Issue with incorrect segmentation of objects in 3D ROI Manager

Hi! I am hoping to use the 3D ROI Manager to separate each circle into its own separate object. (For context, the image is an overhead cross-sectional view of many columns, resulting in said circles.) While many of the pillars are correctly identified as their own object, in a few of the images, as above, a large numbers of columns are grouped as one object (where a single object identified by the 3D ROI manager is colored in yellow). However, I don’t want this to happen! I want each circle to be its own object. I’ve tried water shedding the image, as well as playing with the settings in 3D ROI Manager, such as the distance between centers and max contact, to no avail. If anyone has any suggestions as to how to improve the object segmentation for this image so that each circle will be identified as one object and prevent such conglomeration of circles as one object, that would be very helpful. Thank you so much!

Hi @chialan2021,

Actually this is a correct segmentation of touching objects, it seems that you are segmenting the contours of your pillars, not the inside. Since the borders are touching, either in XY or Z if this is a 3D image, they will be part of a same segmented object.

I may suggest you to try segmenting the inside of your pillars, by simply inverting the image, as a result the objects should not be touching any more.