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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 Windows 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 double click to open the suh_pipelines2021a.exe file

1.Open exe

3.  It alers that publisher is unknown. Click More info and then click Run anyway to the below alert. Subsequent lauches will not show this alert.

2.Run anyway

4. SUH_pipelines is launched. 

3 SUH launched

6. Choose a method, say Subset unsupervised & supervised identification via parameter reduction(UMAP/UST). 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

6.Run UMAP

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

7.UMAP Arg

8. Press Yes to confirm

8.Confirm UMAP

9. Brings up the result which shows the parameters reduced by UMAP

9.UMAP Result