GemStone™ is a revolutionary approach to high-dimensional flow, spectral, and mass cytometry data analysis. Based on patented Probability State Modeling™ technology*, GemStone's approach is science-based, scalable, and reproducible. GemStone is built from the ground up for automation and unlimited measurements.

Simple wizards guide you through model development and automatically generate beautiful reports. Cen-se' ™ and overlay plots reveal the hidden correlations in your data.

Try GemStone free for 30 days and see the difference.

Windows Win 10+    macOS macOS 10.14, 11.x, 12.x +
*US Patent 7,653,509, EU Patent EP2183681


No gates? Really?

With GemStone, you create a model to represent the biology of your cells, and then read samples into the model to quantify marker expression. GemStone uses Probability State Modeling to assign each cell to its most probable population. Each cell belongs to one and only one population, so there is no double-counting. Unlike gating, there are no hard boundaries, and continuous populations are allowed to overlap.


Features and Benefits



Probability State Modeling is an objective, science-based approach.


Different users at different sites get the same results.

Cell type wizard

Identifying populations is a breeze, and report pages are created automatically.

Batch files

Drop in your files and go! Easy, versatile, and automated batch processing.

HD ready

From the ground up, GemStone is built for high dimensional data.


Adding a measurement only requires one additional plot in a cell type.


An objective, statistical assessment of how well each cell type in the model is performing.


Create ratios and other calculated measurements quickly and easily.


Automatic analysis

Designed for automation, GemStone adjusts your model to your data, along with saving graphics, reports, and database.

Unlimited files

Your experiment can be as large as you want!

Easy batch setup

Choose batch options from simple selections.

Save graphics

Export the graphics where you want them to go, in the format you want!

Dimensionality Reduction


Based on t-SNE, the Cen-se' algorithm provides better separation and much better performance. You need to see 300,000 events? Not a problem.

Automatic labels

Because Cen-se' is integrated with the model, it can display population labels on the plot automatically. No other solution provides this level of integration.

High speed

Cen-se' is multi-threaded, allowing it to process more events in less time.

Consistent locations

Cen-se' uses the model to determine where populations are oriented on the plot, so you'll find them in the same location each time you run the model.

User Interface

Project based

Keep all your project files together. FCS, PDF, graphics, templates, results - all within the same project.

Ribbon interface

A ribbon with clean, vibrant, and meaningful icons makes finding what you want easy.

Measurement wizard

Easily edit measurement names, setup transforms and scaling, and check staining.

Context menus

Right-click any object to perform related actions.

Quality Control

Fully tested

Written under the strictest quality guidelines, GemStone doesn't go out the door until it passes extensive testing.

Stain assessment

Select positive and negative populations for each stain and get detailed stain assessment plots and results.


Flag out-of-range values and missing measurements and include flags in reports.

No double-counting

Each event belongs to one and only one cell type. You never have to worry about double-counting due to overlapping gate definitions.

Built-in QC

Reduced Chi-Square for each cell type, customizable alerts for out-of-range stats, and a model performance table provide solid QC.

Statistics and Database

Custom equations

Create user-defined equations to compute additional statistics for reports and database.


GemStone creates a comprehensive database of results which can be automatically exported for integration with LIM systems.


Medians, means, SD, robust SD, event counts, percent of total, percent of cell type, SSMD, and more.


Create tables to display results and sample information.


Popular formats

Save graphics in PDF, SVG, PNG, JPG, and all other popular formats.


Get high-quality hard copy of your reports at any printer resolution.


Generate PDF output with user-defined resolution.

Publication quality

Output in vector format with SVG, or up to 1200dpi for raster formats.

Overlay plot

Unique to GemStone, the overlay plot allows visualization of correlated markers in one graph to examine changes in staging, timing of marker expression, and progression.

Summary map

The summary map is a force-directed graph of all cell type populations, with labels and frequencies.


Automatic pages

The Cell Type wizard generates a clean and comprehensive report page for each population automatically.


A master page makes it easy to add logos and header text to all pages. All elements can be customized, and new elements added to any page.


Add 1P and bivariate plots, expression profiles, Cen-se', TriCOM™, and overlay plots. Other objects include tables, legends, text, lines, arrows, boxes, ellipses.


Report layouts can be saved and reused for other projects.

Import and Export

FCS files

Read all popular data file formats from major vendors.

CSV files

Import data from CSV and tab-delimited text files.

Export FCS

Export FCS files for further analysis in other software.

Export database

The database can be exported in tab-delimited text format.


Projects can be archived in ZIP format and tagged with keywords for later retrieval.

Share projects

Projects can be easily shared with collaborators using the ZIP format.


User guide

A comprehensive user guide with meaningful tutorials is included.


Contact us to find out when our next in-house training class will be or to arrange on-site training at your facility.

Video tutorials

Check out our comprehensive library of video tutorials on YouTube.


Our tech support representatives are here to help via phone or email!


" I have had good fortune of working with the staff at Verity Software House since 1987 on a variety of flow cytometry data analysis and management projects. The Verity staff really listen to their user needs, find solutions, and are 100% dedicated to customer service. Most recently we developed in GemStone an unsupervised CD34 quantitative analysis method based on the ISHAGE protocol which added viability and T cell subset measurements. The Verity staff helped us every step of the way, from creating and fine tuning the GemStone algorithm to training us on how to use it and validating it with over 70 patients against our old manual analysis results. Our staff found the automated ISHAGE GemStone routine easy to operate. It increased our efficiencies and completely eliminated individual to individual variation in the results. "

Paul Wallace, Roswell Park Cancer Institute

" I've been looking forward to Gemstone 2.0. I believe that this is the way that cytometry data should be analyzed. It works from first principles rather than arbitrary pattern recognition and should enhance and promote analytical reproducibility within the lab and consistency between labs. A goal for my company, Cleveland Cytometry Services Co., is to implement Gemstone 2.0 as our standard approach. "

Jake Jacobberger, Cleveland Cytometry Services Co.

" I like to work with GemStone as it provides both a robust and reproducible framework for analyzing flow files, and also intuitive visualization tools, such as the overlay progression plot. With the addition of the Cen-se’ maps in GemStone 2, it is also possible to visualize the outliers, which lowers the risk of over-simplifying data by applying too rigid models. Much recommended. "

Jakob Theorell, University of Oxford

" We have been fans and supporters of Gemstone software since its inception. It was the best software for cytometry when it was initially released about ten years ago, and it has only improved and become more robust and easier to use since that time with the release of Gemstone 2! Bravo to the wonderful folks at Verity Software for providing the most powerful analytic software for flow and mass cytometry on the planet!"

Enthusiastic anonymous user in Boston

" GemStone provides a consistent analytical approach for an automated evaluation of flow data with a high degree of reproducibility. The tutorial was well-written, and the supplementary figures were exceedingly helpful, making the software intuitive and easy to learn. While learning the software, Verity provided me with strong technical support that was timely and educational. GemStone generates comprehensive results and the data output was high-quality and publication ready. The embedded clustering analysis tool is extremely useful and helped me to quickly characterize the expression profiles of interrogated cell populations. "

Kah Teong Soh, Roswell Park Comprehensive Cancer Center

" I just wanted to share a quick note and let you know that you Verity Software guys do a really good job. GemStone is excellent software. Right in time. I'm glad I decided to collaborate with you. Gemstone software was created to deal with complex, multi-color flow data, and it is powerful. I will just mention one of GS’s features – Cen-se. It is competitive with Cytobanks’s Vi-sne. It is fast, even when dealing with a whole panel with one million Cytof’s events. Its final graph is crispy! While using Cytobank someone has to pay premium membership of more than $20k a year. "

Grigoriy Losyev, Brigham and Women's Hospital