Slicer Wiki - User contributions [en]

Slicer3:Module:BinaryDilateOperations-Documentation

2008-08-28T18:33:38Z

Bikekilic: /* Screen shots */

[[Documentation|Return to Slicer Documentation]]

==Binary Dilate Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing dilation on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform dilation method in order to make two different labeled separate objects closer to each other after erosion. At the end, we want to see these objects touched but not overwritten.

This method uses a structuring element in order to cover the object border with given foreground value. It grows the object with this structuring element. For this project, the structuring element is neighborhood structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is neighborhood structuring element with radius 2. It took 7 iterations in order to get closer images with different colors.

The input of this module is the output of BinaryErodeOperations module at the beginning. For the following iterations, the input is the dilated binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelDilate.PNG|thumb|280px|The GUI panel for BinaryDilateOperations Module after binary dilation]]
|}

In this case, the eroded image which is the input for BinaryDilateOperations Module has the pixel value 255 inside and 0 outside.

==DEVELOPMENT==

===Dependencies===

The BinaryDilateOperations Module uses four ITK classes. One of them is for binary dilation, which is called itkBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryDilateImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for dilation the neighborhood structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of dilation depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after dilation. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of neighborhood structuring element. Therefore, neighborhood structuring element was used in BinaryDilateOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive.

Another problem which was encountered with is stemmed from being unable to use labeled images in dilation. Since the binary images are used in dilation, after more than 7 iterations, the spheres become overwritten again and so they can not be labeled differently at the end of the dilation if I use Editor module. Therefore, I lose the connectedness information between spheres which makes me unable to differentiate the different objects. However, even they become overwritten, the labels remain the same as I had after performing LabelBinaryImages module on the last eroded image( background is labeled as 0, the first sphere is labeled as 1 and the second one is labeled as 2).

The results can be observed as seen in the ''Screen shots'' section.

===Screen shots===

{|
|[[Image:Dilate.png|thumb|280px|Binary Dilate Iterations with Neighborhood structuring element with radius 2]]
|[[Image:DilateWithBall.png|thumb|400px|Binary Dilate with Ball Structuring element with radius 5]]
|[[Image:DilateCross.png|thumb|400px|Binary Dilate with Cross Structuring element whose radius is 10]]
|}

Although the above figure shows three steps in dilation, it took 7 steps in order to make them be closer to each other. The neighborhood structuring element with radius 2 was used in dilation process.
In the second figure, the dilation result with ball structuring element which has the radius 5 can be seen. In comparison to the previous case, it took 5 steps in order to get the last dilated image.
The third figure shows the dilation result with cross structuring element whose radius is 10. After 25 iterations I get the last dilated image. In this screen shots, we see the first, the 25th and the last dilated image. In the case of using cross structuring element,the shape of the image is damaged more than the dilation with neighborhood and ball structuring elements.

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

On the other hand, although BinaryDilateImageFilter class has been used for this project, another ITK class which is called itkFastIncrementalBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1FastIncrementalBinaryDilateImageFilter.html] can be used in order to make the dilation faster. I did not use that one because when I make it faster the spheres become overwritten, which I don't want to have in the conclusion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Architecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:BinaryDilateOperations-Documentation-3.2

2008-08-28T18:33:38Z

Bikekilic: /* Screen shots */

Slicer3:Module:BinaryDilateOperations-Documentation

2008-08-28T18:31:22Z

Bikekilic: /* Dependencies */

[[Documentation|Return to Slicer Documentation]]

==Binary Dilate Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing dilation on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform dilation method in order to make two different labeled separate objects closer to each other after erosion. At the end, we want to see these objects touched but not overwritten.

This method uses a structuring element in order to cover the object border with given foreground value. It grows the object with this structuring element. For this project, the structuring element is neighborhood structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is neighborhood structuring element with radius 2. It took 7 iterations in order to get closer images with different colors.

The input of this module is the output of BinaryErodeOperations module at the beginning. For the following iterations, the input is the dilated binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelDilate.PNG|thumb|280px|The GUI panel for BinaryDilateOperations Module after binary dilation]]
|}

In this case, the eroded image which is the input for BinaryDilateOperations Module has the pixel value 255 inside and 0 outside.

==DEVELOPMENT==

===Dependencies===

The BinaryDilateOperations Module uses four ITK classes. One of them is for binary dilation, which is called itkBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryDilateImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for dilation the neighborhood structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of dilation depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after dilation. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of neighborhood structuring element. Therefore, neighborhood structuring element was used in BinaryDilateOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive.

Another problem which was encountered with is stemmed from being unable to use labeled images in dilation. Since the binary images are used in dilation, after more than 7 iterations, the spheres become overwritten again and so they can not be labeled differently at the end of the dilation if I use Editor module. Therefore, I lose the connectedness information between spheres which makes me unable to differentiate the different objects. However, even they become overwritten, the labels remain the same as I had after performing LabelBinaryImages module on the last eroded image( background is labeled as 0, the first sphere is labeled as 1 and the second one is labeled as 2).

The results can be observed as seen in the ''Screen shots'' section.

===Screen shots===

{|
|[[Image:Dilate.png|thumb|280px|Binary Dilate Iterations with Neighborhood structuring element with radius 2]]
|[[Image:DilateWithBall.png|thumb|400px|Binary Dilate with Ball Structuring element with radius 5]]
|[[Image:DilateCross.png|thumb|400px|Binary Dilate with Cross Structuring element whose radius is 10]]
|}

Although the above figure shows three steps in dilation, it took 7 steps in order to make them be closer to each other. The neighborhood structuring element with radius 2 was used in dilation process.
In the second figure, the dilation result with ball structuring element which has the radius 5 can be seen. In comparison to the previous case, it took 5 steps in order to get the last dilated image.
The third figure shows the dilation result with cross structuring element whose radius is 10. After 25 iterations I get the last dilated image. In the case of using cross structuring element,the shape of the image is damaged more than the dilation with neighborhood and ball structuring elements.

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

On the other hand, although BinaryDilateImageFilter class has been used for this project, another ITK class which is called itkFastIncrementalBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1FastIncrementalBinaryDilateImageFilter.html] can be used in order to make the dilation faster. I did not use that one because when I make it faster the spheres become overwritten, which I don't want to have in the conclusion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Architecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:BinaryDilateOperations-Documentation

2008-08-28T18:30:57Z

Bikekilic: /* Quick Tour of Features and Use */

[[Documentation|Return to Slicer Documentation]]

==Binary Dilate Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing dilation on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform dilation method in order to make two different labeled separate objects closer to each other after erosion. At the end, we want to see these objects touched but not overwritten.

This method uses a structuring element in order to cover the object border with given foreground value. It grows the object with this structuring element. For this project, the structuring element is neighborhood structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is neighborhood structuring element with radius 2. It took 7 iterations in order to get closer images with different colors.

The input of this module is the output of BinaryErodeOperations module at the beginning. For the following iterations, the input is the dilated binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelDilate.PNG|thumb|280px|The GUI panel for BinaryDilateOperations Module after binary dilation]]
|}

In this case, the eroded image which is the input for BinaryDilateOperations Module has the pixel value 255 inside and 0 outside.

==DEVELOPMENT==

===Dependencies===

The BinaryDilateOperations Module uses four ITK classes. One of them is for binary erosion, which is called itkBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryDilateImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for dilation the neighborhood structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of dilation depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after dilation. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of neighborhood structuring element. Therefore, neighborhood structuring element was used in BinaryDilateOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive.

Another problem which was encountered with is stemmed from being unable to use labeled images in dilation. Since the binary images are used in dilation, after more than 7 iterations, the spheres become overwritten again and so they can not be labeled differently at the end of the dilation if I use Editor module. Therefore, I lose the connectedness information between spheres which makes me unable to differentiate the different objects. However, even they become overwritten, the labels remain the same as I had after performing LabelBinaryImages module on the last eroded image( background is labeled as 0, the first sphere is labeled as 1 and the second one is labeled as 2).

The results can be observed as seen in the ''Screen shots'' section.

===Screen shots===

{|
|[[Image:Dilate.png|thumb|280px|Binary Dilate Iterations with Neighborhood structuring element with radius 2]]
|[[Image:DilateWithBall.png|thumb|400px|Binary Dilate with Ball Structuring element with radius 5]]
|[[Image:DilateCross.png|thumb|400px|Binary Dilate with Cross Structuring element whose radius is 10]]
|}

Although the above figure shows three steps in dilation, it took 7 steps in order to make them be closer to each other. The neighborhood structuring element with radius 2 was used in dilation process.
In the second figure, the dilation result with ball structuring element which has the radius 5 can be seen. In comparison to the previous case, it took 5 steps in order to get the last dilated image.
The third figure shows the dilation result with cross structuring element whose radius is 10. After 25 iterations I get the last dilated image. In the case of using cross structuring element,the shape of the image is damaged more than the dilation with neighborhood and ball structuring elements.

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

On the other hand, although BinaryDilateImageFilter class has been used for this project, another ITK class which is called itkFastIncrementalBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1FastIncrementalBinaryDilateImageFilter.html] can be used in order to make the dilation faster. I did not use that one because when I make it faster the spheres become overwritten, which I don't want to have in the conclusion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Architecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:BinaryDilateOperations-Documentation

2008-08-28T18:30:13Z

Bikekilic: /* Module Description */

[[Documentation|Return to Slicer Documentation]]

==Binary Dilate Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing dilation on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform dilation method in order to make two different labeled separate objects closer to each other after erosion. At the end, we want to see these objects touched but not overwritten.

This method uses a structuring element in order to cover the object border with given foreground value. It grows the object with this structuring element. For this project, the structuring element is neighborhood structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is neighborhood structuring element with radius 2. It took 7 iterations in order to get closer images with different colors.

The input of this module is the output of BinaryErodeOperations module at the beginning. For the following iterations, the input is the dilated binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelDilate.PNG|thumb|280px|The GUI panel for BinaryDilateOperations Module after binary erosion]]
|}

In this case, the eroded image which is the input for BinaryDilateOperations Module has the pixel value 255 inside and 0 outside.

==DEVELOPMENT==

===Dependencies===

The BinaryDilateOperations Module uses four ITK classes. One of them is for binary erosion, which is called itkBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryDilateImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for dilation the neighborhood structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of dilation depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after dilation. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of neighborhood structuring element. Therefore, neighborhood structuring element was used in BinaryDilateOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive.

Another problem which was encountered with is stemmed from being unable to use labeled images in dilation. Since the binary images are used in dilation, after more than 7 iterations, the spheres become overwritten again and so they can not be labeled differently at the end of the dilation if I use Editor module. Therefore, I lose the connectedness information between spheres which makes me unable to differentiate the different objects. However, even they become overwritten, the labels remain the same as I had after performing LabelBinaryImages module on the last eroded image( background is labeled as 0, the first sphere is labeled as 1 and the second one is labeled as 2).

The results can be observed as seen in the ''Screen shots'' section.

===Screen shots===

{|
|[[Image:Dilate.png|thumb|280px|Binary Dilate Iterations with Neighborhood structuring element with radius 2]]
|[[Image:DilateWithBall.png|thumb|400px|Binary Dilate with Ball Structuring element with radius 5]]
|[[Image:DilateCross.png|thumb|400px|Binary Dilate with Cross Structuring element whose radius is 10]]
|}

Although the above figure shows three steps in dilation, it took 7 steps in order to make them be closer to each other. The neighborhood structuring element with radius 2 was used in dilation process.
In the second figure, the dilation result with ball structuring element which has the radius 5 can be seen. In comparison to the previous case, it took 5 steps in order to get the last dilated image.
The third figure shows the dilation result with cross structuring element whose radius is 10. After 25 iterations I get the last dilated image. In the case of using cross structuring element,the shape of the image is damaged more than the dilation with neighborhood and ball structuring elements.

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

On the other hand, although BinaryDilateImageFilter class has been used for this project, another ITK class which is called itkFastIncrementalBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1FastIncrementalBinaryDilateImageFilter.html] can be used in order to make the dilation faster. I did not use that one because when I make it faster the spheres become overwritten, which I don't want to have in the conclusion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Architecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:BinaryDilateOperations-Documentation

2008-08-28T18:29:38Z

Bikekilic:

[[Documentation|Return to Slicer Documentation]]

==Binary Dilate Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing dilation on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform erosion method in order to make two different labeled separate objects closer to each other after erosion. At the end, we want to see these objects touched but not overwritten.

