How to save only the overlays without the image?

imagej
roi
tracing
root

#1

Hi, I am a beginner in ImageJ. I am currently hand tracing plant roots in images, creating multiple overlaid lines on the image. I was wondering whether it is possible to save all the overlaid lines in their respective positions in one image without the original image underneath it?

Thank you!


#2

Welcome to the forum @castanopsis,

A way to do would be to run Image>Overlay>To ROI Manager, once your traced lines are stored in the ROI Manager you can then display them on any image, including a black canvas File>New>Imageā€¦

However, there should never be a need to trace an image without no automation. Please have a look this recent annoucement on SNT. If you post a representative image, others will probably have other suggestions.


#3

Thanks @tferr! Regarding automating the tracing process, I tried automating the process initially, but my images seem to contain too much background noise for automation to be possible. Nevertheless, here is a sample image I am working on, do you have any particular suggestions?


#4

You could try the pre-release SNT distributed through the Neuroanatomy update site. It allows you to trace in full manual mode. The main advantage being the convenience of a suitable GUI to do