SNT and Sholl are popular plugins that have been distributed in Fiji through the default update-site. So far they have been developed as independent projects which complicates maintenance and development, and is a source of conflicts (see e.g., this thread).
After much thought, @arshadic and I decided to merge these related projects. At the same time, I realized that the situation was not really helping the current clutter of Fiji menus (discussed e.g. here and here). Case in point: Among the two projects, there were a dozen of menu entries spread across the Fiji’s Plugins> and Analysis> menus! As such we decided to do the following:
Distribute all neuronatomy-related plugins through the Neuroanatomy update site. This means that in order to use the Sholl Analysis plugins you will have to subscribe to the Neuroanatomy update site
Restrict commands only to the Plugins>Neuroanatomy> submenu. While this submenu only lists the most popular commands, it also features a “Neuroanatomy Shortcuts Window” that list all commands related to Neuroanatomy. The “Shortcuts Window” also includes a neat mechanism that lists any local macro or script with “SNT” or “neuroanatomy” in the filename. This is how it looks:
We understand that this change has the potential to break existing macros, however do note that the legacy versions of Sholl and Simple Neurite Tracer are still being distributed through Fiji;s default (“Java-8”) update site. It is just, that they no longer register commands in the menu structure. Do reach out if you need help upgrading any existing macro.