This method uses a structuring element in order to cover the object border with given foreground value. It grows the object with this structuring element. For this project, the structuring element is neighborhood structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is neighborhood structuring element with radius 2. It took 7 iterations in order to get closer images with different colors.

The input of this module is the output of BinaryErodeOperations module at the beginning. For the following iterations, the input is the dilated binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelDilate.PNG|thumb|280px|The GUI panel for BinaryDilateOperations Module after binary erosion]]
|}

In this case, the eroded image which is the input for BinaryDilateOperations Module has the pixel value 255 inside and 0 outside.

==DEVELOPMENT==

===Dependencies===

The BinaryDilateOperations Module uses four ITK classes. One of them is for binary erosion, which is called itkBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryDilateImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for dilation the neighborhood structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of dilation depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after dilation. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of neighborhood structuring element. Therefore, neighborhood structuring element was used in BinaryDilateOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive.

Another problem which was encountered with is stemmed from being unable to use labeled images in dilation. Since the binary images are used in dilation, after more than 7 iterations, the spheres become overwritten again and so they can not be labeled differently at the end of the dilation if I use Editor module. Therefore, I lose the connectedness information between spheres which makes me unable to differentiate the different objects. However, even they become overwritten, the labels remain the same as I had after performing LabelBinaryImages module on the last eroded image( background is labeled as 0, the first sphere is labeled as 1 and the second one is labeled as 2).

The results can be observed as seen in the ''Screen shots'' section.

===Screen shots===

{|
|[[Image:Dilate.png|thumb|280px|Binary Dilate Iterations with Neighborhood structuring element with radius 2]]
|[[Image:DilateWithBall.png|thumb|400px|Binary Dilate with Ball Structuring element with radius 5]]
|[[Image:DilateCross.png|thumb|400px|Binary Dilate with Cross Structuring element whose radius is 10]]
|}

Although the above figure shows three steps in dilation, it took 7 steps in order to make them be closer to each other. The neighborhood structuring element with radius 2 was used in dilation process.
In the second figure, the dilation result with ball structuring element which has the radius 5 can be seen. In comparison to the previous case, it took 5 steps in order to get the last dilated image.
The third figure shows the dilation result with cross structuring element whose radius is 10. After 25 iterations I get the last dilated image. In the case of using cross structuring element,the shape of the image is damaged more than the dilation with neighborhood and ball structuring elements.

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

On the other hand, although BinaryDilateImageFilter class has been used for this project, another ITK class which is called itkFastIncrementalBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1FastIncrementalBinaryDilateImageFilter.html] can be used in order to make the dilation faster. I did not use that one because when I make it faster the spheres become overwritten, which I don't want to have in the conclusion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Architecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:BinaryErodeOperations-Documentation

2008-08-28T18:29:19Z

Bikekilic:

[[Documentation|Return to Slicer Documentation]]

==Binary Erode Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing erosion on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform erosion method in order to make the two different objects separate in a given image. After separating them, the next step will be creating a label map and changing the labels to specify different regions.

This method uses a structuring element in order to cover the object border with given foreground value. It shrinks the object with this structuring element. For this project, the structuring element is ball structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is ball structuring element with radius 5. It took 7 iterations in order to get the desired output before creating different labels.

The input of this module is the output of the BinaryThresholding( or LabelBinaryImages) module at the beginning. For the following iterations, the input is the eroded binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelErode.PNG|thumb|280px|The GUI panel for BinaryErodeOperations Module after binary thresholding]]
|[[Image:GUIPanelErodeLabel.PNG|thumb|280px|The GUI panel for BinaryErodeOperations Module after LabelBinaryImages Module]]
|}

As seen above, the first figure shows the GUI panel if the user implements BinaryThresholding Module before erosion, whereas the second one shows the GUI panel of BinaryErodeOperations module in the case of using LabelBinaryImages module before erosion.

==DEVELOPMENT==

===Dependencies===

The BinaryErodeOperations Module uses four ITK classes. One of them is for binary erosion, which is called itkBinaryErodeImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryErodeImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for erosion the ball structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of erosion depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after erosion. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of ball structuring element. Therefore, ball structuring element was used in BinaryErodeOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive. The difference between the performance of structuring elements can be seen in ''Screen shots'' section.

In addition to the problems, I encountered with a problem when I used binary labeled image as an input to BinaryErodeOperations Module. The problem is that I could not create a label map by using Editor Module in Slicer 3. The reason may be due to the output I have after LabelBinaryImages Module. The inside pixel is 1 and the outside pixel is 0 for the binary labeled images. The erosion worked well these images but at the end of the erosion, I could not define two different labels by using Editor Module. Therefore, without having different labels, I could not continue on dilation because in dilation my aim is to see different labeled images touched each other but not overwritten after several steps. However, the failure in creating labels is the reason of not using the binary labeled images for my project. The detailed information is given in the section of ''the Problems'' in [[Slicer3:Module:LabelBinaryImages-Documentation|LabelBinaryImages]].

===Screen shots===

{|
|[[Image:Erode.png|thumb|280px|Binary Erode Iterations]]
|[[Image:AfterLabelChange.PNG|thumb|280px|Creating two different labels after erosion processes]]
|[[Image:AfterModelMaker.PNG|thumb|280px|Creating 3D model of separated and different labeled binary images by using Model Maker Module]]
|[[Image:Erosion1.png|thumb|300px|The results of erosion;neighborhood, ball, cross in order]]
|}

Although the first figure shows four steps in erosion, it took 7 steps in order to make them totally separate. The ball structuring element with radius 5 was used in erosion process.
The last figure shows the different results by using three different structuring elements:neighborhood, ball, cross in order. It can be observed that the shape is better when ball structuring element is used compared to the cases of using either neighborhood or cross structuring element.

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Arcitecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:BinaryErodeOperations-Documentation-3.2

2008-08-28T18:29:19Z

Bikekilic:

[[Documentation|Return to Slicer Documentation]]

==Binary Erode Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing erosion on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform erosion method in order to make the two different objects separate in a given image. After separating them, the next step will be creating a label map and changing the labels to specify different regions.

This method uses a structuring element in order to cover the object border with given foreground value. It shrinks the object with this structuring element. For this project, the structuring element is ball structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is ball structuring element with radius 5. It took 7 iterations in order to get the desired output before creating different labels.

The input of this module is the output of the BinaryThresholding( or LabelBinaryImages) module at the beginning. For the following iterations, the input is the eroded binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelErode.PNG|thumb|280px|The GUI panel for BinaryErodeOperations Module after binary thresholding]]
|[[Image:GUIPanelErodeLabel.PNG|thumb|280px|The GUI panel for BinaryErodeOperations Module after LabelBinaryImages Module]]
|}

As seen above, the first figure shows the GUI panel if the user implements BinaryThresholding Module before erosion, whereas the second one shows the GUI panel of BinaryErodeOperations module in the case of using LabelBinaryImages module before erosion.

==DEVELOPMENT==

===Dependencies===

The BinaryErodeOperations Module uses four ITK classes. One of them is for binary erosion, which is called itkBinaryErodeImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryErodeImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for erosion the ball structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of erosion depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after erosion. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of ball structuring element. Therefore, ball structuring element was used in BinaryErodeOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive. The difference between the performance of structuring elements can be seen in ''Screen shots'' section.

In addition to the problems, I encountered with a problem when I used binary labeled image as an input to BinaryErodeOperations Module. The problem is that I could not create a label map by using Editor Module in Slicer 3. The reason may be due to the output I have after LabelBinaryImages Module. The inside pixel is 1 and the outside pixel is 0 for the binary labeled images. The erosion worked well these images but at the end of the erosion, I could not define two different labels by using Editor Module. Therefore, without having different labels, I could not continue on dilation because in dilation my aim is to see different labeled images touched each other but not overwritten after several steps. However, the failure in creating labels is the reason of not using the binary labeled images for my project. The detailed information is given in the section of ''the Problems'' in [[Slicer3:Module:LabelBinaryImages-Documentation-3.2|LabelBinaryImages]].

===Screen shots===

{|
|[[Image:Erode.png|thumb|280px|Binary Erode Iterations]]
|[[Image:AfterLabelChange.PNG|thumb|280px|Creating two different labels after erosion processes]]
|[[Image:AfterModelMaker.PNG|thumb|280px|Creating 3D model of separated and different labeled binary images by using Model Maker Module]]
|[[Image:Erosion1.png|thumb|300px|The results of erosion;neighborhood, ball, cross in order]]
|}

Although the first figure shows four steps in erosion, it took 7 steps in order to make them totally separate. The ball structuring element with radius 5 was used in erosion process.
The last figure shows the different results by using three different structuring elements:neighborhood, ball, cross in order. It can be observed that the shape is better when ball structuring element is used compared to the cases of using either neighborhood or cross structuring element.

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Arcitecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:LabelBinaryImages-Documentation-3.2

2008-08-28T18:28:50Z

Bikekilic:

[[Documentation|Return to Slicer Documentation]]

==Binary Thresholding and Labeling==

{|
|+
|__TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

The type of this module is CLI and is under the category Segmentation in Slicer 3. The name of this module is LabelBinaryImages in Slicer 3.

===Authors, Collaborators&Contact===

*Author: Bike Kilic, MSc student in Northeastern University
*Contact: kilicbike@gmail.com

===Module Description===

The purpose of this module is defining different labels in an image after morphological operations. This module performs thresholding in the first step and then implements labeling by using the information of connectedness in given input.

The input of this module is the last eroded image. And after this process, the labeled binary image is taken to dilation process. After LabelBinaryImages module, the output shows us different labeled areas. For instance, in this project, the input is eroded spheres and then after this module the output is an image with three different labeled areas:background as 0, one of the spheres as 1 and the other one as 2. The sphere with bigger area is labeled as 1.

The results can be seen in the section called ''Screen shots'' in this page.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:LabelGUI.png|thumb|280px|The GUI panel for LabelBinaryImages Module]]
|}

==DEVELOPMENT==

===Dependencies===

In this module, there are 3 ITK classes which are used.

One of them is for binary thresholding which is called itkBinaryThresholdImageFilter[http://www.itk.org/Doxygen/html/classitk_1_1BinaryThresholdImageFilter.html]. It takes two user inputs which are LowerThreshold and UpperThreshold values. The output is a binary images with 0 outside and 255 inside.

The other class which is for labeling the objects in a binary image is itkConnectedComponentImageFilter class [http://www.itk.org/Doxygen/html/classitk_1_1ConnectedComponentImageFilter.html].Each distinct object is assigned a unique label. The filter experiments with some improvements to the existing implementation, and is based on run length encoding along raster lines. The final object labels start with 1 and are consecutive. Objects that are reached earlier by a raster order scan have a lower label. This is different to the behavior of the original connected component image filter which did not produce consecutive labels or impose any particular ordering. The input of this algorithm is the output of binary thresholding.

The last one is used for remapping the labels associated with the objects in an image. The input comes from the output of ConnectedComponentImageFilter. The name of this last class is itkRelabelComponentImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1RelabelComponentImageFilter.html]. The output of this method is used for BinaryDilateOperations module.

===The Problems===

The problem with this module is that I could not create a 3D model after dilation processes with given labels by using Editor module of Slicer 3. As I had the output of the dilation, I created a label map by using Editor module but what I has as an output is just a black screen labeled as 0. Therefore, I could not perform thresholding tool in Editor so could not able to change the labels and then using Model Maker module.

===Screen shots===

{|
|[[Image:LabelingTrial.png|thumb|400px|The output of LabelBinaryImagesModule and then dilation]]
|}

In the first square, the output of dilation by using BinaryDilateOperations module and label mapping by using Editor module can be seen. Second one indicates the output of LabelBinaryImages module. As mentioned in the section ''Module Description'' in this page, the background is labeled as 0 whereas the separated spheres are labeled as 1 and 2 consecutively.

As we keep on dilating the image, the spheres are still labeled as 1 and 2 and the background as 0.

==MORE INFORMATION==

===Results&Comments===

In this part, I tried to explain if we are able to use LabelBinaryImages module in morphological operations. What I have seen after using this module is that even I continue on dilation of the separated images and make them overwritten, the labels of the objects does not change. The label numbers remain the same as I had seen after I performed the algorithms in LabelBinaryImages module on the last eroded image.

What the user should be careful is that if user has the output of BinaryThresholding module as an input for BinaryDilateOperations module, the dilate value should be chosen as 255. However, if user chooses the output of LabelBinaryImages module as an input for dilation, the dilate value should be the same as label numbers. The reason is that as I have seen from my experiments, when I entered 255 for dilate value to dilate the output image of LabelBinaryImages module, there was no change in the output image. However, when I chose 1 or 2 for the dilate value, the image has been dilated by given structuring element. In my opinion, the reason is that the output of LabelBinaryImages module is formed by the label values 0, 1 and 2, whereas the output of BinaryThresholding module has 255 inside and 0 outside.

