Page history Edit this page How do I edit this website?
Original MediaWiki page

Simple Neurite Tracer › "Export to SWC" Tutorial

The content of this page has not been vetted since shifting away from MediaWiki. If you’d like to help, check out the how to help guide!

DEPRECATION NOTICE: This page describes Simple Neurite Tracer, which is no longer supported or maintained. Please use SNT instead.

This short tutorial shows you how to export a connected set of paths in the Simple Neurite Tracer plugin to an SWC file. This may be useful for analyzing a structure in other tools (e.g. L-measure) or uploading to a database like (n.b. for use in L-measure you will have to set the SWC type for each path - see #Setting_the_SWC_point_types)

Export all connected path sets as SWC files

To export each connected set of paths as a separate SWC file, you can now select the “Export all as SWC…” menu option - you will be prompted for the prefix of the file names:


Export a single connected path set as an SWC file

Often, you will just want to export one set of connected paths. As an example of this, suppose we have a partially traced image like this:


Those are actually three disconnected groups of paths, as you can see from the path list:


In other words, there is one large group of neurons which are all connected, with “Path (0)” as the primary path, there is a single disconnected path (“Path (15)” and group of 6 paths with “Path (16)” as the primary path.

(Paths are connected when you start one path on another one (branching) or end one path on another one (joining). To find out how to do that, see the Simple Neurite Tracer: Step-By-Step Instructions.)

The SWC file format describes a single neuron’s morphology (so every point is connected to another one), whereas a .traces file in Simple Neurite Tracer can describe multiple disconnected structures. This means that in this plugin you can only export a complete connected set of paths to SWC. So, in this example, you could only export three different SWC files, since there are three connected groups of paths. To do that, select all of the paths in that structure (using ⇧ Shift or ⌃ Ctrl when selecting items in the list) - that should look like this:


… and then click the “Export to SWC” button in the bottom right of that window. If you haven’t selected a completely connected set of paths, then you will get an error at this point - otherwise you will be prompted to save the SWC file.

Setting the SWC point types

There is now support in Simple Neurite Tracer for setting the type of SWC points contained in each path. You can do this by selecting a set of paths and then choosing a value from the SWC Type context menu:


You can set each path to a different type in this way, e.g.:


Note: setting an SWC type for every point is required by some software, such as L-measure.

Further Notes

  • You should only export your tracings to SWC for analysis in other tools, or or for uploading to databases that require that format. The SWC format is very simple and you lose a lot of information if you don’t save your tracings in the plugin’s native format.
  • The root node in an exported SWC file will be the first point in the primary path of the group in Simple Neurite Tracer. So, if you care about this, then before saving you should pick the path in the group which starts with what you consider to be the root node, and click “Make Primary” in the Path Window before exporting.