Until now, we have just assumed that API scripting would be the best way to trace and analyze dynamics of neuronal growth. But after feedback from you and others we have recognized that it would be indeed convenient to have GUI commands to facilitate 4D tracing. Yesterday @arshadic, and I released v3.1.105 that implements several commands that should be very useful here. Since the documentation is currently read-only, here is a forum-tutorial of the new commands (I’ll be using the
4-n-test-trace.traces file you provided above):
GUI Support for Timelapse and 4D Imagery in SNT
When tracing the same neurite across time, it is be convenient to duplicate a path from one frame to another. But to be effective, the duplication should take into account retraction and elongation events between frames. SNT’s Edit>Duplicate… command handles this by ‘cloning’ sections of paths between frames. Such sections can be defined by length, or branch point-boundaries, etc. Here is how the Duplicate Prompt looks like:
If a neurite extends between frame t and t+n, one can duplicate the full length of the traced path to frame t+n. If it retracts, one would choose a suitable sub-section. In both cases, the Continue Extending Path option (right-click menu) can then be used to complete the tracing.
It is worth noticing that all of the analysis commands are aware of time when tracing time sequences. E.g., To monitor the tracing progress across the video, one can run Analyze>Frequency Analysis>Distribution of Path Properties… (using Path frame as measurement) which outputs:
More advanced commands can be found under Analyze>Time-Lapse Utilities> namely:
Color Code Paths Across Time
Colors paths by mapping their position in the time-sequence to a lookup-table. E.g.,
(warmer hues corresponding to more recent time-points)
Match Paths Across Time
Looks at all the paths in a time-range, and groups (by means of “group tags”) those that are associated with the same origin. To accommodate for motion artifacts (focus drift, etc.), a tolerance range can be specified.
Retrieves morphometric traits as a function of time. This allows to e.g., monitor the amount of branching across time, or the total amount of cable length as in this example:
If paths have been “Matched Across Time”, it is also possible to directly look into the dynamics of individual neurites: