a data grid was gated on did not cause the data grid to refresh properly (93717)
  76. Fixed a problem with specific layouts that led to them being unable to be loaded (93745)
  77. Fixed crash in unmixing setup when no positive controls were selected (93757)
  78. Fixed bug where scaling formula was incorrectly applied to time parameter (93844)
  79. Removed warning about invalid spillover keyword with just one parameter (94016)
  80. Improved the ability for FCS Express to use files with very long paths (94075)
  81. Fixed bug where max number of invalid password attempts was not respected (94183)
  82. Fixed crash when calculating stats on a file that has no events (94386)
  83. Fixed crash in automatic peak detection with data piled up in first channel (94397)
  84. Fixed crash when copying an overlay item from a navigator (94497)
  85. Improved ability to relocate single stained control files in auto-comp/unmixing (94630)
  86. Transformation drop down list on overlay formatting category did not refresh when transformations where changed (94650)
  87. Fixed the direction of movement when dragging the corners of marker gates (94745)
  88. Added ability to calculate SD and robust SD related statistics on calibrated data (94959)
  89. Fixed crash when closing layout when spreadsheet autocomplete window was open (95052)
  90. Fixed bug that dragging regression plot onto regular plot would copy the regression overlays (95096)
  91. Previously, changing the display type of a token was not undoable (95114)
  92. Fixed bug where compensation wizard would give erroneous warning if negative controls where not specified last (95158)
  93. Previously, if multiple density plots were formatted together, then viewing the Specific Options category could cause them to change without making an explicit change in properties (95603)
  94. Fixed "parent does not have control" crash that could happen (95835)
  95. Fixed bug occasional bug that could happen when moving docking navigators (95962)
  96. Fixed a crash that could occur on layouts with a large set of data files in the list and a large number of gates and batch iterations. (96021)
  97. Fixed bug that Gate change permission was not changed properly when modifying DSG (96154)
  98. Fixed crash in parameter heat maps if no data was loaded (96362)
  99. Fix crash in KMeans if you have more than 50,000 cells and run kmeans multiple times (96512)
  100. Set the default for associating axis scaling with parameters to true (96822)
  101. Fixed bug that radius parameter was disabled when non-parameter requiring stat was selected (96843)
  102. Fixed a crash that could occur after switching a regular histogram to be a Multicycle plot, then deleting a marker (96910)
  103. Prevented a crash that could occur in rare cases when loading old layouts with multiple pages showing statistics (97141)
  104. Fixed bug wheres spillover coefficients from ZE5 instruments were sometimes a factor of 100 off (97221)
  105. Fixed a crash that could occur in cases when multi-selecting plots and the quadrants formatter is open (97327)
  106. Fixed a crash that could occur when opening a combo box for a custom token if there are no list entries defined (97505)
  107. Fixed bug that intermittently happened on 64 bit release when dealing with dongle drivers (97628)
Version 7.04.0014 - March 30, 2020 (RUO) - April 27, 2020 (IVD)
Enhancements

  1. New functions added to custom token formulas for reporting Channel Calibration details (68191)
  2. Added the ability to search through parameter lists in transformations (69934)
  3. added ability to import Flowjo exported compensation matrices (72417)
  4. Added ability to overlay contour plots (75398)
  5. Security users now store their creation date (81797)
  6. Added parameter heat maps (81998)
  7. Added new multiplot feature to show plots with color by parameter for each parameter (82004)
  8. Moved some of the data loading options, such as LogStartMode, DisplayNameSource and MatchingNameSource, into the instrument specific settings (82018)
  9. Added option about which Cytek files to load (82289)
  10. Fixed error message to be more useful in Auto-Comp setup (83186)
  11. Formatting changes that cause warnings can now be applied to plots instead of being treated as errors (84072)
  12. Introduced unmixing and auto-unmixing (87354, 90045)
  13. Allow import of gatingML files (89088)
  14. Added ability to change the gate line width on a gate by gate basis (89215)
  15. improved PDF stability (89735)
  16. Added integration with R to allow to adjust gates via R in between iterations (89988)
  17. Edit field in KMeans properties now has delayed application (90061)
  18. Added new customer token IsCurrentUserMemberOf (90076)
  19. Made "allow self logout" the default for new users (90087)
  20. Sped up the program when moving gates when the gate navigator is open (90128)
