Pipelines

Data quality and transparency in methods are essential to any scientific workflow. However, despite the need for greater control and visibility over the algorithms that process your data, today's researchers are often met with algorithmic black boxes and complex programming requirements when reaching for the latest or most appropriate method to prepare and analyze their data.

FCS Express offers a solution tailored to the individual needs of all researchers with Pipelines. Skip the complex scripts, and stop worrying about how to learn to program. FCS Express has the right tools for the job built into the software without the need for external plugins. Pipelines work for both Flow and Image cytometry data sets giving you the ultimate flexibility and ability to visualize cells of interest from pipeline derived parameters back on your images!

Although not required for embedded algorithms, FCS Express 7 allows users keen in programming to integrate their own R/Python scripts in their layout.

Pipelines give you control over data processing

Pipelines 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.

Go from raw data to results step-by-step. Pipelines provide control and flexibility in data processing.

Pipeline steps for many data processing needs

Pre-defined steps for common algorithms

Easy to Use Interface - No Plugins or Programming Required!

Pipelines enable researchers to use the flexible and intuitive interface of FCS Express to perform advanced data analysis and processing steps, without the need for external applications such as R or Python. No more writing complex programming scripts and having to rely on plugins. With FCS Express you have access to many of the most common and cutting-edge data analysis tools directly within the software.

Customize Your Data Processing Workflow

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.

Customize each step of your algorithm. Arrange the order of your data processing steps. Implement unique and flexible transformations that fit your data. Pipelines enable you to fully explore the results you care about!

Learn more about Pipelines in the FCS Express manual.

Compatibility with Image Cytometry Data Sets

Video Overviews of Pipelines

Full Overview of Pipelines

Pipelines Quick Start

Virtual Spectra Full Overview

FlowSOM Full Overview

FlowAI Quick Start

FlowSOM Quick Start