SmartRoot plugin installation and usage

I am very new to ImageJ and have been having difficulties uploading/using the SmartRoot plugin. Might this have anything to do with the ongoing ImageL system upgrade? Or if not, is there anyone out there that can give me some idea of how to go about getting SmartRoot up and running? I should mention that I am not a computer expert and totally new to Java/ImageJ/SmartRoot - and also new to MacOS and my new laptop]. Any help would be greatly appreciated.

Hi @Colin_Hindmarch and welcome to the forum!

Do you mean this one?

It’s highly unlikely, I would say. You can use ImageJ/Fiji locally and install plugins without being dependent on the ImageJ web site.

Did you follow the instructions here?

If so, where did you get stuck? Do you see any error messages?

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Hi, Thanks for getting back, much appreciated.

In ‘(Fiji Is Just) ImageJ’ I went to ‘Plugins’, then down to ‘Install Plugin’, which takes me to a SmartRoot [window] with five *.jar files. When I click the one called ‘Smart_Root.jar’ [a random, uninformed choice], I get a message: “NOTICE: Please restart ImageJ to complete plugin or macro installation, add new commands to the menus, etc…”
When I restart, as instructed, I am back to square one. I fear I have no idea what I am doing wrong and well out of my depths on this one. By the way, I have also uploaded MySQL Workbench.


@Colin_Hindmarch Thanks for the additional details.

Instead of using the Plugins › Install Plugin menu command, I suggest just dropping the .jar files directly into your folder directly, as indicated by the documentation.

Since you are using Fiji, though, I recommend skipping the jcommon and jfreechart libraries, because Fiji already includes those. So the steps are:

  • Download and unpack it.
  • Navigate into the unpacked SmartRoot folder.
  • Drag Image_Explorer.jar, mysql-connector-java-5.1.7-bin.jar, and Smart_Root.jar into the plugins folder of your installation.
  • Start Fiji.
  • Run Plugins › SR Explorer to start SmartRoot.

@guillaumelobet Have you considered making an ImageJ update site for SmartRoot? It would make installation and updates easier for users.

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Okay, I shall try all that - hope it works; thanks, Colin.

Thank you, Ctrueden,
I seemed to have got things working - at some point I will attempt to make an ImageJ update site.

Many thanks for your efforts.


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