Tracing Neurites in 2017 (Simple Neurite Tracer update)

fiji
imagej
neuroanatomy
segmentation

#1

After an hiatus of almost 5 years without significant updates, Simple Neurite Tracer (SNT) - the IJ framework for semi-automated tracing of tubular structures - has been updated to version 3.1.0, which implements several features that will improve the efficiency and quality of your tracings. The update is available through the Java 8 update site. Some of the highlights:

  • Cursor that “auto-snaps” to neurites in 2D or 3D
  • Paths can be exported as ImageJ ROIs (an immediate application of this feature is e.g., intensity measurements along traced neurites)
  • Color schemes for traced paths
  • Improved handling of SWC files and support for ESWC files
  • Improved GUI with better support for multiple displays and extended keyboard shortcuts
  • New bundled plugins, including a batch processing plugin for Sholl analysis, and a new plugin to render paths as topographic skeletons.
  • Post-tracing operations can be performed on subsets of paths filtered by SWC type or positioning in image.
  • Several bug fixes, including several issues that did allow volume fitting to work properly on Java 8

A couple of notes on this release:

  • Updating the (rather vast) SNT documentation is a really burden for a single individual. If you find something unclear, we would be very happy if you would click the Edit link on the problematic wiki page to improve it. Don’t be shy about doing this: Any changes can always be reverted if needed.

  • (Knowing that I obviously have a bias towards SNT) I’ve used several other tracing programs in the past (including closed-sourced-science-impeding software), but remain deeply impressed by SNT’s flexibility. However, it always strikes me the lack of feedback from users: Only ~2 bug reports in five years, despite being a rather popular plugin, and despite several severe bugs plagued earlier versions. This new version will not be an exception, and it will also be affected by bugs: Please remember that we can only correct the issues that we are aware of.

If you want to know more about SNT’s development: Have a look at the releases page, and the list of known issues.

We really hope SNT continues to be useful for your research!


Automated tracing with Simple Neurite Tracer
#2

Where should I be able to download this? When I go to the Java 8 site I’m not seeing it. I’ve downloaded the latest version of Fiji but I’m still getting the error message saying that the plugin doesn’t work for 2D or 3D images.


#3

Sorry for the long delay in reply, @TWestbrook! Did you get it working? The latest Simple Neurite Tracer does ship with Fiji.

If it’s still not working, can you please post a minimal, complete, verifiable example so that we can try to reproduce it?


#4