===Future work===

As a future work, it will be better to add an algorithm which makes label mapping in LabelBinaryImages module instead of using Editor module in Slicer 3. The reason is that the thresholding in Editor module and the one in LabelBinaryImages module works different so creating label maps and then coloring these maps with different labels fails by using Editor module. In 2D plane, I can see that the labels which are defined by LabelBinaryImages module by performing on the separated binary spheres after erosion processes do not change even they overwrite after many dilation processes. However, when I want to color these different labeled objects, at that point I can not achieve my goal and am not be able to see the result in 3D space.

===References===

#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G.,''Label object representation and manipulation with ITK'', 2007. [http://www.insight-journal.com/]

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T18:28:50Z

Bikekilic:

Slicer3:Module:BinaryThresholding-Documentation

2008-08-28T18:28:31Z

Bikekilic:

[[Documentation|Return to Slicer Documentation]]

==Binary Thresholding==

{|
|+
|__TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

Type of this module is CLI and is under the category named Segmentation in Slicer 3.

===Authors, Collaborators&Contact===

*Author: Bike Kilic, MSc student in Northeastern University
*Contact: kilicbike@gmail.com

===Module Description===

The purpose of this module is implementing simple binary thresholding in order to get a binary image at the end. In this project, the input is two spheres which are connected to each other and after this process, the pixel value of the inside of the connected spheres becomes 255, whereas the outside value is 0.

In order to add the input, from the File tab of Slicer 3, the inputted volume is added to the data module. In this project the input is "spheres.nrrd" as seen in the part of Screen shots in [[Slicer3:Module:Binary Morphological Operations-Documentation|Binary Morphological Operations]]. The output of binary thresholding is then used for erosion.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelThreshold.PNG|thumb|280px|The GUI panel of BinaryThresholding Module]]
|}

==DEVELOPMENT==

===Dependencies===

In order to implement binary thresholding, itkBinaryThresholdImageFilter class has been used.[http://www.itk.org/Doxygen/html/classitk_1_1BinaryThresholdImageFilter.html]

This module is used to binarize an input image by thresholding.

The ITK filter produces an output image whose pixels are either one of two values ( OutsideValue or InsideValue ), depending on whether of not the corresponding input image pixel lie between the two thresholds ( LowerThreshold and UpperThreshold ). Values equal to either threshold is considered to be between the thresholds.

As seen in the GUI panel uploaded below, the LowerThreshold is 35 and the UpperThreshold value is 255. The InsideValue is 255, whereas OutsideValue is 0.

===The Problems===

No problem has been occurred in this module. However, the performance of this module depends on the data. If data does not have good contrast, the thresholding does not work as expected. Therefore, there should be another algorithm which helps the user to look at the grey-level values of the data in order to pick the correct threshold intervals. On the other hand, if the data is noisy, has low contrast, blurred, in this module any smoothing or reconstruction method can be included before binary thresholding in order to enhance the image.

==MORE INFORMATION==

===Future work===

As a future work, another ITK class can be added into this module which can help reducing the unexpected noises in the input image before performing binary thresholding.

===References===

#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Arcitecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.

Slicer3:Module:BinaryThresholding-Documentation-3.2

2008-08-28T18:28:31Z

Bikekilic:

[[Documentation|Return to Slicer Documentation]]

==Binary Thresholding==

{|
|+
|__TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

Type of this module is CLI and is under the category named Segmentation in Slicer 3.

===Authors, Collaborators&Contact===

*Author: Bike Kilic, MSc student in Northeastern University
*Contact: kilicbike@gmail.com

===Module Description===

The purpose of this module is implementing simple binary thresholding in order to get a binary image at the end. In this project, the input is two spheres which are connected to each other and after this process, the pixel value of the inside of the connected spheres becomes 255, whereas the outside value is 0.

In order to add the input, from the File tab of Slicer 3, the inputted volume is added to the data module. In this project the input is "spheres.nrrd" as seen in the part of Screen shots in [[Slicer3:Module:Binary Morphological Operations-Documentation-3.2|Binary Morphological Operations]]. The output of binary thresholding is then used for erosion.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelThreshold.PNG|thumb|280px|The GUI panel of BinaryThresholding Module]]
|}

==DEVELOPMENT==

===Dependencies===

In order to implement binary thresholding, itkBinaryThresholdImageFilter class has been used.[http://www.itk.org/Doxygen/html/classitk_1_1BinaryThresholdImageFilter.html]

This module is used to binarize an input image by thresholding.

The ITK filter produces an output image whose pixels are either one of two values ( OutsideValue or InsideValue ), depending on whether of not the corresponding input image pixel lie between the two thresholds ( LowerThreshold and UpperThreshold ). Values equal to either threshold is considered to be between the thresholds.

As seen in the GUI panel uploaded below, the LowerThreshold is 35 and the UpperThreshold value is 255. The InsideValue is 255, whereas OutsideValue is 0.

===The Problems===

No problem has been occurred in this module. However, the performance of this module depends on the data. If data does not have good contrast, the thresholding does not work as expected. Therefore, there should be another algorithm which helps the user to look at the grey-level values of the data in order to pick the correct threshold intervals. On the other hand, if the data is noisy, has low contrast, blurred, in this module any smoothing or reconstruction method can be included before binary thresholding in order to enhance the image.

==MORE INFORMATION==

===Future work===

As a future work, another ITK class can be added into this module which can help reducing the unexpected noises in the input image before performing binary thresholding.

===References===

#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Arcitecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.

Slicer3:Module:BinaryThresholding-Documentation

2008-08-28T18:27:09Z

Bikekilic: /* Module Type&Category */

==Binary Thresholding==

{|
|+
|__TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

Type of this module is CLI and is under the category named Segmentation in Slicer 3.

===Authors, Collaborators&Contact===

*Author: Bike Kilic, MSc student in Northeastern University
*Contact: kilicbike@gmail.com

===Module Description===

The purpose of this module is implementing simple binary thresholding in order to get a binary image at the end. In this project, the input is two spheres which are connected to each other and after this process, the pixel value of the inside of the connected spheres becomes 255, whereas the outside value is 0.

In order to add the input, from the File tab of Slicer 3, the inputted volume is added to the data module. In this project the input is "spheres.nrrd" as seen in the part of Screen shots in [[Slicer3:Module:Binary Morphological Operations-Documentation|Binary Morphological Operations]]. The output of binary thresholding is then used for erosion.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelThreshold.PNG|thumb|280px|The GUI panel of BinaryThresholding Module]]
|}

==DEVELOPMENT==

===Dependencies===

In order to implement binary thresholding, itkBinaryThresholdImageFilter class has been used.[http://www.itk.org/Doxygen/html/classitk_1_1BinaryThresholdImageFilter.html]

This module is used to binarize an input image by thresholding.

The ITK filter produces an output image whose pixels are either one of two values ( OutsideValue or InsideValue ), depending on whether of not the corresponding input image pixel lie between the two thresholds ( LowerThreshold and UpperThreshold ). Values equal to either threshold is considered to be between the thresholds.

As seen in the GUI panel uploaded below, the LowerThreshold is 35 and the UpperThreshold value is 255. The InsideValue is 255, whereas OutsideValue is 0.

===The Problems===

No problem has been occurred in this module. However, the performance of this module depends on the data. If data does not have good contrast, the thresholding does not work as expected. Therefore, there should be another algorithm which helps the user to look at the grey-level values of the data in order to pick the correct threshold intervals. On the other hand, if the data is noisy, has low contrast, blurred, in this module any smoothing or reconstruction method can be included before binary thresholding in order to enhance the image.

==MORE INFORMATION==

===Future work===

As a future work, another ITK class can be added into this module which can help reducing the unexpected noises in the input image before performing binary thresholding.

===References===

#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Arcitecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.

Slicer3:Module:Binary Morphological Operations-Documentation

2008-08-28T18:26:39Z

Bikekilic: /* Future work */

[[Documentation|Return to Slicer Documentation]]

==Binary Morphological Operations==
{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

In order to implement morphological operations which are erosion and dilation, the four new modules have been integrated to Slicer 3 by using ITK commands which are explained in [[Slicer3:Module:Binary_Morphological_Operations-Documentation|Module Description]].The types of those modules are CLI and the category of them is Segmentation.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

The modules in this framework are used in order to segment a given image by morphological operations:

-The first step is to binarize given gray-level image. The inside of the object is white and the outside is black. In order to do binarization, in this project there are two modules integrated into Slicer 3. The one called "LabelBinaryImages" uses general thresholding which makes the inside pixel equal to 1 and outside pixels equal to 0 and then creates a labeled binary image. The other one called "BinaryThresholding" thresholds the gray-level image by given upper and lower values in order to binarize the image. However in this case, the inside pixels values are 255 and the ones which are in the outside of the object have the value 0.

-After having binary image, the second step is performing erode operation to this image in order to make the different objects separate with the module called "BinaryErodeOperations". For instance, in this project I have two intersected spheres which are already binary image. However in order to make them smooth, the spheres are thresholded by general thresholding firstly and then by binary erode operation the spheres are totally separated to specify two different labels. The label map is created by using Editor module of Slicer 3.

-As we have two separate images, the dilation operation is used in order to make them touch each other but not onto each other. The name of the module is "BinaryDilateOperations". The aim of this module is to make the totally separated objects touch each other but not overwritten.

-The final step is to create the label map and make 3D model of touching but different labeled objects. The Editor and Model Maker modules are used in order to achieve this goal.

The output of the algorithms is two different labeled binary image.

==USAGE==

===Examples, Use Cases & Tutorials===

The "BinaryThresholding" module can be used in segmentation of foreground and background in an image. The problem might be stemmed from the values chosen for upper and lower threshold. In that case, the histogram equalization or some reconstruction methods can be used beforehand in order to enhance the image.

The "LabelBinaryImages" module is useful in order to find the connected pixels and label the image depending on the connectedness. After thresholding even we see different objects the program does not understand that they are different images so this module helps the program to label the objects in a binary image.

The morphological operations which are "BinaryErodeOperations" and "BinaryDilateOperations" can be used for several aspects such as segmentation, reconstruction, enhancement. What we have to be careful is choosing the best structuring element because both erosion and dilation depends on the structuring element. As I have seen in ITK documentation, there are three different structuring elements which are used for morphological operations. In this project, erosion is made by ball structuring element and the dilation uses neighborhood structuring element. The other included class for structuring element is binary cross structuring element. In addition to choosing structuring element, the properties of them have crucial role in the performance of these operations. For instance, if the radius of the binary ball structuring element is increased, the edge of the image has more square shape so it does not preserve the shape information. Therefore, in order to preserve the shape, some thresholding or smoothing algorithms can be performed.

===Quick Tour of Features and Use===

In the first step, the binary thresholding uses the gray level image as an input. In this project, our input is two intersected spheres with different radius sizes.

The second step, "BinaryErodeOperations", uses the output of binary thresholding which is a binary image as an input. This module should be repeated until we have two totally separate images because we need to create a label map and mark the different objects with different labels. The input for the repeated erosion is the eroded image from the previous one. User also identifies the radius size of structuring element.

The label map and label images are created by using Editor module. The input for label map is the last eroded image. After creating label map, the tools of Editor module help us to change the labels and create different labels. Then by using Model Maker, we can observe the separate images in 3D surface.

The next step is "BinaryDilateOperations". This module uses the last eroded image which is the output of BinaryErodeOperations as an input. Like erosion case, this module is also repeated until we get touched but not overwritten binary images. At the end of this method, what we want to see is to have different colored images which are touched each other.

The last step is again creating label map and 3D model by using Editor and Model Maker modules in order.

The input and output images of above algorithms are given in the Screen shots part.

==DEVELOPMENT==

===Dependencies===

The modules for thresholding and morphological operations are taken from ITK website, [http://www.itk.org/Doxygen/html/classes.html].

For thresholding. itkBinaryThresholdImageFilter class is included. The user chooses lower and upper threshold values. The detailed information is given in [[Slicer3:Module:BinaryThresholding-Documentation|BinaryThresholding]]

If the user wants to both binarize and label the image before morphological operations, the "LabelBinaryImages" module uses three ITK classes. itkBinaryThresholdImageFilter is for binary thresholding. itkConnectedComponentImageFilter and itkRelabelComponentImageFilter are for labeling the image. Please see the page [[Slicer3:Module:LabelBinaryImages-Documentation|LabelBinaryImages]] for more information.

