Step 3: Automatic Segmentation
- Select Primary Object and set up suitable parameters to detect the objects, i.e. threshold, area, separation.
- As soon as objects are detected, the ZOI and Ring are automatically created around each primary object with the preset parameters.
- To modify Ring Distance and Width, select the Ring Element class.
- Now, you can define the location and dimension of the ring flexibly. You can set it at the edge of the main object or inside the main object. You can also define an arbitrary distance.
- Define the following parameters:
- Ring Distance: Distance from surface of the primary object. Negative values means that the ring starts at the defined distance within the primary object. Ring Width: Defines the width of the ring.
- The ZOI is automatically adapted to exceed the class with the larger diameter, i.e. either ring or primary object, by at least 3 pixels (default setting).
Modifying the ZOI Width
- Select ZOI-class, and with the ZOI Width slider, set the distance. You can set the distance between the outer border of the ZOI and the outer border of either ring or primary object, respectively. The ZOI Width is at least 3 pixels larger than either the ring or the primary object, whichever is larger. The ZOI area incorporates also the area of the ring and the primary object, and thus can serve for example for measuring features over the complete cell.
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