What’s New in FCS Express 7

What's New in FCS Express 7?

FCS Express 7 is the result of close collaborations between De Novo Software and scientists around the world. Version 7 builds on 20+ years of experience in flow and image cytometry data analysis. Customers have asked for new visualizations for experiments, easier ways to distill highly multi-parametric data sets, more speed, and many other improvements to help facilitate getting results. The team at De Novo Software has responded with the latest release of the FCS Express legacy. Please read about some of the new and exciting features below and see our extensive list of improvements in the FCS Express 7 release notes.

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What's New in the Latest 7.18.0015 Release

7.18.0015 was released May 2023 including some of the major enhancements below and many bug fixes.

Research customers who purchased standalone (including internet dongle) FCS Express Flow or Image licenses in the past, will now have access to all product features for both Flow and Image, and also to the High Content and Advanced Multicycle add-ons. Learn more...

New Logo
Support for MacOS 13.3 (Ventura) and greater
Gate Navigator and Data List will be displayed by default on new layouts
Added toolbar buttons to Gate Navigator
Simplified appearance of Create Gate dialog
Added icons to the plot type selection dialog displayed after dragging and dropping data files
The Format Ribbon Tab will now only appear when a layout object is selected
Updated Help Ribbon Tab
Improved panning and zooming on picture plots
Added Proxy support

Spectrum plots improvements:
- When adding overlays on spectrum plots, the new overlays will show the same spectrum as the base overlay
- Added Median as an option in the Overlay to Show options for Spectrum plots

Added Aurora CS to the Instrument Specific Settings
Added ability for classification output parameters to be treated as numeric within Pipelines

And much more! Please see the full release notes for version 7.18.0015 for additional details.

What's New in the Latest 7.16.0035 Release

7.16.0035 was released November 2022 including some of the major enhancements below and many bug fixes.

Improvements for Mac M1 compatibility and performance
New Notes tool added
New color levels for Density and Contour plots (Inferno, Magma, Plasma, Viridis)
No Gate root gate added to hierarchies
Classification Folders add the ability to run pipeline steps independently on each data set within a merged file (learn more in our recent webinar)
Greater control over axis line formatting
Speed optimizations for Mac, well gates, applying transformations, loading CellProfiler data sets, and more
New default instrument specific settings for Bigfoot instrument
Improvements to pipeline steps
Improvements to tokens including customized token error text and improved time format compatibility

And much more! Please see the full release notes for version 7.16.0035 for additional details.

New functionality from previous FCS Express 7 releases below

Version 7.14.0020 was released in June 2022 and included some of the major updates listed below:

Phenograph and Lovuain Communities
ThermoFisher .TMO file compatibility
Instrument specific settings for Fluidigm CytofXT
New statistics naming options
Ability to show/hide gates in views/navigators
Speed improvements for NxN, KNN, Heatmaps, tSNE, and unmixing
Overall speed improvements
Improvements to audit trails
Added password complexity requirements to security systems
Color by parameter multi-plot options for heatmaps
Additional gate hierarchy expand and collapse options
Keyword dropdown dialog with recently used keywords

FCS Express 7.12.0005 was released in December 2021 shortly after the release of 7.10.0007. Updates below are inclusive of both releases. The release contains compatibility, performance, new feature improvements. The latest update provides:

ARM-based Mac "M1" computer support
macOS 12.x Monterey support
Allows for hyperlinking to layouts; URL; and other documents
Enables ability to view the data source of tokens
Progress bar and mid-run cancellation feature for data transformations/pipelines
Improved speed for tSNE and uMAP
Additional variance based parameter selection pipeline steps
Jaccard Similarity pipeline step
Improved automatic identification of compensation controls for Bio-Rad data sets
and much more...

FCS Express 7.08.0018 was released in July 2021 and contains numerous enhancements based on customer input as well as many performance improvements. The update included new Summary Charts (Beeswarm and Violin), Levey Jennings plots, "live" updating compensation and unmixing, automatic spillover spreading matrix, automatic cross staining index, and many additions to pipelines. Check out the new features from 7.08.0018 below and in our full release notes.

Spreadsheet and Charts

The new version of FCS Express 7 allows to easily create Summary charts in Violin and Beeswarm style. Both styles may be combined with the already-existing Box and Whisker style.

Levey Jennings plots allow you to visualize quality control data to ensure test metrics are stable over time and fall within a predetermined range.

The new Export to Spreadsheet batch actions allows users to batch statistics directly into integrated spreadsheets to facilitate and speed up formula/chart creation.

Pipelines and transformations

New pipeline steps and pipeline-related features have been just released!

See the full list of all available pipeline steps or scroll down to look at the newest ones.

Enhanced Self-Organizing Map algorithm with Batch SOM.
	New Python Transformation step to run Python scripts in your pipeline. Have a look at some script examples in our Python Transformation web page!
New Graph Layout Method to graph cluster nodes with either tSNE or UMAP layout.
	New Gate Downsampling step to apply a gate in a specific position of the pipeline.
Ability to add Gated Data to the Data List to facilitate batch processing across gates. Although this feature can help in many different scenario, one of the best application is to create artificial iterations from gates, to then run Batch Processing on them.
	FlowCut is now available FCS Express 7 as Pre-Defined pipeline algorithm. FlowCut allows to perform quality control on flow cytometry data in order to improve both manual and automated downstream analysis.

Compensation and Unmixing

The Compensation and Unmixing wizard has been completely revamped "under the hood" to improve usability, speed, and will now allow for "live updating" compensation calculations as variables change.
	Normalized spectra are automatically graphed at the end of the Unmixing wizard.
Spillover Spreading Matrix (SSM) and Cross Staining Index (CSI) matrices are both automatically calculated at the end of the Compensation/Unmixing wizard.

