Big Sur and Monterey are the current macOS releases that support Macs with M1 chips (instead of more common Intel chips). Many users have contacted FlowJo about upgrading to these OS, or the M1 Macs, and we recommend delaying the upgrade of any technology until it has been well tested and deemed stable. That stated, we would like to convey our current understanding of the situation to our users.  

Based on the press releases from Apple, they created a translator for Intel chip-based programs to be translated to the M1, called Rosetta 2, which should handle the compatibility. FlowJo is written in Java, which due to its prevalence should have been a priority for their testing. We have users that have given us feedback using the M1 Macs and we have been told that they appear to be fully compatible, so we are optimistic that we will be able to recommend the M1 processor once we have completed our testing of FlowJo on the M1 chips.

We have not found or had any reports of issues with the new processors or the macOS when using FlowJo Portal, FlowJo Dongle, or serial numbers to authenticate FlowJo.

We are still testing to confirm OS stability with all of our features. Users that have given us feedback have reported the some issues and we are working to understand those issues in more detail to fix them:

The first major issue reported in Big Sur is a new setting, “Prefer tabs”, that groups similar windows into tabs. This also causes FlowJo to crash when trying to open the Table Editor. If you have already upgraded to Big Sur, please change this option to “never” and restart FlowJo.  

If you use FlowJo plugins, for some R-4.0 Mac installations on MacOS Big Sur, the symbolic link to the executable file in /usr/local/bin/r is not created. If you try to set the R path to /usr/local/bin/r without the symLink, FlowJo will not be able to find it. You can work around this by creating a symbolic link to /usr/local/bin/r by entering the following command in the Terminal app on your Mac:

sudo ln -s /Library/Frameworks/R.framework/Resources/bin/R /usr/local/bin/R

After this, check again in Terminal by entering: “where r” (if using zsh shell in Terminal). You should then see the new R path “/usr/local/bin/r” returned. You can then try running plugin again.

If you have any feedback to provide us, please email us at