New Features in FCS Express 7
Contents
In addition to the new features described in the other sections of the manual, FCS Express has major improvements summarized below:
•Speed
oSignificantly improved speed in the loading of data files, layouts, and saving of layouts (up to 2X increase over previous version).
•User Interface
oLive Updating Dockable Formatting Interface
▪New look for the formatting window that updates as you make changes
▪New tools and reorganized features to improve ease of use and efficiency
oNew Color Blind Color Level Option for Density and Contour Plots, Gate Heat Maps, and Plate Heat Maps
oThe Refresh tool is particularly useful when editing or adding keywords, adjusting data loading preferences, modifying parameter labels, or any other changes where removing cached data and replacing it with updated data from FCS Express is useful.
oSystem Level Audit Trails (logging/audit trails add-on only)
▪Allows users to track system level actions to an audit trail for further improving compliance with regulatory requirements such as 21 CFR Part 11
•Pipelines
oPipelines in FCS Express are a set of data processing steps that stand alone or are connected in series. The output of a step can be applied to a data file or utilized as the input of the next step, or series of steps, that may be applied to your data.The vast majority of commonly used algorithms for data analysis are actually pipelines, with tSNE (and its variants) and SPADE being two examples. However, when those algorithms are implemented as a one calculation, user customizations are limited to the what the specific implementation allows. Pipelines in FCS Express increase the computational flexibility and granularity of running algorithms and data transformations while giving users the unique ability to create their own transformations.
▪UMAP
▪Merge to Spectra (for virtual unmixing)
▪Ability to store transformation results within the layout when saving, to save time when the layout is re-opened.
▪...and much more...
•Compensation and Unmixing
▪Added the ability to perform spectral unmixing with live updating wizard
oUnmixing Visualized Matrix builder
▪The Visualized Matrix builder creates a new page showing a chart displaying the Detector vs Intensity for each single stained control added in the wizard, as well as a spreadsheet with the charted values (each detector is labeled by Detector # and Wavelength).
oImproved Automatic Compensation Interface and performance
▪New options, improved workflow and live updating capabilities for automatic compensation
oSpillover Spreading Matrix and Cross Staining Index matrix
oImproved Data Fitting for Automatic Compensation
▪Improved stained and unstained automatic peak identification
oAutomatic Data File and Parameter Matching
▪Parameters automatically matched for single stained controls
oImproved Scatter Gate Selection
▪Set default scatter gate parameters in automatic compensation setup
oAbility to Choose Multiple Internal and Universal Negative Controls
▪Select the same tube as both a stained and unstained (self as negative) control
oCompensation Options to append or overwrite compensated parameters
▪Added the ability to append compensated parameters to uncompensated parameter list or overwrite existing parameters as compensated (current and previous default)
•Batch processing
oAbility to batch process to Internal Spreadsheet
oAbility to add Gated Data to Data List to facilitate batch processing across gates
•Data File Compatibility and Support
▪Automatically recognize and set scaling for data files
▪Improved support for Cytek Spectral Data
oMACSQuant MQD File Compatibility
▪Load and analyze MQD files directly in FCS Express
oImproved support for Cytek Aurora and BioRad ZE5 volumetric keyword concentration calculations
•New Plot Types and Enhancements
oGates Heat maps and Parameter Heat Maps
▪Create array style heat maps for gated populations and parameters
▪Allows for multiple subtraction, addition, division, and multiplication data fitting. Replaces Histogram Subtraction Tool from previous versions.
▪Create plots for every combination of parameters in a data file.
▪Five new multi-plot options available: NxN Plots, NxN Plots compensated, All Parameters by X, All Parameters by Y, Histograms for all parameters
▪Quickly create overlays for all parameters on a single histogram for a data file.
oBox and Whisker, Violin and Beeswarm Plots
▪Visualize the distribution of your data according to quartiles, where the middle two quartiles are represented by a mean- or median-bisected box, and the outer two by whiskers. Individual data points within each set may be denoted by points, and the appearance of outliers can also be visually emphasized.
▪Visualize quality control data to ensure test metrics are stable over time and fall within a predetermined range.
•Data Transformations and Statistics
oUsability Improvements for Transformations
▪New Apply to all/selected button for transformations
▪Improved PCA for data sets with more parameters than cells
▪Improved K-means clustering
oToken Multiplication Grouping
▪Improves ability to add multiple statistics from different gates, markers, quadrants, and parameters in spreadsheets and token tables.
▪Better grouping of statistics from multiple files in spreadsheets
oAnalysis of Variance or ANOVA
▪Perform single factor or one way ANOVA directly within Integrated Spreadsheets to test for statistical differences between multiple groups
▪Ability to perform a Tukey's range test, also known as Tukey's test, directly within the Integrated Spreadsheets.
▪Create markers and gates for any percentile value
▪When typing a formula a dialog will appear providing hints and links on how to use available formula references
•General Usability and Tokens
▪Use blank tubes as placeholders for additional samples when creating or working with panels
▪Change gate and plot positions with keyboard arrows
▪Create data specific gate with keystroke
oAbility to view the Source or Formula of Tokens and Custom Tokens
oNew User Options
▪Defer changes for MultiCycle plot formatting
oNew Tokens
▪New token for status of iteration flags
▪New token for current time zone
▪New Color token that allows users to create customized color gradients based on the value of any token. May be used in conjunction with new custom object background tokens.
▪New token to return whether files in the data list are empty
oVisualize any FCS file on a Spectrum Plot as a "Virtual Spectral" data file
oSingle download for all versions of FCS Express (Flow, Image, Plus)
oNew slider bars for biexponential transformation to adjust transitions points
oView data specific gates and plot navigator items from the gate view
oImprovements to gates when drawn on bi-exponential scales
▪Gates no longer need to be replaced for data files where biexponential scaling and data ranges are different.
oAxis Scaling for parameters are retained and updated across all plots when formatted.
oDisplay File and Classification Identifiers on plots
oAbility to control well/node size on Plate Heat Maps
oImproved Multicycle plot model summaries
oEdit number of decimal places for spreadsheet tokens
oExport site license and internet dongle users in CSV report format
oAbility to insert images into Standard Operating Procedure steps
oAbility to add rules to control permissions for signing/unsigning specific signatures
oOptionally display a dialog when creating markers to allow the user to name the markers
oAbility to control the "off page" color