For morphological operations, itkBinaryDilateImageFilter and itkBinaryErodeImageFilter classes are used. In order to create structuring element, ITK classes are also used. BinaryBallStructuringElement, BinaryCrossStructuringElement and Neighborhood classes are included in this project. The radius is given by the user. If user labels the image as 1 and 0 in the first step, the both erode and dilate value should be chosen as 1. Otherwise, if user wants to just threshold the image by using "BinaryThresholding" module, erode and dilate values should be the same as the upper value of the threshold. The reason is that these values represent the foreground value which is also the inner pixel value of the image. Please see the page [[Slicer3:Module:BinaryErodeOperations-Documentation|BinaryErodeOperations]] for erosion and [[Slicer3:Module:BinaryDilateOperations-Documentation|BinaryDilateOperations]] for dilation.

===The problems===

The problems I encountered with are stemmed from the values given by user in all sub-modules.

In the first step, the problems in binary thresholding are explained in the part [[Slicer3:Module:BinaryThresholding-Documentation|BinaryThresholding]]. And if user wants to use labeling in addition to thresholding, the problems I had should be known and the detailed information is given in [[Slicer3:Module:LabelBinaryImages-Documentation|LabelBinaryImages]].

In the second step, the problems in erosion are explained in the part [[Slicer3:Module:BinaryErodeOperations-Documentation|BinaryErodeOperations]].

In the third and last step, the problems in dilation are explained in the part [[Slicer3:Module:BinaryDilateOperations-Documentation|BinaryDilateOperations]].

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

===Screen shots===

{|
|[[Image:Sphere.png|thumb|280px|Input image for the module]]
|[[Image:ModelBeforeMorpho.png|thumb|280px|The output of model maker before morphological operations after thresholding]]
|}
The screen shot which show the input panel of binary thresholding operation can be shown in [[Slicer3:Module:BinaryThresholding-Documentation|BinaryThresholding]].

The screen shot which show the input and output of labeling binary images can be shown in [[Slicer3:Module:LabelBinaryImages-Documentation|LabelBinaryImages]].

The screen shots which show the input and result of erode operation can be shown in [[Slicer3:Module:BinaryErodeOperations-Documentation|BinaryErodeOperations]].

The screen shots which show the input and result of dilate operation can be shown in [[Slicer3:Module:BinaryDilateOperations-Documentation|BinaryDilateOperations]].

===Acknowledgment===

Most of the development took place in the Surgical Planning Laboratory, Harvard Medical School and Brigham and Women's Hospital, under the supervision of Mr. Steve Pieper Ph.D.

==MORE INFORMATION==

===Results&Comments===

In this project, the aim is to make the overwritten spheres separate by using erosion. After erosion, label them with different colors by using Editor module is the second goal. After having different labeled objects, dilation makes these objects touch together but not overwritten. At the end, we want to see different labeled objects which touch each other but not neither onto nor into each other.

Binary Thresholding, Binary Erosion worked very well. However, in binary dilation, I encountered with a problem. When I increased the iteration of dilation after the objects got closer, the objects became overwritten. And therefore, I could not label them differently. The problems and screen shots can be followed from [[Slicer3:Module:BinaryDilateOperations-Documentation|BinaryDilateOperations]].

The solution can be changing the algorithm in "BinaryDilateOperations" module. For instance, the input for the dilation could be labeled objects instead of binary eroded images. Another solution could be giving some constraints in growing forces of dilation.

===Future work===

For this project. in the future, the dilation algorithm should be improved. Instead of using binary eroded images, the binary labeled eroded images can be used as an input for dilation operation.For detailed information please look at [[Slicer3:Module:LabelBinaryImages-Documentation|LabelBinaryImages]]

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Arcitecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:Binary Morphological Operations-Documentation-3.2

2008-08-28T18:26:39Z

Bikekilic: /* Future work */

[[Documentation|Return to Slicer Documentation]]

==Binary Morphological Operations==
{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

In order to implement morphological operations which are erosion and dilation, the four new modules have been integrated to Slicer 3 by using ITK commands which are explained in [[Slicer3:Module:Binary_Morphological_Operations-Documentation-3.2|Module Description]].The types of those modules are CLI and the category of them is Segmentation.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

The modules in this framework are used in order to segment a given image by morphological operations:

-The first step is to binarize given gray-level image. The inside of the object is white and the outside is black. In order to do binarization, in this project there are two modules integrated into Slicer 3. The one called "LabelBinaryImages" uses general thresholding which makes the inside pixel equal to 1 and outside pixels equal to 0 and then creates a labeled binary image. The other one called "BinaryThresholding" thresholds the gray-level image by given upper and lower values in order to binarize the image. However in this case, the inside pixels values are 255 and the ones which are in the outside of the object have the value 0.

-After having binary image, the second step is performing erode operation to this image in order to make the different objects separate with the module called "BinaryErodeOperations". For instance, in this project I have two intersected spheres which are already binary image. However in order to make them smooth, the spheres are thresholded by general thresholding firstly and then by binary erode operation the spheres are totally separated to specify two different labels. The label map is created by using Editor module of Slicer 3.

-As we have two separate images, the dilation operation is used in order to make them touch each other but not onto each other. The name of the module is "BinaryDilateOperations". The aim of this module is to make the totally separated objects touch each other but not overwritten.

-The final step is to create the label map and make 3D model of touching but different labeled objects. The Editor and Model Maker modules are used in order to achieve this goal.

The output of the algorithms is two different labeled binary image.

==USAGE==

===Examples, Use Cases & Tutorials===

The "BinaryThresholding" module can be used in segmentation of foreground and background in an image. The problem might be stemmed from the values chosen for upper and lower threshold. In that case, the histogram equalization or some reconstruction methods can be used beforehand in order to enhance the image.

The "LabelBinaryImages" module is useful in order to find the connected pixels and label the image depending on the connectedness. After thresholding even we see different objects the program does not understand that they are different images so this module helps the program to label the objects in a binary image.

The morphological operations which are "BinaryErodeOperations" and "BinaryDilateOperations" can be used for several aspects such as segmentation, reconstruction, enhancement. What we have to be careful is choosing the best structuring element because both erosion and dilation depends on the structuring element. As I have seen in ITK documentation, there are three different structuring elements which are used for morphological operations. In this project, erosion is made by ball structuring element and the dilation uses neighborhood structuring element. The other included class for structuring element is binary cross structuring element. In addition to choosing structuring element, the properties of them have crucial role in the performance of these operations. For instance, if the radius of the binary ball structuring element is increased, the edge of the image has more square shape so it does not preserve the shape information. Therefore, in order to preserve the shape, some thresholding or smoothing algorithms can be performed.

===Quick Tour of Features and Use===

In the first step, the binary thresholding uses the gray level image as an input. In this project, our input is two intersected spheres with different radius sizes.

The second step, "BinaryErodeOperations", uses the output of binary thresholding which is a binary image as an input. This module should be repeated until we have two totally separate images because we need to create a label map and mark the different objects with different labels. The input for the repeated erosion is the eroded image from the previous one. User also identifies the radius size of structuring element.

The label map and label images are created by using Editor module. The input for label map is the last eroded image. After creating label map, the tools of Editor module help us to change the labels and create different labels. Then by using Model Maker, we can observe the separate images in 3D surface.

The next step is "BinaryDilateOperations". This module uses the last eroded image which is the output of BinaryErodeOperations as an input. Like erosion case, this module is also repeated until we get touched but not overwritten binary images. At the end of this method, what we want to see is to have different colored images which are touched each other.

The last step is again creating label map and 3D model by using Editor and Model Maker modules in order.

The input and output images of above algorithms are given in the Screen shots part.

==DEVELOPMENT==

===Dependencies===

The modules for thresholding and morphological operations are taken from ITK website, [http://www.itk.org/Doxygen/html/classes.html].

For thresholding. itkBinaryThresholdImageFilter class is included. The user chooses lower and upper threshold values. The detailed information is given in [[Slicer3:Module:BinaryThresholding-Documentation-3.2|BinaryThresholding]]

If the user wants to both binarize and label the image before morphological operations, the "LabelBinaryImages" module uses three ITK classes. itkBinaryThresholdImageFilter is for binary thresholding. itkConnectedComponentImageFilter and itkRelabelComponentImageFilter are for labeling the image. Please see the page [[Slicer3:Module:LabelBinaryImages-Documentation-3.2|LabelBinaryImages]] for more information.

For morphological operations, itkBinaryDilateImageFilter and itkBinaryErodeImageFilter classes are used. In order to create structuring element, ITK classes are also used. BinaryBallStructuringElement, BinaryCrossStructuringElement and Neighborhood classes are included in this project. The radius is given by the user. If user labels the image as 1 and 0 in the first step, the both erode and dilate value should be chosen as 1. Otherwise, if user wants to just threshold the image by using "BinaryThresholding" module, erode and dilate values should be the same as the upper value of the threshold. The reason is that these values represent the foreground value which is also the inner pixel value of the image. Please see the page [[Slicer3:Module:BinaryErodeOperations-Documentation-3.2|BinaryErodeOperations]] for erosion and [[Slicer3:Module:BinaryDilateOperations-Documentation-3.2|BinaryDilateOperations]] for dilation.

===The problems===

The problems I encountered with are stemmed from the values given by user in all sub-modules.

In the first step, the problems in binary thresholding are explained in the part [[Slicer3:Module:BinaryThresholding-Documentation-3.2|BinaryThresholding]]. And if user wants to use labeling in addition to thresholding, the problems I had should be known and the detailed information is given in [[Slicer3:Module:LabelBinaryImages-Documentation-3.2|LabelBinaryImages]].

In the second step, the problems in erosion are explained in the part [[Slicer3:Module:BinaryErodeOperations-Documentation-3.2|BinaryErodeOperations]].

In the third and last step, the problems in dilation are explained in the part [[Slicer3:Module:BinaryDilateOperations-Documentation-3.2|BinaryDilateOperations]].

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

===Screen shots===

{|
|[[Image:Sphere.png|thumb|280px|Input image for the module]]
|[[Image:ModelBeforeMorpho.png|thumb|280px|The output of model maker before morphological operations after thresholding]]
|}
The screen shot which show the input panel of binary thresholding operation can be shown in [[Slicer3:Module:BinaryThresholding-Documentation-3.2|BinaryThresholding]].

The screen shot which show the input and output of labeling binary images can be shown in [[Slicer3:Module:LabelBinaryImages-Documentation-3.2|LabelBinaryImages]].

The screen shots which show the input and result of erode operation can be shown in [[Slicer3:Module:BinaryErodeOperations-Documentation-3.2|BinaryErodeOperations]].

The screen shots which show the input and result of dilate operation can be shown in [[Slicer3:Module:BinaryDilateOperations-Documentation-3.2|BinaryDilateOperations]].

===Acknowledgment===

Most of the development took place in the Surgical Planning Laboratory, Harvard Medical School and Brigham and Women's Hospital, under the supervision of Mr. Steve Pieper Ph.D.

==MORE INFORMATION==

===Results&Comments===

In this project, the aim is to make the overwritten spheres separate by using erosion. After erosion, label them with different colors by using Editor module is the second goal. After having different labeled objects, dilation makes these objects touch together but not overwritten. At the end, we want to see different labeled objects which touch each other but not neither onto nor into each other.

Binary Thresholding, Binary Erosion worked very well. However, in binary dilation, I encountered with a problem. When I increased the iteration of dilation after the objects got closer, the objects became overwritten. And therefore, I could not label them differently. The problems and screen shots can be followed from [[Slicer3:Module:BinaryDilateOperations-Documentation-3.2|BinaryDilateOperations]].

The solution can be changing the algorithm in "BinaryDilateOperations" module. For instance, the input for the dilation could be labeled objects instead of binary eroded images. Another solution could be giving some constraints in growing forces of dilation.

