How to save only the overlays without the image?



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!


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.


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?


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