Analysis of hyperstacks

I have some 3D time-lapse images and I imported them as one hyperstack into SNT. I was trying to analyze them all at once but it appears that SNT only allows me to do one at a time (determined by the data source under the option menu). Right now I am manually analyzing them one by one but I wonder if there is a faster way for doing this?


Perhaps @tferr is the best person to give you some advice here… I’ve never used SNT myself - nor annotated neurons.

But perhaps you can help us help you more by sharing an image for example and what you aim to do exactly? Maybe I can still help…

Hi! Thank you so much for your response.

So here is an example,

I am trying to analyzing a time-lapse image with 200 time points and each time point has 69 stacks. While I am able to extract a plot profile under analyze menu of path manager, it only analyzes one time point at a time. So I wonder if there is a more efficient way that allows me to analyze them once for all.

Hi @Martin_Feng, sorry for the late reply. The best way to expedite things would be through a script that calls the API directly (have a look at some of the examples in Fiji’s Script Editor: Templates> Neuroanatomy>). If you would like to interact with the API as little as possible, you could write a simpler script that calls menu commands programmatically. I don’t think those type of scripts are included in the the Script Editor, but you can find and example for a 5D image here. Do let us know how it goes!