===Future work===

For this project. in the future, the dilation algorithm should be improved. Instead of using binary eroded images, the binary labeled eroded images can be used as an input for dilation operation.For detailed information please look at [[Slicer3:Module:LabelBinaryImages-Documentation-3.2|LabelBinaryImages]]

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Arcitecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:Binary Morphological Operations-Documentation

2008-08-28T18:25:16Z

Bikekilic: /* Screen shots */

[[Documentation|Return to Slicer Documentation]]

==Binary Morphological Operations==
{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

In order to implement morphological operations which are erosion and dilation, the four new modules have been integrated to Slicer 3 by using ITK commands which are explained in [[Slicer3:Module:Binary_Morphological_Operations-Documentation|Module Description]].The types of those modules are CLI and the category of them is Segmentation.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

The modules in this framework are used in order to segment a given image by morphological operations:

-The first step is to binarize given gray-level image. The inside of the object is white and the outside is black. In order to do binarization, in this project there are two modules integrated into Slicer 3. The one called "LabelBinaryImages" uses general thresholding which makes the inside pixel equal to 1 and outside pixels equal to 0 and then creates a labeled binary image. The other one called "BinaryThresholding" thresholds the gray-level image by given upper and lower values in order to binarize the image. However in this case, the inside pixels values are 255 and the ones which are in the outside of the object have the value 0.

-After having binary image, the second step is performing erode operation to this image in order to make the different objects separate with the module called "BinaryErodeOperations". For instance, in this project I have two intersected spheres which are already binary image. However in order to make them smooth, the spheres are thresholded by general thresholding firstly and then by binary erode operation the spheres are totally separated to specify two different labels. The label map is created by using Editor module of Slicer 3.

-As we have two separate images, the dilation operation is used in order to make them touch each other but not onto each other. The name of the module is "BinaryDilateOperations". The aim of this module is to make the totally separated objects touch each other but not overwritten.

-The final step is to create the label map and make 3D model of touching but different labeled objects. The Editor and Model Maker modules are used in order to achieve this goal.

The output of the algorithms is two different labeled binary image.

==USAGE==

===Examples, Use Cases & Tutorials===

The "BinaryThresholding" module can be used in segmentation of foreground and background in an image. The problem might be stemmed from the values chosen for upper and lower threshold. In that case, the histogram equalization or some reconstruction methods can be used beforehand in order to enhance the image.

The "LabelBinaryImages" module is useful in order to find the connected pixels and label the image depending on the connectedness. After thresholding even we see different objects the program does not understand that they are different images so this module helps the program to label the objects in a binary image.

The morphological operations which are "BinaryErodeOperations" and "BinaryDilateOperations" can be used for several aspects such as segmentation, reconstruction, enhancement. What we have to be careful is choosing the best structuring element because both erosion and dilation depends on the structuring element. As I have seen in ITK documentation, there are three different structuring elements which are used for morphological operations. In this project, erosion is made by ball structuring element and the dilation uses neighborhood structuring element. The other included class for structuring element is binary cross structuring element. In addition to choosing structuring element, the properties of them have crucial role in the performance of these operations. For instance, if the radius of the binary ball structuring element is increased, the edge of the image has more square shape so it does not preserve the shape information. Therefore, in order to preserve the shape, some thresholding or smoothing algorithms can be performed.

===Quick Tour of Features and Use===

In the first step, the binary thresholding uses the gray level image as an input. In this project, our input is two intersected spheres with different radius sizes.

The second step, "BinaryErodeOperations", uses the output of binary thresholding which is a binary image as an input. This module should be repeated until we have two totally separate images because we need to create a label map and mark the different objects with different labels. The input for the repeated erosion is the eroded image from the previous one. User also identifies the radius size of structuring element.

The label map and label images are created by using Editor module. The input for label map is the last eroded image. After creating label map, the tools of Editor module help us to change the labels and create different labels. Then by using Model Maker, we can observe the separate images in 3D surface.

The next step is "BinaryDilateOperations". This module uses the last eroded image which is the output of BinaryErodeOperations as an input. Like erosion case, this module is also repeated until we get touched but not overwritten binary images. At the end of this method, what we want to see is to have different colored images which are touched each other.

The last step is again creating label map and 3D model by using Editor and Model Maker modules in order.

The input and output images of above algorithms are given in the Screen shots part.

==DEVELOPMENT==

===Dependencies===

The modules for thresholding and morphological operations are taken from ITK website, [http://www.itk.org/Doxygen/html/classes.html].

For thresholding. itkBinaryThresholdImageFilter class is included. The user chooses lower and upper threshold values. The detailed information is given in [[Slicer3:Module:BinaryThresholding-Documentation|BinaryThresholding]]

If the user wants to both binarize and label the image before morphological operations, the "LabelBinaryImages" module uses three ITK classes. itkBinaryThresholdImageFilter is for binary thresholding. itkConnectedComponentImageFilter and itkRelabelComponentImageFilter are for labeling the image. Please see the page [[Slicer3:Module:LabelBinaryImages-Documentation|LabelBinaryImages]] for more information.

For morphological operations, itkBinaryDilateImageFilter and itkBinaryErodeImageFilter classes are used. In order to create structuring element, ITK classes are also used. BinaryBallStructuringElement, BinaryCrossStructuringElement and Neighborhood classes are included in this project. The radius is given by the user. If user labels the image as 1 and 0 in the first step, the both erode and dilate value should be chosen as 1. Otherwise, if user wants to just threshold the image by using "BinaryThresholding" module, erode and dilate values should be the same as the upper value of the threshold. The reason is that these values represent the foreground value which is also the inner pixel value of the image. Please see the page [[Slicer3:Module:BinaryErodeOperations-Documentation|BinaryErodeOperations]] for erosion and [[Slicer3:Module:BinaryDilateOperations-Documentation|BinaryDilateOperations]] for dilation.

===The problems===

The problems I encountered with are stemmed from the values given by user in all sub-modules.

In the first step, the problems in binary thresholding are explained in the part [[Slicer3:Module:BinaryThresholding-Documentation|BinaryThresholding]]. And if user wants to use labeling in addition to thresholding, the problems I had should be known and the detailed information is given in [[Slicer3:Module:LabelBinaryImages-Documentation|LabelBinaryImages]].

In the second step, the problems in erosion are explained in the part [[Slicer3:Module:BinaryErodeOperations-Documentation|BinaryErodeOperations]].

In the third and last step, the problems in dilation are explained in the part [[Slicer3:Module:BinaryDilateOperations-Documentation|BinaryDilateOperations]].

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

===Screen shots===

{|
|[[Image:Sphere.png|thumb|280px|Input image for the module]]
|[[Image:ModelBeforeMorpho.png|thumb|280px|The output of model maker before morphological operations after thresholding]]
|}
The screen shot which show the input panel of binary thresholding operation can be shown in [[Slicer3:Module:BinaryThresholding-Documentation|BinaryThresholding]].

The screen shot which show the input and output of labeling binary images can be shown in [[Slicer3:Module:LabelBinaryImages-Documentation|LabelBinaryImages]].

The screen shots which show the input and result of erode operation can be shown in [[Slicer3:Module:BinaryErodeOperations-Documentation|BinaryErodeOperations]].

The screen shots which show the input and result of dilate operation can be shown in [[Slicer3:Module:BinaryDilateOperations-Documentation|BinaryDilateOperations]].

===Acknowledgment===

Most of the development took place in the Surgical Planning Laboratory, Harvard Medical School and Brigham and Women's Hospital, under the supervision of Mr. Steve Pieper Ph.D.

==MORE INFORMATION==

===Results&Comments===

In this project, the aim is to make the overwritten spheres separate by using erosion. After erosion, label them with different colors by using Editor module is the second goal. After having different labeled objects, dilation makes these objects touch together but not overwritten. At the end, we want to see different labeled objects which touch each other but not neither onto nor into each other.

Binary Thresholding, Binary Erosion worked very well. However, in binary dilation, I encountered with a problem. When I increased the iteration of dilation after the objects got closer, the objects became overwritten. And therefore, I could not label them differently. The problems and screen shots can be followed from [[Slicer3:Module:BinaryDilateOperations-Documentation|BinaryDilateOperations]].

The solution can be changing the algorithm in "BinaryDilateOperations" module. For instance, the input for the dilation could be labeled objects instead of binary eroded images. Another solution could be giving some constraints in growing forces of dilation.

===Future work===

For this project. in the future, the dilation algorithm should be improved. Instead of using binary eroded images, the binary labeled eroded images can be used as an input for dilation operation.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Arcitecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T18:22:35Z

Bikekilic: /* Future work */

==Binary Thresholding and Labeling==

{|
|+
|__TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

The type of this module is CLI and is under the category Segmentation in Slicer 3. The name of this module is LabelBinaryImages in Slicer 3.

===Authors, Collaborators&Contact===

*Author: Bike Kilic, MSc student in Northeastern University
*Contact: kilicbike@gmail.com

===Module Description===

The purpose of this module is defining different labels in an image after morphological operations. This module performs thresholding in the first step and then implements labeling by using the information of connectedness in given input.

The input of this module is the last eroded image. And after this process, the labeled binary image is taken to dilation process. After LabelBinaryImages module, the output shows us different labeled areas. For instance, in this project, the input is eroded spheres and then after this module the output is an image with three different labeled areas:background as 0, one of the spheres as 1 and the other one as 2. The sphere with bigger area is labeled as 1.

The results can be seen in the section called ''Screen shots'' in this page.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:LabelGUI.png|thumb|280px|The GUI panel for LabelBinaryImages Module]]
|}

==DEVELOPMENT==

===Dependencies===

In this module, there are 3 ITK classes which are used.

One of them is for binary thresholding which is called itkBinaryThresholdImageFilter[http://www.itk.org/Doxygen/html/classitk_1_1BinaryThresholdImageFilter.html]. It takes two user inputs which are LowerThreshold and UpperThreshold values. The output is a binary images with 0 outside and 255 inside.

The other class which is for labeling the objects in a binary image is itkConnectedComponentImageFilter class [http://www.itk.org/Doxygen/html/classitk_1_1ConnectedComponentImageFilter.html].Each distinct object is assigned a unique label. The filter experiments with some improvements to the existing implementation, and is based on run length encoding along raster lines. The final object labels start with 1 and are consecutive. Objects that are reached earlier by a raster order scan have a lower label. This is different to the behavior of the original connected component image filter which did not produce consecutive labels or impose any particular ordering. The input of this algorithm is the output of binary thresholding.

The last one is used for remapping the labels associated with the objects in an image. The input comes from the output of ConnectedComponentImageFilter. The name of this last class is itkRelabelComponentImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1RelabelComponentImageFilter.html]. The output of this method is used for BinaryDilateOperations module.

===The Problems===

The problem with this module is that I could not create a 3D model after dilation processes with given labels by using Editor module of Slicer 3. As I had the output of the dilation, I created a label map by using Editor module but what I has as an output is just a black screen labeled as 0. Therefore, I could not perform thresholding tool in Editor so could not able to change the labels and then using Model Maker module.

===Screen shots===

{|
|[[Image:LabelingTrial.png|thumb|400px|The output of LabelBinaryImagesModule and then dilation]]
|}

In the first square, the output of dilation by using BinaryDilateOperations module and label mapping by using Editor module can be seen. Second one indicates the output of LabelBinaryImages module. As mentioned in the section ''Module Description'' in this page, the background is labeled as 0 whereas the separated spheres are labeled as 1 and 2 consecutively.

As we keep on dilating the image, the spheres are still labeled as 1 and 2 and the background as 0.

==MORE INFORMATION==

===Results&Comments===

In this part, I tried to explain if we are able to use LabelBinaryImages module in morphological operations. What I have seen after using this module is that even I continue on dilation of the separated images and make them overwritten, the labels of the objects does not change. The label numbers remain the same as I had seen after I performed the algorithms in LabelBinaryImages module on the last eroded image.

What the user should be careful is that if user has the output of BinaryThresholding module as an input for BinaryDilateOperations module, the dilate value should be chosen as 255. However, if user chooses the output of LabelBinaryImages module as an input for dilation, the dilate value should be the same as label numbers. The reason is that as I have seen from my experiments, when I entered 255 for dilate value to dilate the output image of LabelBinaryImages module, there was no change in the output image. However, when I chose 1 or 2 for the dilate value, the image has been dilated by given structuring element. In my opinion, the reason is that the output of LabelBinaryImages module is formed by the label values 0, 1 and 2, whereas the output of BinaryThresholding module has 255 inside and 0 outside.

===Future work===

As a future work, it will be better to add an algorithm which makes label mapping in LabelBinaryImages module instead of using Editor module in Slicer 3. The reason is that the thresholding in Editor module and the one in LabelBinaryImages module works different so creating label maps and then coloring these maps with different labels fails by using Editor module. In 2D plane, I can see that the labels which are defined by LabelBinaryImages module by performing on the separated binary spheres after erosion processes do not change even they overwrite after many dilation processes. However, when I want to color these different labeled objects, at that point I can not achieve my goal and am not be able to see the result in 3D space.

