FCS Express Features

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!

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.

Pre-defined pipeline steps (FlowAI, FlowCut, FlowSOM, SPADE,...) 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.

Have you ever wished you could link up your statistics from files, gates, and plots directly to Excel? FCS Express provides integrated spreadsheets that update in real-time as gates or data change using tokens.

Drag and drop gated populations to populate a spreadsheet. Pull many data files from the Data List into the spreadsheet to compare samples and generate results automatically.
	You already know how to use spreadsheets since you are an expert in Excel.
Customize spreadsheets with many of the advanced Excel tools you know, including conditional formatting, so you can get to your results easier and faster.
	Looking for a formula function? FCS Express has you covered with many of the same formulas provided in Excel.

Spreadsheets Formula Hints provide all the details needed to get started on your analysis. Skip the manual lookups and go straight to results!

When it comes to your data, publication-quality results are important. FCS Express provides publication-ready graphics every time you analyze a sample in several formats at any resolution.

The right plot for your analysis is always at your fingertips.
	Customize every aspect of your plots as you are analyzing or by creating defaults, so you are ready to move instantly from the raw data to your publication.
Format your any axis with custom labels and gridlines or tick marks.
	Use black and white or grayscale plots to avoid color page fees.

FCS Express IVD is the first third party flow cytometry data analysis software listed with the FDA.  De Novo Software is committed to the high quality of FCS Express by creating and adhering to policies and procedures to satisfy the strictest requirements and complex regulations of 21 CFR §820.

Make qualitative assessments about the data automatically with statistic classifiers.
	Use conditional statements and tokens to control automatically when a batch process action is run.
Describe the analysis and outcome with canned comments.  Drag and drop to add your interpretation to the layout and batch to the LIS.
	Verify the analysis and layout status with time-stamped, electronic signatures.

Ensure your flow cytometry data analysis complies with CFR Part 11 by incorporating security and logging features. Along with sophisticated encryption, print logging, print tagging, password aging, and many other features, FCS Express saves time and many in compliance efforts.

Control hundreds of actions in the software at the user- and layout-level.
	Record every action made.  Logging in FCS Express generates digital, time-stamped files recording every action made for auditing.  Print or save as PDF to archive audit trails.
Create electronic signatures for your users to verify layout status and export the information directly to your LIS. Using tokens, a Signature Order can be enforced in which a signature from one particular signature group must be signed before a signature from another signature group is allowed.
	Track and report system level actions in an audit trail and enhance your compliance with regulatory requirements.

Take advantage of the only third-party software capable of displaying your spectral data from Cytek and Sony instruments.

Apply gates to visualize subsets of interest along spectra.
	Create gates to analyze populations further or backgate on other plots.
Overlay multiple samples or populations in a single plot for easy visual comparison.

Perform Spectral Unmixing from single stained controls directly in FCS Express.  As adjustments are made to the compensation setup, and/or directly to the matrix, your flow cytometry analysis will update immediately to help you visualize changes based on your controls without delay.

A Visualized Matrix can also be created for any created or imported unmixing matrix added to a layout.  FCS Express will automatically generate a Visualized Matrix by simply using a right-click on the desired unmixing matrix in the Compensation and Unmixing editor by choosing Build Visualized Matrix.  The Visualized matrix page includes a spreadsheet with charted values and a chart displaying the Detector vs Intensity for each single stained control added in the Automatic Unmixing Setup.

FCS Express makes it easy and convenient to view unmixed spectral signatures.  The Visualized Matrix is one of many new features that takes your analysis in FCS Express to the next level.

Spillover Spreading Matrix (SSM) and Cross Staining Index (CSI) matrix are both automatically calculated at the end of the Compensation/Unmixing wizard.

With FCS Express, take advantage of the widely-used tools for flow cytometry data analysis to speed up your image cytometry data analysis.  Go further with picture plots and data grids to drill down from populations to single cells with a click.

Gate regions of interest on your images in Picture Plots and view backgating of other gates from your analysis.
	Select cell(s) of interest or create cell galleries within data grids.

Data transformations allow you to create custom parameters through various algorithms in FCS Express as well as integrate directly with R.  The Transformations navigator is an intuitive dialog and makes it easy to apply your transformations to plots via a quick drag-and-drop.

