9.74. ITK Threshold Maximum Connected Components Image Filter
Finds the threshold value of an image based on maximizing the number of objects in the image that are larger than a given minimal size.
Group (Subgroup)
ITKConnectedComponents (ConnectedComponents)
Description
This method is based on Topological Stable State Thresholding to calculate the threshold set point. This method is particularly effective when there are a large number of objects in a microscopy image. Compiling in Debug mode and enable the debug flag for this filter to print debug information to see how the filter focuses in on a threshold value. Please see the Insight Journal’s MICCAI 2005 workshop for a complete description. References are below.
Parameters
The MinimumObjectSizeInPixels parameter is controlled through the class Get/SetMinimumObjectSizeInPixels() method. Similar to the standard itk::BinaryThresholdImageFilter the Get/SetInside and Get/SetOutside values of the threshold can be set. The GetNumberOfObjects() and GetThresholdValue() methods return the number of objects above the minimum pixel size and the calculated threshold value.
Automatic Thresholding in ITK
There are multiple methods to automatically calculate the threshold intensity value of an image. As of version 4.0, ITK has a Thresholding ( ITKThresholding ) module which contains numerous automatic thresholding methods.implements two of these. Topological Stable State Thresholding works well on images with a large number of objects to be counted.
References
Urish KL, August J, Huard J. “Unsupervised segmentation for myofiber counting in immunofluorescent microscopy images”. Insight Journal. ISC/NA-MIC/MICCAI Workshop on Open-Source Software (2005) https://insight-journal.org/browse/publication/40
Pikaz A, Averbuch, A. “Digital image thresholding based on topological stable-state”. Pattern Recognition, 29(5): 829-843, 1996.
Questions
email Ken Urish at ken.urish(at)gmail.com Please cc the itk list serve for archival purposes.
Input Parameter(s)
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Minimum Object Size In Pixels |
Scalar Value |
UInt32 |
The pixel type must support comparison operators. Set the minimum pixel area used to count objects on the image. Thus, only objects that have a pixel area greater than the minimum pixel area will be counted as an object in the optimization portion of this filter. Essentially, it eliminates noise from being counted as an object. The default value is zero. |
Upper Boundary |
Scalar Value |
Float64 |
The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity. |
Inside Value |
UInt8 |
The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity. |
|
Outside Value |
UInt8 |
The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity. |
Input Cell Data
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Image Geometry |
Geometry Selection |
Image |
Select the Image Geometry Group from the DataStructure. |
Input Cell Data |
Array Selection |
Allowed Types: int8, uint8, int16, uint16, int32, uint32, int64, uint64, float32, float64 |
The image data that will be processed by this filter. |
Output Cell Data
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Output Image Data Array |
DataObjectName |
The result of the processing will be stored in this Data Array. |
Example Pipelines
License & Copyright
Please see the description file distributed with this plugin.
DREAM3D Mailing Lists
If you need help, need to file a bug report or want to request a new feature, please head over to the DREAM3DNX-Issues GitHub site where the community of DREAM3D-NX users can help answer your questions.