Other improvements

Features for regulated-environment applications

Rules may now be created to enforce signature signing order control via permissions for signing/unsigning specific electronic signatures.
A new token type is now available to return whether files in the data list are empty tubes.

General usability improvements

New user option allows users to define naming markers when markers are created.

Many more...

Transformation results are now stored in the layout so that the transformation will not be recalculated when the layout is re-opened.
Speed improvements, especially for layout opening and spreadsheet operations.
New spreadsheet functions including Tukey's test.
Improvements to gates on files with different ranges.
New option to change the background color for Data Grids. Especially useful when the Data Grids are used to display single-cell images.
New option to change the “off page color”.
Custom denominators for gates to further increase the flexibility while retrieving statistics.
New plot theme to automatically report the Current Gate in the plot title.
Improvements for visualizing Fluidigm Helios time parameters.
See the Release Note for the full enhancement list......

The 7.06.0015 release of FCS Express 7 included tons of new functionality and over 100 improvements based on the feedback from cytometry professionals. See what was released below.

Pipelines

Pipelines 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. No plugins, no programming, just results! See our full list of all available steps.

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.

A pipeline is made of individual data processing steps with each step performing a specific calculation/transformation. To get started using Pipelines for your analysis TODAY, please click here.

Pre-defined pipeline steps make accessing commonly used algorithms and data processing steps easy.
	FCS Express provides a wide variety of pipeline steps for you to choose from. See our full list of all available steps and contact us if there are steps you are interested incorporating into FCS Express that are not yet available.

Pre-defined algorithms - FlowSOM, FlowAI, SPADE

Virtual Spectra from non-spectral data

Using the Merge to Spectra pipeline step allows users to create a virtual spectrum parameter by combining multiple input detectors, generally from an overdetermined system. The derived spectrum parameter can then be displayed using a Spectrum Plot and results used for the Unmixing pipeline step. Please see our chapter on Virtual Spectrum in the FCS Express manual for additional information.

For additional information and resources on Virtual Spectra, please click here.

Unmixing Visualized Matrix Builder

Usability Improvements

Automatic well/classification gates

Create Well Gates on each single well or cluster automatically. FCS Express can create individual gates across the entire plate or based on a selection of wells. If cluster assignments are present on the Heat Map, common with transformations such as KMeans or SPADE, each well gate will be based on an individual cluster.

Data Refresh Button.

Instantly update User Preferences, change how Compensation is applied, or even display newly added keywords with just a single click using the Data Refresh button. The Refresh button lets you refresh any data loaded onto the layout, including any preferences you have recently changed. No more closing and re-opening layouts to apply new settings, just click the Refresh button.

Hints for Spreadsheet formulas

Discover hints for each Spreadsheet formula. Once inserted into a Spreadsheet cell, click inside the formula's parentheses to reveal tips on usage. Each formula hint displays the name, equation, and input requirements along with an example entry and link to the manual for complete description.

New Plot Types

Box and Whisker Plots

Box and Whisker Plots allow you to 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.

Gates Heat Maps

Create array style heat maps for gated populations across multiple data files.

Parameter Heat Maps

Create array style heat maps for parameters and populations across multiple data files.

Subtraction Plots

Subtraction plots automatically calculate channel by channel subtraction, addition, division, and overton results with a single click.

NxN Plots

With a single click automatically visualize all parameters across a sample or multiple overlaid samples in histograms, parameters arranged by X axis, parameters arranged by Y axis, all combinations, all combinations used during compensation, or Color by All Parameters used in a tSNE transformation. Pick and choose which parameters to plot easily and quickly in all NxN plot types.

Parameter Overlays

Quickly create overlays for all parameters in a data file in a histogram.

Automatic and General Compensation and Unmixing Improvements

Support for Spectral Unmixing
Match single-stained controls to parameters automatically
Define default scatter parameters in wizard
Choose from different internal and universal negative controls easily
Gate scatter populations automatically
Improved automatic peak detection for stained and unstained populations
Other compensation improvments:
- Assigning compensation as a layout preference
- Density plots used by default in the compensation wizard
- Visual alerts for adjusted compensation values

Formatting and Data Display Improvements

Live, Dockable Formatting Controls The new dockable formatting interface allows for real time control of formatting on any plots and objects. Multiple formatting categories may be nested together for easy access as you perform analysis. With the new formatting controls you will never have to open a separate window or wait for an update to see changes applied.
	Instrument Specific Settings Automatically recognize your cytometer and set scaling accordingly
Multicycle Plot Improvements Defer changes when editing Multicycle plot(s) without applying modeling changes in real time Improved model summaries
	Biexponential Slider Easily adjust transition point for manual biexponential scaling
New Color Levels for Color Blindness Updated color palettes for some forms of color blindness
	Contour Plot Overlays Create color overlays for different populations on contour plots.

Data File Compatibility and Display

New Statistics and Tokens

Enhanced User Interface and Experience

Speed
- Significantly improved speed in the loading of data files, layouts, and saving of layouts (up to 2X increase over previous version)
Reorganized ribbon
- New tools and reorganized features to improve ease of use and efficiency
New keyboard shortcuts
Token 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
New color level for color blindness
View Data Specific Gates and plot navigator items in the Gate View
Add blank tubes to Data List
- Use blank tubes as placeholders for additional samples when creating or working with panels
New buttons in Transformations Dialog: Apply to All or Selected

Other Enhancements

Edit number of decimals for values displayed in spreadsheets
No need to replace gates in plots displaying data files with different biexponential scalings and data ranges
Can enable option to create Data Specfic Gate when moving gate in Create or Edit Gate dialogs
Improved PCA for data sets with more parameters than cells
Improved K-means clustering
Installer for FCS Express
User lists can be exported as CSV files for site licenses and internet dongle licenses

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