error message on files previously good to go with Fast4DReg

[smohline]

This is the error I am getting now using Fast4DReg in Fiji. I have updated my Nano J Core and Bioformats to be current at the same time I updated Fast4DReg.

In case the screenshot doesn't work,

The error says;

Unregonized command: "F4DR Estimate Drift" in line 181.

run( "F4DR Estimate Drift", "time - " + etc.

Please help.

Thanks,
Shane

[guijacquemet]

Hi,

Thanks for reaching out. This is most likely an installation issue. Could you confirm that the Fast4DReg JAR is installed in Fiji? The correct steps are:

Use the Fast4DReg Fiji update site (recommended): In Fiji, go to Help > Update… > Manage update sites, find and enable the Fast4DReg update site. This should install the correct JAR automatically.

If you still have an issue after that could you try to removing the Nano J Core?

[smohline]

Thanks for your response.

We installed it exactly as you specify above. I have also tried removing Nano J Core, but I receive the same error message both times. One thing is that the Fast4DReg shows up at the bottom of my plugin list as a separate group of 4 or so. I am also running from a core ondemand version of Fiji.

Thanks for your help.

Shane

[guijacquemet]

Hi @smohline,

Thanks for the follow-up and the screenshot. that's very helpful. The fact that you're running a "core on-demand" version of Fiji imay be the root cause here.

On shared/on-demand Fiji environments (common in HPC or institutional setups), the update site mechanism can successfully install the Fast4DReg macro files (which is why you see Fast4DReg entries in your Plugins menu) but fail to properly install or persist the Fast4DReg JAR file. The F4DR Estimate Drift command is registered by the JAR, not the macros. So if the JAR isn't loaded, you'll see exactly this "unrecognised command" error.

Here are some things to try:

Check if the JAR is present: In your Fiji installation directory, look for a file named something like Fast4DReg_.jar (or Fast4DReg-*.jar) in the plugins/ folder. If it's missing, that confirms the problem.

Check Fiji's startup log for errors: Go to Window > Console in Fiji immediately after startup and look for any errors mentioning Fast4DReg or NanoJ. A ClassNotFoundException or NoSuchMethodError would indicate a JAR loading failure.

Contact your IT/sysadmin: On-demand Fiji environments often reset between sessions or have read-only plugin directories. Your sysadmin may need to pre-install the Fast4DReg JAR in the shared Fiji installation, or you may need to use a local (non-shared) copy of Fiji with write access.

Try a local Fiji install: Download a fresh copy of Fiji to your own machine or a directory you control, enable the Fast4DReg update site from scratch (Help > Update… > Manage update sites), and test again. This will confirm whether the issue is specific to your on-demand environment.

Manual JAR installation (if update site doesn't persist): You can manually download the latest Fast4DReg_.jar from the Fast4DReg update site and place it directly into Fiji's plugins/ folder, then restart Fiji.

Let us know what you find — especially whether the JAR file is present and whether there are any errors in the console. That will help us narrow it down further.