Operation: count nuclei - watershed

Author:

Volker Baecker, uses the Watershed plugin from Christopher Mei.

Example

Description

Finds the objects in the active image and adds them to the roi-manager. If the roi-manager already contains rois, they are deleted before the application is executed. A watershed algorithm is used to separate touching objects.

Options

To change options either press the O-button of the application or open the application (right click on the top of the application tile and select open from the context menu) and press the O-button of one operation of the application


Important options are smoothing diameter, and the min. size and max. size.

The smoothing diameter is the radius of the kernel of a smoothing filter that is applied before the watershed. It needs to be big enough to make disappear internal structures of the objects you want to count, since otherwise objects will be split too much. It should not be bigger than necessary since otherwise the contours of the objects become imprecise and touching objects may not be split.

The min. and max. size can be used to eliminate wrong objects that are either too small or too big. The area of the objects you want to measure must be between the min. and the max. value.

Results

The applications opens the roi-manager, removes any rois from it and adds the rois of the objects found in the active image.