  21. Improved speed of exact local density calculator (90276)
  22. Added red-green gradient palette for heat maps (90284)
  23. Implemented Opt-tSNE (90345)
  24. Added typing delay to the Legend text editor in the overlays category (90399)
  25. Added security code for enabling or disabling batch action (90409)
  26. Fixed bug where parameters from Helios files were defaulting to biex and not linear (90581)
  27. Improved Merge FCS loading options so it was available for every specific instrument (91157)
  28. Added instrument-specific settings for CYTOF (91505)
Bugs Fixes

  1. Fixed bug that if you were hiding the error bar line by setting the line style to "no line", the Y axis was still adjusting as if the error bars were being drawn (67530)
  2. Stopped showing multiple error messages if inserting gates/makers when user does not have permission to show errors (12398)
  3. Fixed alternating highlight color in data list so that it was not confused with the inactivated selection color (18745)
  4. Fixed bug that the axis scaling on spectral plots with multiple overlays was not correct (75221)
  5. In cases with where pie charts overlapped other plots, changing data on the other plots sometimes resulted in only a portion of the pie chart being redrawn (77023)
  6. Fixed mouse wheel scrolling on format screens (80276)
  7. Now able to insert multiple tokens in the title field when several plots are selected together (81206)
  8. Erased old spillover keyword when exporting data so data was not compensated twice upon reload. (81272)
  9. Data can now be changed in the Reader on published layouts if the publisher has granted permission (81652)
  10. Improved error message when trying to export merged files as FCS (82528)
  11. Fixed flickering when typing into treeview node editors (83932)
  12. fixed crash in Weighted density downsampling (88087)
  13. Fixed a bug where the resolution of exported parameters would sometimes change when doing batch export (88211)
  14. Added functionality to auto-detect the LDAP settings from the users local computer (88272)
  15. Fixed bug that the "modify contents of a data file" permission was not always respected when editing spreadsheets (88607)
  16. Gate heatmaps now display percentage statistics relative to the full sample, rather than relative to only the subset (88644)
  17. Fixed bug that the "color based on" drop-down was still available when converting a density plot to contour plot (88858)
  18. Improved code to not perform transformations for plots on invisible pages when layout loads (88888)
  19. Fixed alignment of axis labels with the center (89000)
  20. Permissions for creating new plots are now checked when dragging data files from the Data Navigator onto a blank part of the layout (89203)
  21. enhanced ability to allow to easily open multiple plots from the same spreadsheet (89515)
  22. Enhanced ability to delete invalid config files from the config wizard (89658)
  23. Added ability for Configuration file Setup Wizard to show serial number of available demo downloads (89888)
  24. Fixed bug where dragging gate, marker, or plot to Batch Actions Excel Action results in all gates being selected in Edit Statistics dialog (89924)
  25. Fixed a refreshing problem in the Parameters to Display formatting category that occurred after inserting a new data grid (90053)
  26. Fixed text for "compensation to use" in layout info and user options (90097)
  27. Y Axis labels are now changed to be horizontal when the overlays are stacked while adding overlays (90098)
  28. Fixed tab order on marker frame (90138)
  29. Fixed resetting the toolbar to default state (90143)
  30. Adding ability to change the "category" of box and whisker plots by clicking on the axis titles (90151)
  31. Fixed bug where Multicycle plot id not refresh after changing the model (90166)
  32. In legend text field, added delayed editing, and in Gate Heatmap overlays formatting, reduced the number of times all overlays get automatically selected (90232)
  33. Fixed formatting screens for box and whisker plot to make it clearer which options were being applied (90262)
  34. Properly centered the Group names in box and whisker plots (90263)
  35. Fixed a crash that could occur when inserting a marker if a formatter window was open on the markers category (90265)
  36. Fixed audit trail to entries for changes to "Compensation to use" to more closely match the user interface (90286)
  37. Fixed the spacing for axis title width to make sure that each title in stacked histograms can be read (90375)
  38. Fixed fonts on compensation matrix screen so modified compensation matrix values are underlined instead of being red (90398)
  39. Fixed bug where the parameter names in the parameter selection dialog for multi-plots would sometimes be incorrect (90401)
