Neuroanatomy: Moving of Sholl/Strahler/Tracing Plugins

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:

  1. 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

  2. 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.

3 Likes

Thanks Tiago,
That’s excellent news. I have just updated to the latest version of SNT and can confirm that it resolves the issues regarding the Sholl analysis on selected path that I previously reported (Simple Neurite Tracer - Sholl Analysis on selected paths).
I also noticed that the new version now remembers the settings in the Sholl analysis dialogue, which is a nice feature.
I just noticed one slightly odd behaviour. When I accidently click on a column heading in the output table, the table gets re-sorted, but the re-sorting is a bit odd - it appears to use the first digit in each cell rather that the cell value (see screenshot below). So, sorting by the first column sorts the values 1,10,11,12,13,4,15,16,17,18,19,2,20,21, etc.
Is there an easy way to change the sorting behaviour so that it sorts them 1,2,3,…,9,10,11, etc?
Thanks,
Volko
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