Generate stunning tSNE/viSNE plots with an easy-to-use interface.
	Create SPADE trees from your data that update in real-time as gates and data  change.
Cluster analysis is simplified with integrated k-means tools.
	Principal Component Analysis is available in the transformations navigator.
When your analysis needs a customized approach, execute R scripts directly in FCS Express.

FCS Express allows you to create and apply compensations easily by reading data files, adjusting manually, or building from scratch with controls.

Load and edit compensations in any way you need.
	Rapidly progress through the Automatic Compensation Setup with your single-stained and unstained controls to create the compensation.
Quickly edit or adjust compensation directly from the plot with slider bars or defining cofactors within the compensations navigator.  The results will update in real time whenever anything affecting the compensation setup changes, or to the matrix itself.

Spillover Spreading Matrix (SSM) and Cross Staining Index (CSI) matrices are both automatically calculated at the end of the Compensation/Unmixing wizard.

Use batch processing to not only speed through bulk analysis of many samples but also create PDF, PPT, XLS, and more with a single click.

Generate report documents simultaneously when analyzing samples with the same gating strategy.
	Control when batch actions are run with conditional statements and tokens in FCS Express IVD.
Define how and where to save each report created from the batch by customizing its options.

Save time by using the standard statistics ,statistical tests, or create custom calculations in FCS Express.  Use integrated spreadsheets to get your statistics in a format similar to Excel.  All values will update in real-time when gates move or data change.

Avoid the tedium of writing statistics down on paper for further analysis by adding them to a batch process.
	Insert statistics anywhere in the layout - plots, text boxes, custom tables, and spreadsheets.
Make live-updating qualitative assessments from statistics with classifiers in FCS Express IVD.

Avoid manually defining generations for your proliferation data with integrated modeling in FCS Express.  Using a sophisticated linear least-squares fitting process, the model extracts the information and statistics you need.

Make your data pop with custom color schemes     or...     simplify the graph for publishing in black and white or grayscale.
	Adjust fit parameters to optimize the modeling for your data.
Statistics and information about the model's fit can be inserted into the layout and included with batch processing.

Import your experiments for BD FACSDiva™ and Accuri™ instruments to save time by no longer needing to recreate plots and gates after acquisition.  Update the gating strategy or customize plots as needed and run a batch process to create results from all samples in the experiment.

Diva to FCS Express
All acquisition templates and analysis worksheets The native, high resolution, floating point FCS data All gates with the proper gating hierarchy All compensation settings All markers and quadrants	Diva FCS Express
Accuri to FCS Express
Accuri FCS Express	All plots on the Collect and Analyze tab The native, high resolution, 24 bit FCS data All gates with the proper gating hierarchy All compensation settings All markers and quadrants All plot formatting settings

Easily visualize and analyze plate-based data sets, index sorting, and screening for flow and image cytometry assays with heat maps in FCS Express.

Represent multiple statistics and parameters for many samples in a single plot
	Apply gates to display only events of interest only or  create gates to aggregate wells/samples of interest, such as replicates.
Choose the color scheme and define color levels to customize your heat map and make it stand out.

Let FCS Express create gates automatically for all or selected wells and clusters from your heat map.

FCS Express provides exceptional quality control tools to standardize your data analysis and improve consistency across the team.

Ensure FCS Express is installed, configured, and operating properly for your validated work through the IQ/OQ program.
	Run quality control checks on demand or automatically during batch processing with alerts.
Define which actions are permitted, by whom, and when with authorizations and permission rules. Combine with the Standard Operating Procedure (SOP) builder to standardize an analysis.
	Control when objects - plots, gates, pages, and more - are visible on the layout.

Merging data files is a convenient way to load and visualize multiples files on a single plot and can be particularly useful when performing transformations in FCS Express.  Textual information or Classification File Identifiers can be used to identify each data file contained within a merged data file.  The Classification File Identifiers can now be displayed on 2D plots to make the identification of specific files using gates and/or markers straightforward. FCS Express makes working with merged data files trouble-free.

FCS Express remembers manually adjusted scaling.  No longer will users have to adjust each plot, once a change has been made to a plot parameter all plots displaying the same parameter will automatically update.  Optimizing how data is displayed on your plot has never been easier.