  40. Make sure that when the user does not have permissions for modifying transformations, that the transformation window doesn't become unresponsive (90451)
  41. Fixed Labkey to conform with new requirement for CORS authentication (90476)
  42. Fixed a crash that occurred when setting the biex value of a plot too high using the slider (90484)
  43. Fixed crash that happened when deleting the last control on autoComp frame and extra targets were visible (90493)
  44. Fixed crash when performing undo after deleting auto compensation control when extra targets checklist is showing (90500)
  45. Mouse scroll wheel now works correctly in the formatting windows (90557)
  46. Improved logging for dragging gates to new locations in the gating hierarchy (90562)
  47. Fixed bug in tSNE algorithm where momentum switch occured one iteration after exaggeration ended (90573)
  48. Fixed crash that occured when typing a value > 100% in the overlay transparency edit box 90574)
  49. Fixed a crash that could occur when cutting a histogram subtraction plot (90578)
  50. Prevented a crash that could occur when dragging and dropping a batch action while batch processing was running (90605)
  51. Fixed bug that Diva importer did not respect "do not show this choice again" (90614)
  52. Fixed a crash that could occur when inserting a spectrum plot if the formatter is open and displaying the Axes category (90615)
  53. Fixed crash when exporting a text box as RTF via the batch actions and the text box was not on a currently showing page (90617)
  54. Fixed bug that "create output folder" checkbox was not visible on MacOS (90634)
  55. Made Batch Export window shorter (90635)
  56. Fixed crash in autocomp setup for certain data files (90726)
  57. Fix bug in auto-comp wizard when building auto-comp gates in the case that there were duplicated parameter names in the data file (90743)
  58. Fixed bug where FCS Express froze on Mac when opening the manual from the Help menu (90778)
  59. Fixed a crash that could occur in the Overlays formatting category occur when clicking on the Reorder or Remove buttons quickly (90816)
  60. Fixed that the wrong number of days left in demo was reported in Help->about (90837)
  61. Fixed crash when trying to log in without specifying a user name (90848)
  62. Fixed bug where you could not type into the spin edit on the zoom form (90860)
  63. Improved error message when an FCS file with an invalid spillover matrix (90887)
  64. Fixed scaling of Cytek data in rare cases that had huge negative values (90962)
  65. Fixed a crash that could be triggered when changing data files on a data grid using the right-click menu, while a layout navigator is open (91000)
  66. Fixed spelling mistake in Cytek Instrument specific settings (91028)
  67. fixed crash when copying Box and Whisker plots to the clipboard (91032)
  68. Fixed a bug that could prevent loading layouts saved in version 6, if the layouts had data-specific marker gates (91044)
  69. Fixed crash in kinetics plots where there was only a single data point in a given time slice (91077)
  70. Fixed bug where spectral Exclusion gates did not return the correct results (91092)
  71. Fixed spelling mistake in instrument specific settings dialog (91137)
  72. fixed crash when inserting multiple tokens and not specifying the stat to use (91151)
  73. Fixed bug that outlier dot size for contour plot overlays did not match what it said on format screen (91156)
  74. Fixed bug where histograms did not graph data with small data range properly (91177)
  75. Fixed crash when loading compensation files with unrecognized extensions (91212)
  76. Fixed bug importing compensation matrix files if the parameter names contained a space (91217)
  77. Fixed bug that anonymizer user interface did not always reflect the current settings in the layout (91267)
  78. If scatter plots were overlapping with data plots, then when you switched data iterations, the scatter plots did not always update immediately (91275)
  79. Fixed memory leak in parsing Sony spectral data (91303)
  80. Fix Instrument Specific settings for ZE5 instrument (91329)
  81. Enhanced ZE5 instrument specific settings to have more accurate division factor (91333)
  82. Fixed sizing of Biexponential options (91389)
Version 7.01.0018 - November 5, 2019 (RUO Only)
Enhancements

  1. FCS Express 7 now supports MacOS Catalina
  2. Range max and min fields now allow delays before values are applied to the plot (84311)
  3. Added ability for user to control the minimum peak threshold in Proliferation fitting (88445)
  4. Added ability to select parameters to use for NxN plots (88535)
  5. Added expiration date to the about box (88836)
  6. Improved speed of KMeans for large datasets (88963)
  7. Added serial number to message about renewals. (89073)
  8. Added Box and whisker plots (72757)
