Modules:OtsuThresholdSegmentation-Documentation-3.6
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Module Name
Otsu Threshold Segmentation
General Information
Module Type & Category
Type: CLI
Category: Segmentation
Authors, Collaborators & Contact
- Author: Bill Lorensen
- Contact: bill.lorensen at gmail.com
Module Description
This filter creates a labeled image from a grayscale image. First, it calculates an optimal threshold that separates the image into foreground and background. This threshold separates those two classes so that their intra-class variance is minimal (see http://en.wikipedia.org/wiki/Otsu%27s_method). Then the filter runs a connected component algorithm to generate unique labels for each connected region of the foreground. Finally, the resulting image is relabeled to provide consecutive numbering.
The original reference is: N.Otsu, ‘‘A threshold selection method from gray level histograms,’’ IEEE Trans.Syst.ManCybern.SMC-9,62–66 1979.
Usage
OtsuThresholdSegmentation [--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--minimumObjectSize <int>]
[--faceConnected] [--numberOfBins
<int>] [--brightObjects] [--]
[--version] [-h] <std::string>
<std::string>
Where:
--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).
--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)
--xml
Produce xml description of command line arguments (default: 0)
--echo
Echo the command line arguments (default: 0)
--minimumObjectSize <int>
Minimum size of object to retain. This parameter can be used to get
rid of small regions in noisy images. (default: 0)
--faceConnected
This is an advanced parameter. Adjacent voxels are face connected.
This affects the connected component algorithm. If this parameter is
false, more regions are likely to be identified. (default: 0)
--numberOfBins <int>
This is an advanced parameter. The number of bins in the histogram
used to model the probability mass function of the two intensity
distributions. Small numbers of bins may result in a more conservative
threshold. The default should suffice for most applications.
Experimentation is the only way to see the effect of varying this
parameter. (default: 128)
--brightObjects
Segmenting bright objects on a dark background or dark objects on a
bright background. (default: 0)
--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.
--version
Displays version information and exits.
-h, --help
Displays usage information and exits.
<std::string>
(required) Input volume to be segmented
<std::string>
(required) Output filtered
Source code & documentation
Source Code: OtsuThresholdSegmentation.cxx
XML Description: OtsuThresholdSegmentation.xml
More Information
Acknowledgement
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from National Centers for Biomedical Computing.
