I read from the bioXriv preprint (https://doi.org/10.1101/2020.07.13.179325) that the new SNT toolbox will allow " With timelapse sequences, traced paths can be automatically matched across frames so that growth dynamics of individual neurites can be monitored across time." This is great news! however, I was unable to use this plugin (unsuccesful matching, each path was assigned to its own group) and could not find any explanation how to do that in the SNT Manual page in Fiji website.
For example, I have time sequences of a growing neuron from t0 to t30, where dendrites are growing and retracting. Do I have to trace the neurites in each image first and then then can be matched accross the timelapse? Is there any documentation or walkthrough about this that somehow I am missing?
Thanks a lot and thank you for the new SNT toolbox again!
Welcome to the forum @yunus
With imagej.net read only, we did not have yet the chance to update the documentation. The short answer is yes, SNT’s matching assumes you have traced neurites at each time point. A couple of resources that may be useful:
See this older thread, where tracing across a time-sequence is discussed
The figures in the preprint can be generated programmatically. Have a look at the manuscript’s companion repository. There you will find a script that generates the time profile described on Figure 1. It will download both the timelapse video, and the traces file. You can use it as a demo dataset.
- Download the companion repository (direct link), and unzip it locally on your computer
- Then locate the ‘Fig01’ directory and run the time_profile.py script. NB: You can drag-and drop the script into Fiji’s main window: It will open in Fiji’s script editor. From there press the ‘Run’ button, or use Ctrl + R (Cmd + R on MacOS).