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User Guide

To make it easier for the flow community, we have developed a package, known as (Stanford University Herzenberg_pipelines) which allows access to our key methods EPP, UMAP & QFMatch and notably, can be used outside of AutoGate.

This package is available in different Matlab versions namely 2021a, 2020a, 2019a, 2017a and importantly, on both Mac and Windows.

Prior to installing this package, it is required that users have corresponding Matlab Runtime version available on their computer. To download Matlab Runtime, click here -


Below are the steps to access the package on Mac OS.

1. Download the package (.tar) file from

The 4 digit number in the URL references the Matlab Runtime version that will be supported. If you have Matlab Runtime 2019a on your computer, then simply replace the 4 digit with 2019a  To remind, this number can only be the four Matlab Runtime versions listed above. 

 2. Go to the downloads folder and open the suh_pipelines2021a.tar file to create/extract the .app file

1.Extract Tar

3. Right click on the file and click Open . It alers that developer cannot be verified. Click Cancel to the below alert

2.Open App

4. Right click again on the and click Open. This time, click on Open

3 Reopen App

5. SUH_pipelines app is launched. 

4.SUH Launched

6. Choose a method, say Subset unsupervised identification via Exhaustive Projection Pursuit (EPP). By default, it uses the sample experiment file (eliverlabeled.cvs). To continue with this sample, specify an argument type whose values can be customized by clicking on Refine x arguments button

5.EPP settings

7. Once satifisied with the selection & arguments, click Run with arguments

5a SUH EPP Arguments

8. Press Yes to confirm

6.EPP confirm

9. If Matlab prompts for access to folder, press OK to allow

7.Allow Access


10. Brings up the EPP gates with overlap (F-Measure) and similarity (QF Match) graphs.

7a.EPP result