Accessing SNT from FIJI (Answered, Archive)

Original questions: I found the version I am using seems not the same version shown in the instruction ( I got the program from the FIJI package (the latest update). The location of SNT in my FIJI is plugins/segmentation/SNT, instead of plugins/Neuroanatomy/SNT. Also when I right click on the tracing window, I didn’t see the contextual menu. Is there a different version?
[answered by Tiago~ Thank you]
Because SNT has been completely rewritten, we decided to only replace
the legacy Simple Neurite Tracer version once we were sure all the
major bugs were ironed out. So in order to have access to the “beta”
version of the software you have to subscribe to the NeuroAnatomy
update site. In the following weeks we’ll to make SNT available in core
Fiji (so that users don’t need to do anything to run it), so this will
no longer be required.

To subscribe to the NeuroAnatomy update site:

  1. Run Help > Update… (Note that the help menu contains a couple of
    other commands (“Update” [notice the absence of ellipsis] and “Update

  2. Click Manage update sites

  3. Select the Neuroanatomy checkbox (see also list of update sites)

  4. Click Apply changes and Restart ImageJ.

If I misunderstood you, and you are already subscribed to the update
site, then I really don’t know how you ended up with an outdated
version. Lots of files were moved around recently, and we pushed a
series of successive updates. Could be that somehow you are caught in
some weird state. Then I would suggest two things:

  • Download a new Fiji and subscribe to the NeuroAnatomy update site
    repeating the procedure above. (you can rename the new “”
    directory something like “” and have it side-by-side
    with your previous installation. It is perfectly fine to do that.

  • Alternatively, you can run the updater, click on “advanced mode” and
    then go through the list of “local files”, “modified files” and "files
    from the NeuroAnatomy update site. and look at their “status” message.
    Hopefully, by doing so you will caught which file failed to update
    properly. You can then flag the culprits for reinstall.