Manually refining detected ridges



Sorry this is a reviving of an old post that you may have thought was dead. But I am seeking more help for my macro. I’ve made some adjustments to my macro . Besides learning to write functions, my main addition since has been to add a basic ‘user interaction step’ to pick which blobjects should be measured and create new blobjects. (For some reason ~25% of the chromosomes are not built into Blobjects.)

The major accuracy issue now is with the ridge detection. Inserting this ridge detection into my macro was an Amazing :heart_eyes: improvement for ‘detangling’ the overlapping objects. However, my macro still can’t produce reliable data since ridge detection still makes mistakes and there’s no way for me to change them before the measurements are reported. Ideally I would like to find a way to interact / change / update the objects produced into the ROI manager by ridge detection (Cs and JPs) to remove mistake ridges and keep the good ones.

My naive questions for editing Ridge Detection are;
How hard would it be to insert a step during the Ridge Detection to pause and edit some of the identified ridges?
Could there a way for the user to input ‘start and end’ points for a given ridge?

I’m sorry if my macro is hard to read and very long. I have not refined the final output sections since improving the accuracy of ridge detection should be addressed before I produce results I wish to use.
I appreciate any advice regarding these questions or how to start playing with the java classes in Ridge Detection to address these issues.


Creating object class with rois from multiple channels
Batch mode exception error

No worries! I split it to a new topic which stays linked with the old one.

The link is dead now; it looks like you deleted the ImageJ_macro repository. I guess you didn’t get the help you needed? Sorry for that! :disappointed:

If this is still something you’re struggling with, it would be helpful to see an example image with A) the segmentation you are getting from the automation/macro; and B) a manual segmentation which illustrates what you want to have happen instead.


I am trying to get back into the swing of things with macro.
But I am having issues opening my images after updating Fiji this morning. I can’t open any of my images and I’m getting a long Exception window. I’ll have to investigate this new issue before compiling some examples and illustrations.


Please feel welcome to start a new thread on the forum here, and we’ll help troubleshoot!