Watershed

Watershed segmentation in MIPAV is an interactive algorithm that allows automatically segment the image regions of interest. The watershed transformation performs gray scale segmentation using the topographical approach. Interpreting an image as a topographical relief, the algorithm performs flooding starting from regional minima, which are seen as plateaus of constant altitude surrounded only by pixels of higher gray levels. Dams or watershed lines are built when pixels from different basins meet or when the pixel's gray level reaches a certain threshold value which represents the image's background.

Background

An example of watershed segmentation: (a) grey level profile of the image data, (b) watershed segmentation


The user is, first, asked to identify the background pixels and initial region(s) using VOIs. At least two VOIs are required - the first one to specify the image's background and the second one to outline the image region(s) the user wish to segment (this VOI(s) represents the initial region(s)).

Note: The order in which VOIs are defined on the image is important. The first VOI must always outline background pixels.

Watershed algorithm: (a) - the original image with two VOIs: the VOI1 highlights the image background and VOI2 is a group of three VOI delineated inside the objects we wish to segment
(b) this figure illustrates the main steps of the algorithm
(c) the result segmented image


Raw watershed segmentation produces a severely over segmented image with hundreds or thousands of catchment basins

To overcome that problem the following techniques are used in this implementation of the algorithm:

Image types

You can apply this algorithm to 2D and 3D gray-scale images.

Watershed dialog box

The Watershed dialog box


Energy file - the energy file is generally a gradient magnitude image and the intensity peaks in this image are the watersheds boundaries. The algorithm creates and saves the energy file automatically when you first time run the algorithm for a chosen image.

Use pre-calculated energy file - when you run the algorithm for the same image next time you have an option to open and use the previously saved energy file for your segmentation.


Scale of the Gaussian - specify the scale of the Gaussian for each dimension. The Z Dimension option is only available for 3D images.

Use image resolutions to normalize Z scale - if checked, this option allows using the image resolutions to normalize the voxel size in Z dimension.

OK - applies the Watershed algorithm according to the specifications in this dialog box.

Cancel - disregards any changes that you made in the dialog box and closes this dialog box.

Help - displays online help for this dialog box.

Applying Watershed

Before applying the algorithm,

To run the algorithm

See also

Morphology

Segmenting Images Using Contours and Masks

References

The following sources were used to create this help.

Watershed ICAEN IOWA - http://www.icaen.uiowa.edu/~dip/LECTURE/Segmentation3.html#watershed]

Watershed ITC.ORG - http://www.itk.org/HTML/WatershedSegmentationExample.html]