Hi Both (@odinsbane & @etadobson), and thank you for the responses!
I have been trying to use the plug-in “Snake to ROI” but am unfortunately not having much success.
After saving the snake produced in the Jfilament window as a .txt, I then select the image window and run the snakes to roi plugin.
The image I am running the plug-in on is a duplicate of the one I created the snake with, and when I check the .txt doc the snake is present for this frame. However, no ROI becomes selected in my image or in the ROI manager.
Instead I get the following box shown:
I’m not sure if I am doing something wrong? but any tips would be appreciated.
B) Yep I have read the document, but I’m not sure to what magnitude to change the settings by? I have used the following settings which deforms the snake nice and smoothly.
However, the problem is that between frames the snake does not follow my filament of interest as it moves through X,Y. Instead, if another filament comes close to the snake, the snake snaps to this filament instead.
As in, as the filamentOI moves through space the snake doesn’t move to the same extent. Can this be solved through editing the plug-in parameters or do I need to increase the temporal sampling rate when acquiring the images so the movement between frames is minimised?
Thanks a lot for the help! it’s greatly appreciated.