I am trying to see if I can migrate our quantification workflow from NeuronJ, which is not really maintained, to Simple Neurite Tracer. We are tracing segments of neuronal processes on tens of 2D images before quantifying length, intensities etc.
The one thing I don’t manage to do with SNT is to process one 2D image after another in a fast way, without closing the image, closing SNT, opening the next image and relaunching SNT, all this manually. Is there a shortcut in SNT to do this (open the next image in the current folder in SNT)? I can’t group the images by z-stack (they would be interpreted as a 3D image) or t-stacks (SNT refuses to process them).
Ideally there would be an option to process a whole open stack in forced 2D mode as just a series of 2D images, exporting all the traces as ROIs that would be affected to the right slice (the corresponding 2D image) - that would allow instant quantification downstream.
Thanks for your help - I guess I should tag @tferr here.