export binary mask of region

[khaled benaggoune]

Hello everyone,

maybe my question seems a repetition, but sorry i am new in groovy and i appreciate your help.

in our project we try to annotate regions of interest, we lock these regions, and annotate cells inside each region. now we want to extract each region with the associated mask of the cells inside. and if it is possible to extract this images with tiles. i just tried the scripts in the blog about extracting binary masks but this gives the mask of the overall locked region.

thank you

[micros...@gmail.com]

The new forum location is listed at the top of this forum, all new questions should be directed there.

Playing with Pete's script, it should export both the larger annotation and all of the smaller annotations independently. If you wanted to change the smaller objects into detections, this thread might help: https://groups.google.com/d/msg/qupath-users/_A2wz3dUFxc/SiD1mjfUDgAJ