  9. Added visual indicator and tokens denoting that a compensation matrix has been manually adjusted (79985)
  10. Changed scatter gate plots from auto-compensation wizard to be density plots (79931)
  11. Allowed choosing Y-axis title type on stacked-overlay plots at the time of parameter addition (81764)
  12. Added ability to run KMeans multiple times with random initial guesses to find the best result (89478)
  13. If, when creating NxN plots you specify file name in legend, the legend now appears automatically (89900)
  14. Fixed default minimum cluster percent for SPADE to 0.1% (83857)
  15. Added ability to shift+click to select multiple checkboxes in checkListBoxes at once on Windows (89469)
  16. Added Gate Color and overlay color to statistics window (19100)
  17. Allowed using the slider in the biex formatting category for values > 10000 (89214)
  18. Improved speed of downsampling (89494)
  19. Converted the error logging window a floating/dockable window (89875)
  20. Added option to KMeans whether or not to use results that did not converge (89876)
  21. Improved LDAP integration to work against a wider variety of authentication options (89175)
Bug Fixes

  1. Full sessions report was not previously reporting correct session time and hour sum (88579)
  2. Legend text on Gates heat map will now properly display FCS Express-related keywords (88609)
  3. Fixed a bug that a new spreadsheet could be inserted even if you did not have permission (88670)
  4. Fixed bug where people spreadsheet cells could be changed even without permissions (88671)
  5. When adding data files is prohibited due to security permission settings, made the error message clearer (88673)
  6. Fixed bug that empty permission rules formula were evaluated as True (88717)
  7. Added ability to specify Sender name, Reply to and Sender email to notification emails (89113)
  8. Fixed bug where security notifications were missing the merge data (89139)
  9. Added option to not try to merge spectral data file when loading Cytek data (89191)
  10. Fixed crash when autocomp is run on spectral data file where preferences are set for extra spectra parameters to be deleted (89239)
  11. Fixed bug where Failed Logins where being logged when LDAP Single Sign On was being used (89604)
  12. Improved speed when resizing plots with textboxes (81231)
  13. Fixed bug where the text on the channel calibration tool is wrong at high DPI (81256)
  14. Increased width of autocompensation list boxes to accomodate longer file names (83159)
  15. Fixed bug that Target Density Downsampling would return different results if using different numbers of threads (87525)
  16. Layout history entries for changes to channel calibration plot settings were improved (88309)
  17. Fixed bug getting time zone on Mac under certain circumstances (89923)
  18. Data Export dialog was previously losing the file type extension in some circumstances (75318)
  19. Fixed bug where width parameters in Cytek data were not deleted properly. (89834)
  20. Fixed Layout icon on Mac (89971)
  21. Improved error message when loading invalid Amnis XML files (88486)
  22. Enabled obtaining a network countercode from any computer running FCS Express (89732)
  23. Fixed a crash that could occur when pasting a countercode obtained via the web site (89788)
  24. Hid Color Scaling combo box for Color Levels that do not support color scaling (89797)
  25. Speed up drawing of the gate navigator when there are large numbers of gates (89800)
  26. Fixed bug that density plots created for auto-compensation setup did not use outlier mode from the user preferences (90024)
  27. Improved how SPADE tries multiple attempts at K-means (90047)
  28. Fixed the URL in the configuration wizard for obtaining a config file manually (90081)
  29. Fixed a crash that happened when you apply a snapshot and the snapshot is trying to modify gates to display for a plot that had been deleted (90094)
  30. Fixed a crash that could occur when switching axes between hyperlog and log scale formulas, and back (90107)
  31. Optimizated formatter refreshes (89844)
  32. Fixed bug where certain images could not be loaded on mac (89863)
  33. If the Matching name did not match the display name, you could not change parameters on plots (89896)
  34. Fixed a crash that could happen when deleting a page with a plot where the stats grid is on another page (89921)
  35. Fixed crash when that happened when magnifying plots (89969)
  36. Fixed crash when clipboard had invalid data (89970)
  37. Fixed bug that you could load new data files into a layout even if you did not have permission to do so (89663)
Version 7.00.0037 - August 11, 2019 (RUO Only)
Bug Fixes

  1. Fixed the address that FCS Express uses to communicate with the internet dongle server
Version 7.00.0035 - August 11, 2019 (RUO Only)
Enhancements

What's new in FCS Express 7?