===References===

#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G.,''Label object representation and manipulation with ITK'', 2007. [http://www.insight-journal.com/]

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T18:20:26Z

Bikekilic:

==Binary Thresholding and Labeling==

{|
|+
|__TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

The type of this module is CLI and is under the category Segmentation in Slicer 3. The name of this module is LabelBinaryImages in Slicer 3.

===Authors, Collaborators&Contact===

*Author: Bike Kilic, MSc student in Northeastern University
*Contact: kilicbike@gmail.com

===Module Description===

The purpose of this module is defining different labels in an image after morphological operations. This module performs thresholding in the first step and then implements labeling by using the information of connectedness in given input.

The input of this module is the last eroded image. And after this process, the labeled binary image is taken to dilation process. After LabelBinaryImages module, the output shows us different labeled areas. For instance, in this project, the input is eroded spheres and then after this module the output is an image with three different labeled areas:background as 0, one of the spheres as 1 and the other one as 2. The sphere with bigger area is labeled as 1.

The results can be seen in the section called ''Screen shots'' in this page.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:LabelGUI.png|thumb|280px|The GUI panel for LabelBinaryImages Module]]
|}

==DEVELOPMENT==

===Dependencies===

In this module, there are 3 ITK classes which are used.

One of them is for binary thresholding which is called itkBinaryThresholdImageFilter[http://www.itk.org/Doxygen/html/classitk_1_1BinaryThresholdImageFilter.html]. It takes two user inputs which are LowerThreshold and UpperThreshold values. The output is a binary images with 0 outside and 255 inside.

The other class which is for labeling the objects in a binary image is itkConnectedComponentImageFilter class [http://www.itk.org/Doxygen/html/classitk_1_1ConnectedComponentImageFilter.html].Each distinct object is assigned a unique label. The filter experiments with some improvements to the existing implementation, and is based on run length encoding along raster lines. The final object labels start with 1 and are consecutive. Objects that are reached earlier by a raster order scan have a lower label. This is different to the behavior of the original connected component image filter which did not produce consecutive labels or impose any particular ordering. The input of this algorithm is the output of binary thresholding.

The last one is used for remapping the labels associated with the objects in an image. The input comes from the output of ConnectedComponentImageFilter. The name of this last class is itkRelabelComponentImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1RelabelComponentImageFilter.html]. The output of this method is used for BinaryDilateOperations module.

===The Problems===

The problem with this module is that I could not create a 3D model after dilation processes with given labels by using Editor module of Slicer 3. As I had the output of the dilation, I created a label map by using Editor module but what I has as an output is just a black screen labeled as 0. Therefore, I could not perform thresholding tool in Editor so could not able to change the labels and then using Model Maker module.

===Screen shots===

{|
|[[Image:LabelingTrial.png|thumb|400px|The output of LabelBinaryImagesModule and then dilation]]
|}

In the first square, the output of dilation by using BinaryDilateOperations module and label mapping by using Editor module can be seen. Second one indicates the output of LabelBinaryImages module. As mentioned in the section ''Module Description'' in this page, the background is labeled as 0 whereas the separated spheres are labeled as 1 and 2 consecutively.

As we keep on dilating the image, the spheres are still labeled as 1 and 2 and the background as 0.

==MORE INFORMATION==

===Results&Comments===

In this part, I tried to explain if we are able to use LabelBinaryImages module in morphological operations. What I have seen after using this module is that even I continue on dilation of the separated images and make them overwritten, the labels of the objects does not change. The label numbers remain the same as I had seen after I performed the algorithms in LabelBinaryImages module on the last eroded image.

What the user should be careful is that if user has the output of BinaryThresholding module as an input for BinaryDilateOperations module, the dilate value should be chosen as 255. However, if user chooses the output of LabelBinaryImages module as an input for dilation, the dilate value should be the same as label numbers. The reason is that as I have seen from my experiments, when I entered 255 for dilate value to dilate the output image of LabelBinaryImages module, there was no change in the output image. However, when I chose 1 or 2 for the dilate value, the image has been dilated by given structuring element. In my opinion, the reason is that the output of LabelBinaryImages module is formed by the label values 0, 1 and 2, whereas the output of BinaryThresholding module has 255 inside and 0 outside.

===Future work===

As a future work, it will be better to add an algorithm which makes label mapping in LabelBinaryImages module instead of using Editor module in Slicer 3. The reason is that the thresholding in Editor module and the one in LabelBinaryImages module works different so creating label maps and then coloring these maps with different labels fails by using Editor module. In 2D plane, I can see that the labels after separation of spheres by erosion processes do not change even they overwrite after many dilation processes. However, when I want to color these different labeled objects, at that point I can not achieve my goal and am not be able to see the result in 3D space.

===References===

#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G.,''Label object representation and manipulation with ITK'', 2007. [http://www.insight-journal.com/]

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T18:12:00Z

Bikekilic:

==Binary Thresholding and Labeling==

{|
|+
|__TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

The type of this module is CLI and is under the category Segmentation in Slicer 3. The name of this module is LabelBinaryImages in Slicer 3.

===Authors, Collaborators&Contact===

*Author: Bike Kilic, MSc student in Northeastern University
*Contact: kilicbike@gmail.com

===Module Description===

The purpose of this module is defining different labels in an image after morphological operations. This module performs thresholding in the first step and then implements labeling by using the information of connectedness in given input.

The input of this module is the last eroded image. And after this process, the labeled binary image is taken to dilation process. After LabelBinaryImages module, the output shows us different labeled areas. For instance, in this project, the input is eroded spheres and then after this module the output is an image with three different labeled areas:background as 0, one of the spheres as 1 and the other one as 2. The sphere with bigger area is labeled as 1.

The results can be seen in the section called ''Screen shots'' in this page.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:LabelGUI.png|thumb|280px|The GUI panel for LabelBinaryImages Module]]
|}

==DEVELOPMENT==

===Dependencies===

In this module, there are 3 ITK classes which are used.

One of them is for binary thresholding which is called itkBinaryThresholdImageFilter[http://www.itk.org/Doxygen/html/classitk_1_1BinaryThresholdImageFilter.html]. It takes two user inputs which are LowerThreshold and UpperThreshold values. The output is a binary images with 0 outside and 255 inside.

The other class which is for labeling the objects in a binary image is itkConnectedComponentImageFilter class [http://www.itk.org/Doxygen/html/classitk_1_1ConnectedComponentImageFilter.html].Each distinct object is assigned a unique label. The filter experiments with some improvements to the existing implementation, and is based on run length encoding along raster lines. The final object labels start with 1 and are consecutive. Objects that are reached earlier by a raster order scan have a lower label. This is different to the behavior of the original connected component image filter which did not produce consecutive labels or impose any particular ordering. The input of this algorithm is the output of binary thresholding.

The last one is used for remapping the labels associated with the objects in an image. The input comes from the output of ConnectedComponentImageFilter. The name of this last class is itkRelabelComponentImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1RelabelComponentImageFilter.html]. The output of this method is used for BinaryDilateOperations module.

===The Problems===

The problem with this module is that I could not create a 3D model after dilation processes with given labels by using Editor module of Slicer 3. As I had the output of the dilation, I created a label map by using Editor module but what I has as an output is just a black screen labeled as 0. Therefore, I could not perform thresholding tool in Editor so could not able to change the labels and then using Model Maker module.

===Screen shots===

{|
|[[Image:LabelingTrial.png|thumb|400px|The output of LabelBinaryImagesModule and then dilation]]
|}

In the first square, the output of dilation by using BinaryDilateOperations module and label mapping by using Editor module can be seen. Second one indicates the output of LabelBinaryImages module. As mentioned in the section ''Module Description'' in this page, the background is labeled as 0 whereas the separated spheres are labeled as 1 and 2 consecutively.

As we keep on dilating the image, the spheres are still labeled as 1 and 2 and the background as 0.

==MORE INFORMATION==

===Results&Comments===

In this part, I tried to explain if we are able to use LabelBinaryImages module in morphological operations. What I have seen after using this module is that even I continue on dilation of the separated images and make them overwritten, the labels of the objects does not change. The label numbers remain the same as I had seen after I performed the algorithms in LabelBinaryImages module on the last eroded image.

What the user should be careful is that if user has the output of BinaryThresholding module as an input for BinaryDilateOperations module, the dilate value should be chosen as 255. However, if user chooses the output of LabelBinaryImages module as an input for dilation, the dilate value should be the same as label numbers. The reason is that as I have seen from my experiments, when I entered 255 for dilate value to dilate the output image of LabelBinaryImages module, there was no change in the output image. However, when I chose 1 or 2 for the dilate value, the image has been dilated by given structuring element. In my opinion, the reason is that the output of LabelBinaryImages module is formed by the label values 0, 1 and 2, whereas the output of BinaryThresholding module has 255 inside and 0 outside.

===Future work===

===References===

#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G.,''Label object representation and manipulation with ITK'', 2007. [http://www.insight-journal.com/]

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T18:05:56Z

Bikekilic: /* Results&Comments */

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T18:03:21Z

Bikekilic:

==Binary Thresholding and Labeling==

{|
|+
|__TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

The type of this module is CLI and is under the category Segmentation in Slicer 3. The name of this module is LabelBinaryImages in Slicer 3.

===Authors, Collaborators&Contact===

*Author: Bike Kilic, MSc student in Northeastern University
*Contact: kilicbike@gmail.com

===Module Description===

The purpose of this module is defining different labels in an image after morphological operations. This module performs thresholding in the first step and then implements labeling by using the information of connectedness in given input.

The input of this module is the last eroded image. And after this process, the labeled binary image is taken to dilation process. After LabelBinaryImages module, the output shows us different labeled areas. For instance, in this project, the input is eroded spheres and then after this module the output is an image with three different labeled areas:background as 0, one of the spheres as 1 and the other one as 2. The sphere with bigger area is labeled as 1.

The results can be seen in the section called ''Screen shots'' in this page.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:LabelGUI.png|thumb|280px|The GUI panel for LabelBinaryImages Module]]
|}

==DEVELOPMENT==

===Dependencies===

In this module, there are 3 ITK classes which are used.

One of them is for binary thresholding which is called itkBinaryThresholdImageFilter[http://www.itk.org/Doxygen/html/classitk_1_1BinaryThresholdImageFilter.html]. It takes two user inputs which are LowerThreshold and UpperThreshold values. The output is a binary images with 0 outside and 255 inside.

The other class which is for labeling the objects in a binary image is itkConnectedComponentImageFilter class [http://www.itk.org/Doxygen/html/classitk_1_1ConnectedComponentImageFilter.html].Each distinct object is assigned a unique label. The filter experiments with some improvements to the existing implementation, and is based on run length encoding along raster lines. The final object labels start with 1 and are consecutive. Objects that are reached earlier by a raster order scan have a lower label. This is different to the behavior of the original connected component image filter which did not produce consecutive labels or impose any particular ordering. The input of this algorithm is the output of binary thresholding.

The last one is used for remapping the labels associated with the objects in an image. The input comes from the output of ConnectedComponentImageFilter. The name of this last class is itkRelabelComponentImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1RelabelComponentImageFilter.html]. The output of this method is used for BinaryDilateOperations module.

===The Problems===

The problem with this module is that I could not create a 3D model after dilation processes with given labels by using Editor module of Slicer 3. As I had the output of the dilation, I created a label map by using Editor module but what I has as an output is just a black screen labeled as 0. Therefore, I could not perform thresholding tool in Editor so could not able to change the labels and then using Model Maker module.

===Screen shots===

{|
|[[Image:LabelingTrial.png|thumb|400px|The output of LabelBinaryImagesModule and then dilation]]
|}

In the first square, the output of dilation by using BinaryDilateOperations module and label mapping by using Editor module can be seen. Second one indicates the output of LabelBinaryImages module. As mentioned in the section ''Module Description'' in this page, the background is labeled as 0 whereas the separated spheres are labeled as 1 and 2 consecutively.

As we keep on dilating the image, the spheres are still labeled as 1 and 2 and the background as 0.

==MORE INFORMATION==

===Results&Comments===

In this part, I tried to explain if we are able to use LabelBinaryImages module in morphological operations. What I have seen after using this module is that even I continue on dilation of the separated images and make them overwritten, the labels of the objects does not change. The label numbers remain the same as I had seen after I performed the algorithms in LabelBinaryImages module on the last eroded image.

What the user should be careful is that if user has the output of BinaryThresholding module as an input for BinaryDilateOperations module, the dilate value should be chosen as 255. However, if user chooses the output of LabelBinaryImages module as an input for dilation, the dilate value should be the same as label numbers. The reason is that as I have seen from my experiments, when I entered 255 for dilate value to dilate the output image of LabelBinaryImages module, there was no change in the output image. However, when I chose 1 or 2 for the dilate value, the output is like as seen in ''Screen shots'' part above.

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T16:23:05Z

Bikekilic: /* Results&Comments */

==Binary Thresholding and Labeling==

{|
|+
|__TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

The type of this module is CLI and is under the category Segmentation in Slicer 3. The name of this module is LabelBinaryImages in Slicer 3.

===Authors, Collaborators&Contact===

*Author: Bike Kilic, MSc student in Northeastern University
*Contact: kilicbike@gmail.com

===Module Description===

The purpose of this module is defining different labels in an image after morphological operations. This module performs thresholding in the first step and then implements labeling by using the information of connectedness in given input.

The input of this module is the last eroded image. And after this process, the labeled binary image is taken to dilation process. After LabelBinaryImages module, the output shows us different labeled areas. For instance, in this project, the input is eroded spheres and then after this module the output is an image with three different labeled areas:background as 0, one of the spheres as 1 and the other one as 2. The sphere with bigger area is labeled as 1.

The results can be seen in the section called ''Screen shots'' in this page.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:LabelGUI.png|thumb|280px|The GUI panel for LabelBinaryImages Module]]
|}

==DEVELOPMENT==

===Dependencies===

In this module, there are 3 ITK classes which are used.

One of them is for binary thresholding which is called itkBinaryThresholdImageFilter[http://www.itk.org/Doxygen/html/classitk_1_1BinaryThresholdImageFilter.html]. It takes two user inputs which are LowerThreshold and UpperThreshold values. The output is a binary images with 0 outside and 255 inside.

The other class which is for labeling the objects in a binary image is itkConnectedComponentImageFilter class [http://www.itk.org/Doxygen/html/classitk_1_1ConnectedComponentImageFilter.html].Each distinct object is assigned a unique label. The filter experiments with some improvements to the existing implementation, and is based on run length encoding along raster lines. The final object labels start with 1 and are consecutive. Objects that are reached earlier by a raster order scan have a lower label. This is different to the behavior of the original connected component image filter which did not produce consecutive labels or impose any particular ordering. The input of this algorithm is the output of binary thresholding.

The last one is used for remapping the labels associated with the objects in an image. The input comes from the output of ConnectedComponentImageFilter. The name of this last class is itkRelabelComponentImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1RelabelComponentImageFilter.html]. The output of this method is used for BinaryDilateOperations module.

===The Problems===

The problem with this module is that I could not create a 3D model after dilation processes with given labels by using Editor module of Slicer 3. As I had the output of the dilation, I created a label map by using Editor module but what I has as an output is just a black screen labeled as 0. Therefore, I could not perform thresholding tool in Editor so could not able to change the labels and then using Model Maker module.

===Screen shots===

{|
|[[Image:LabelingTrial.png|thumb|400px|The output of LabelBinaryImagesModule and then dilation]]
|}

In the first square, the output of dilation by using BinaryDilateOperations module and label mapping by using Editor module can be seen. Second one indicates the output of LabelBinaryImages module. As mentioned in the section ''Module Description'' in this page, the background is labeled as 0 whereas the separated spheres are labeled as 1 and 2 consecutively.

As we keep on dilating the image, the spheres are still labeled as 1 and 2 and the background as 0.

==MORE INFORMATION==

===Results&Comments===

In this part, I tried to explain if we are able to use LabelBinaryImages module in morphological operations. What I have seen after using this module is that even I continue on dilation of the separated images and make them overwritten, the labels of the objects does not change. The label numbers remain the same as I had seen after I performed the algorithms in LabelBinaryImages module on the last eroded image.

What the user should be careful is that if user has the output of BinaryThresholding module as an input for BinaryDilateOperations module, the dilate value should be chosen as 255. However, if user chooses the output of LabelBinaryImages module as an input for dilation, the dilate value should be the same as label numbers. The reason is that as I have seen from my experiments, even I perform dilation on the output image of LabelBinaryImages module

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T16:21:18Z

Bikekilic:

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T16:14:44Z

Bikekilic: /* Screen shots */

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T16:12:56Z

Bikekilic: /* Screen shots */

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T16:08:37Z

Bikekilic: /* Screen shots */

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T16:07:01Z

Bikekilic:

File:LabelingTrial.png

2008-08-28T16:03:15Z

Bikekilic:

Slicer3:Module:BinaryDilateOperations-Documentation

2008-08-28T16:01:18Z

Bikekilic: /* Screen shots */

==Binary Dilate Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing dilation on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform erosion method in order to make two different labeled separate objects closer to each other after erosion. At the end, we want to see these objects touched but not overwritten.

This method uses a structuring element in order to cover the object border with given foreground value. It grows the object with this structuring element. For this project, the structuring element is neighborhood structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is neighborhood structuring element with radius 2. It took 7 iterations in order to get closer images with different colors.

The input of this module is the output of BinaryErodeOperations module at the beginning. For the following iterations, the input is the dilated binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelDilate.PNG|thumb|280px|The GUI panel for BinaryDilateOperations Module after binary erosion]]
|}

In this case, the eroded image which is the input for BinaryDilateOperations Module has the pixel value 255 inside and 0 outside.

==DEVELOPMENT==

===Dependencies===

The BinaryDilateOperations Module uses four ITK classes. One of them is for binary erosion, which is called itkBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryDilateImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for dilation the neighborhood structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of dilation depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after dilation. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of neighborhood structuring element. Therefore, neighborhood structuring element was used in BinaryDilateOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive.

Another problem which was encountered with is stemmed from being unable to use labeled images in dilation. Since the binary images are used in dilation, after more than 7 iterations, the spheres become overwritten again and so they can not be labeled differently at the end of the dilation if I use Editor module. Therefore, I lose the connectedness information between spheres which makes me unable to differentiate the different objects. However, even they become overwritten, the labels remain the same as I had after performing LabelBinaryImages module on the last eroded image( background is labeled as 0, the first sphere is labeled as 1 and the second one is labeled as 2).

The results can be observed as seen in the ''Screen shots'' section.

===Screen shots===

{|
|[[Image:Dilate.png|thumb|280px|Binary Dilate Iterations with Neighborhood structuring element with radius 2]]
|[[Image:DilateWithBall.png|thumb|400px|Binary Dilate with Ball Structuring element with radius 5]]
|[[Image:DilateCross.png|thumb|400px|Binary Dilate with Cross Structuring element whose radius is 10]]
|}

Although the above figure shows three steps in dilation, it took 7 steps in order to make them be closer to each other. The neighborhood structuring element with radius 2 was used in dilation process.
In the second figure, the dilation result with ball structuring element which has the radius 5 can be seen. In comparison to the previous case, it took 5 steps in order to get the last dilated image.
The third figure shows the dilation result with cross structuring element whose radius is 10. After 25 iterations I get the last dilated image. In the case of using cross structuring element,the shape of the image is damaged more than the dilation with neighborhood and ball structuring elements.

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

On the other hand, although BinaryDilateImageFilter class has been used for this project, another ITK class which is called itkFastIncrementalBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1FastIncrementalBinaryDilateImageFilter.html] can be used in order to make the dilation faster. I did not use that one because when I make it faster the spheres become overwritten, which I don't want to have in the conclusion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Architecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:BinaryDilateOperations-Documentation

2008-08-28T15:56:28Z

Bikekilic: /* Screen shots */

==Binary Dilate Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing dilation on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform erosion method in order to make two different labeled separate objects closer to each other after erosion. At the end, we want to see these objects touched but not overwritten.

This method uses a structuring element in order to cover the object border with given foreground value. It grows the object with this structuring element. For this project, the structuring element is neighborhood structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is neighborhood structuring element with radius 2. It took 7 iterations in order to get closer images with different colors.

The input of this module is the output of BinaryErodeOperations module at the beginning. For the following iterations, the input is the dilated binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelDilate.PNG|thumb|280px|The GUI panel for BinaryDilateOperations Module after binary erosion]]
|}

In this case, the eroded image which is the input for BinaryDilateOperations Module has the pixel value 255 inside and 0 outside.

==DEVELOPMENT==

===Dependencies===

The BinaryDilateOperations Module uses four ITK classes. One of them is for binary erosion, which is called itkBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryDilateImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for dilation the neighborhood structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of dilation depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after dilation. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of neighborhood structuring element. Therefore, neighborhood structuring element was used in BinaryDilateOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive.

Another problem which was encountered with is stemmed from being unable to use labeled images in dilation. Since the binary images are used in dilation, after more than 7 iterations, the spheres become overwritten again and so they can not be labeled differently at the end of the dilation if I use Editor module. Therefore, I lose the connectedness information between spheres which makes me unable to differentiate the different objects. However, even they become overwritten, the labels remain the same as I had after performing LabelBinaryImages module on the last eroded image( background is labeled as 0, the first sphere is labeled as 1 and the second one is labeled as 2).

The results can be observed as seen in the ''Screen shots'' section.

===Screen shots===

{|
|[[Image:Dilate.png|thumb|280px|Binary Dilate Iterations with Neighborhood structuring element with radius 2]]
|[[Image:DilateWithBall.png|thumb|400px|Binary Dilate with Ball Structuring element with radius 5]]
|[[Image:DilateCross.png|thumb|400px|Binary Dilate with Cross Structuring element whose radius is 10]]
|}

Although the above figure shows three steps in dilation, it took 7 steps in order to make them be closer to each other. The neighborhood structuring element with radius 2 was used in dilation process.
In the second figure, the dilation result with ball structuring element which has the radius 5 can be seen. In comparison to the previous case, it took 5 steps in order to get the last dilated image.
The third figure shows the dilation result with cross structuring element whose radius is 10. After

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

On the other hand, although BinaryDilateImageFilter class has been used for this project, another ITK class which is called itkFastIncrementalBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1FastIncrementalBinaryDilateImageFilter.html] can be used in order to make the dilation faster. I did not use that one because when I make it faster the spheres become overwritten, which I don't want to have in the conclusion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Architecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:BinaryDilateOperations-Documentation

2008-08-28T15:56:06Z

Bikekilic: /* Screen shots */

==Binary Dilate Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing dilation on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform erosion method in order to make two different labeled separate objects closer to each other after erosion. At the end, we want to see these objects touched but not overwritten.

This method uses a structuring element in order to cover the object border with given foreground value. It grows the object with this structuring element. For this project, the structuring element is neighborhood structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is neighborhood structuring element with radius 2. It took 7 iterations in order to get closer images with different colors.

The input of this module is the output of BinaryErodeOperations module at the beginning. For the following iterations, the input is the dilated binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelDilate.PNG|thumb|280px|The GUI panel for BinaryDilateOperations Module after binary erosion]]
|}

In this case, the eroded image which is the input for BinaryDilateOperations Module has the pixel value 255 inside and 0 outside.

==DEVELOPMENT==

===Dependencies===

The BinaryDilateOperations Module uses four ITK classes. One of them is for binary erosion, which is called itkBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryDilateImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for dilation the neighborhood structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of dilation depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after dilation. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of neighborhood structuring element. Therefore, neighborhood structuring element was used in BinaryDilateOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive.

Another problem which was encountered with is stemmed from being unable to use labeled images in dilation. Since the binary images are used in dilation, after more than 7 iterations, the spheres become overwritten again and so they can not be labeled differently at the end of the dilation if I use Editor module. Therefore, I lose the connectedness information between spheres which makes me unable to differentiate the different objects. However, even they become overwritten, the labels remain the same as I had after performing LabelBinaryImages module on the last eroded image( background is labeled as 0, the first sphere is labeled as 1 and the second one is labeled as 2).

The results can be observed as seen in the ''Screen shots'' section.

===Screen shots===

{|
|[[Image:Dilate.png|thumb|280px|Binary Dilate Iterations with Neighborhood structuring element with radius 2]]
|[[Image:DilateWithBall.png|thumb|280px|Binary Dilate with Ball Structuring element with radius 5]]
|[[Image:DilateCross.png|thumb|300px|Binary Dilate with Cross Structuring element whose radius is 10]]
|}

Although the above figure shows three steps in dilation, it took 7 steps in order to make them be closer to each other. The neighborhood structuring element with radius 2 was used in dilation process.
In the second figure, the dilation result with ball structuring element which has the radius 5 can be seen. In comparison to the previous case, it took 5 steps in order to get the last dilated image.
The third figure shows the dilation result with cross structuring element whose radius is 10. After

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

On the other hand, although BinaryDilateImageFilter class has been used for this project, another ITK class which is called itkFastIncrementalBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1FastIncrementalBinaryDilateImageFilter.html] can be used in order to make the dilation faster. I did not use that one because when I make it faster the spheres become overwritten, which I don't want to have in the conclusion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Architecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

File:DilateCross.png

2008-08-28T15:55:09Z

Bikekilic:

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T15:44:24Z

Bikekilic:

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T15:40:06Z

Bikekilic: /* Dependencies */

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T15:38:35Z

Bikekilic:

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T15:33:18Z

Bikekilic:

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T15:27:29Z

Bikekilic: /* Quick Tour of Features and Use */

File:LabelGUI.png

2008-08-28T15:25:44Z

Bikekilic:

File:GUIPanelLabel.PNG

2008-08-28T15:18:43Z

Bikekilic:

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T15:18:20Z

Bikekilic:

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T15:16:34Z

Bikekilic: /* Module Description */

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T15:16:05Z

Bikekilic: /* Module Description */

Slicer3:Module:LabelBinaryImages-Documentation

2008-08-28T15:15:54Z

Bikekilic: New page: ==Binary Thresholding and Labeling== {| |+ |__TOC__ |} ==GENERAL INFORMATION== ===Module Type&Category=== The type of this module is CLI and is under the category Segmentation in Slice...

Slicer3:Module:BinaryDilateOperations-Documentation

2008-08-28T15:06:29Z

Bikekilic: /* Screen shots */

==Binary Dilate Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing dilation on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform erosion method in order to make two different labeled separate objects closer to each other after erosion. At the end, we want to see these objects touched but not overwritten.

This method uses a structuring element in order to cover the object border with given foreground value. It grows the object with this structuring element. For this project, the structuring element is neighborhood structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is neighborhood structuring element with radius 2. It took 7 iterations in order to get closer images with different colors.

The input of this module is the output of BinaryErodeOperations module at the beginning. For the following iterations, the input is the dilated binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelDilate.PNG|thumb|280px|The GUI panel for BinaryDilateOperations Module after binary erosion]]
|}

In this case, the eroded image which is the input for BinaryDilateOperations Module has the pixel value 255 inside and 0 outside.

==DEVELOPMENT==

===Dependencies===

The BinaryDilateOperations Module uses four ITK classes. One of them is for binary erosion, which is called itkBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryDilateImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for dilation the neighborhood structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of dilation depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after dilation. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of neighborhood structuring element. Therefore, neighborhood structuring element was used in BinaryDilateOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive.

Another problem which was encountered with is stemmed from being unable to use labeled images in dilation. Since the binary images are used in dilation, after more than 7 iterations, the spheres become overwritten again and so they can not be labeled differently at the end of the dilation if I use Editor module. Therefore, I lose the connectedness information between spheres which makes me unable to differentiate the different objects. However, even they become overwritten, the labels remain the same as I had after performing LabelBinaryImages module on the last eroded image( background is labeled as 0, the first sphere is labeled as 1 and the second one is labeled as 2).

The results can be observed as seen in the ''Screen shots'' section.

===Screen shots===

{|
|[[Image:Dilate.png|thumb|280px|Binary Dilate Iterations with Neighborhood structuring element with radius 2]]
|[[Image:DilateWithBall.png|thumb|280px|Binary Dilate with Ball Structuring element with radius 5]]
|}

Although the above figure shows three steps in dilation, it took 7 steps in order to make them be closer to each other. The neighborhood structuring element with radius 2 was used in dilation process.
In the second figure, the dilation result with ball structuring element which has the radius 5 can be seen. In comparison to the previous case, it took 5 steps in order to get the last dilated image.
The third figure shows the dilation result with cross structuring element whose radius is 10. After

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

On the other hand, although BinaryDilateImageFilter class has been used for this project, another ITK class which is called itkFastIncrementalBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1FastIncrementalBinaryDilateImageFilter.html] can be used in order to make the dilation faster. I did not use that one because when I make it faster the spheres become overwritten, which I don't want to have in the conclusion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Architecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:BinaryDilateOperations-Documentation

2008-08-28T15:00:55Z

Bikekilic: /* The Problems */

==Binary Dilate Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing dilation on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform erosion method in order to make two different labeled separate objects closer to each other after erosion. At the end, we want to see these objects touched but not overwritten.

This method uses a structuring element in order to cover the object border with given foreground value. It grows the object with this structuring element. For this project, the structuring element is neighborhood structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is neighborhood structuring element with radius 2. It took 7 iterations in order to get closer images with different colors.

The input of this module is the output of BinaryErodeOperations module at the beginning. For the following iterations, the input is the dilated binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelDilate.PNG|thumb|280px|The GUI panel for BinaryDilateOperations Module after binary erosion]]
|}

In this case, the eroded image which is the input for BinaryDilateOperations Module has the pixel value 255 inside and 0 outside.

==DEVELOPMENT==

===Dependencies===

The BinaryDilateOperations Module uses four ITK classes. One of them is for binary erosion, which is called itkBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryDilateImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for dilation the neighborhood structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of dilation depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after dilation. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of neighborhood structuring element. Therefore, neighborhood structuring element was used in BinaryDilateOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive.

Another problem which was encountered with is stemmed from being unable to use labeled images in dilation. Since the binary images are used in dilation, after more than 7 iterations, the spheres become overwritten again and so they can not be labeled differently at the end of the dilation if I use Editor module. Therefore, I lose the connectedness information between spheres which makes me unable to differentiate the different objects. However, even they become overwritten, the labels remain the same as I had after performing LabelBinaryImages module on the last eroded image( background is labeled as 0, the first sphere is labeled as 1 and the second one is labeled as 2).

The results can be observed as seen in the ''Screen shots'' section.

===Screen shots===

{|
|[[Image:Dilate.png|thumb|280px|Binary Dilate Iterations with Neighborhood structuring element with radius 2]]
|[[Image:DilateWithBall.png|thumb|280px|Binary Dilate with Ball Structuring element with radius 5]]
|}

Although the above figure shows three steps in dilation, it took 7 steps in order to make them be closer to each other. The neighborhood structuring element with radius 2 was used in dilation process.

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

On the other hand, although BinaryDilateImageFilter class has been used for this project, another ITK class which is called itkFastIncrementalBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1FastIncrementalBinaryDilateImageFilter.html] can be used in order to make the dilation faster. I did not use that one because when I make it faster the spheres become overwritten, which I don't want to have in the conclusion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Architecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:BinaryDilateOperations-Documentation

2008-08-28T14:20:31Z

Bikekilic: /* Screen shots */

==Binary Dilate Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing dilation on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform erosion method in order to make two different labeled separate objects closer to each other after erosion. At the end, we want to see these objects touched but not overwritten.

This method uses a structuring element in order to cover the object border with given foreground value. It grows the object with this structuring element. For this project, the structuring element is neighborhood structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is neighborhood structuring element with radius 2. It took 7 iterations in order to get closer images with different colors.

The input of this module is the output of BinaryErodeOperations module at the beginning. For the following iterations, the input is the dilated binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelDilate.PNG|thumb|280px|The GUI panel for BinaryDilateOperations Module after binary erosion]]
|}

In this case, the eroded image which is the input for BinaryDilateOperations Module has the pixel value 255 inside and 0 outside.

==DEVELOPMENT==

===Dependencies===

The BinaryDilateOperations Module uses four ITK classes. One of them is for binary erosion, which is called itkBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryDilateImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for dilation the neighborhood structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of dilation depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after dilation. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of neighborhood structuring element. Therefore, neighborhood structuring element was used in BinaryDilateOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive.

Another problem which was encountered with is stemmed from being unable to use labeled images in dilation. Since the binary images are used in dilation, after more than 7 iterations, the spheres become overwritten again and so they can not be labeled differently at the end of the dilation. Therefore, I lose the connectedness information between spheres which makes me unable to differentiate the different objects.

===Screen shots===

{|
|[[Image:Dilate.png|thumb|280px|Binary Dilate Iterations with Neighborhood structuring element with radius 2]]
|[[Image:DilateWithBall.png|thumb|280px|Binary Dilate with Ball Structuring element with radius 5]]
|}

Although the above figure shows three steps in dilation, it took 7 steps in order to make them be closer to each other. The neighborhood structuring element with radius 2 was used in dilation process.

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

On the other hand, although BinaryDilateImageFilter class has been used for this project, another ITK class which is called itkFastIncrementalBinaryDilateImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1FastIncrementalBinaryDilateImageFilter.html] can be used in order to make the dilation faster. I did not use that one because when I make it faster the spheres become overwritten, which I don't want to have in the conclusion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Architecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

File:DilateWithBall.png

2008-08-28T14:19:17Z

Bikekilic: Dilation with ball structuring element which has the radius 5.

Dilation with ball structuring element which has the radius 5.

Slicer3:Module:BinaryErodeOperations-Documentation

2008-08-27T20:27:45Z

Bikekilic: /* Screen shots */

==Binary Erode Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing erosion on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform erosion method in order to make the two different objects separate in a given image. After separating them, the next step will be creating a label map and changing the labels to specify different regions.

This method uses a structuring element in order to cover the object border with given foreground value. It shrinks the object with this structuring element. For this project, the structuring element is ball structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is ball structuring element with radius 5. It took 7 iterations in order to get the desired output before creating different labels.

The input of this module is the output of the BinaryThresholding( or LabelBinaryImages) module at the beginning. For the following iterations, the input is the eroded binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelErode.PNG|thumb|280px|The GUI panel for BinaryErodeOperations Module after binary thresholding]]
|[[Image:GUIPanelErodeLabel.PNG|thumb|280px|The GUI panel for BinaryErodeOperations Module after LabelBinaryImages Module]]
|}

As seen above, the first figure shows the GUI panel if the user implements BinaryThresholding Module before erosion, whereas the second one shows the GUI panel of BinaryErodeOperations module in the case of using LabelBinaryImages module before erosion.

==DEVELOPMENT==

===Dependencies===

The BinaryErodeOperations Module uses four ITK classes. One of them is for binary erosion, which is called itkBinaryErodeImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryErodeImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for erosion the ball structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of erosion depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after erosion. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of ball structuring element. Therefore, ball structuring element was used in BinaryErodeOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive. The difference between the performance of structuring elements can be seen in ''Screen shots'' section.

In addition to the problems, I encountered with a problem when I used binary labeled image as an input to BinaryErodeOperations Module. The problem is that I could not create a label map by using Editor Module in Slicer 3. The reason may be due to the output I have after LabelBinaryImages Module. The inside pixel is 1 and the outside pixel is 0 for the binary labeled images. The erosion worked well these images but at the end of the erosion, I could not define two different labels by using Editor Module. Therefore, without having different labels, I could not continue on dilation because in dilation my aim is to see different labeled images touched each other but not overwritten after several steps. However, the failure in creating labels is the reason of not using the binary labeled images for my project. The detailed information is given in the section of ''the Problems'' in [[Slicer3:Module:LabelBinaryImages-Documentation|LabelBinaryImages]].

===Screen shots===

{|
|[[Image:Erode.png|thumb|280px|Binary Erode Iterations]]
|[[Image:AfterLabelChange.PNG|thumb|280px|Creating two different labels after erosion processes]]
|[[Image:AfterModelMaker.PNG|thumb|280px|Creating 3D model of separated and different labeled binary images by using Model Maker Module]]
|[[Image:Erosion1.png|thumb|300px|The results of erosion;neighborhood, ball, cross in order]]
|}

Although the first figure shows four steps in erosion, it took 7 steps in order to make them totally separate. The ball structuring element with radius 5 was used in erosion process.
The last figure shows the different results by using three different structuring elements:neighborhood, ball, cross in order. It can be observed that the shape is better when ball structuring element is used compared to the cases of using either neighborhood or cross structuring element.

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Arcitecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:BinaryErodeOperations-Documentation

2008-08-27T20:27:30Z

Bikekilic: /* Screen shots */

==Binary Erode Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing erosion on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform erosion method in order to make the two different objects separate in a given image. After separating them, the next step will be creating a label map and changing the labels to specify different regions.

This method uses a structuring element in order to cover the object border with given foreground value. It shrinks the object with this structuring element. For this project, the structuring element is ball structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is ball structuring element with radius 5. It took 7 iterations in order to get the desired output before creating different labels.

The input of this module is the output of the BinaryThresholding( or LabelBinaryImages) module at the beginning. For the following iterations, the input is the eroded binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelErode.PNG|thumb|280px|The GUI panel for BinaryErodeOperations Module after binary thresholding]]
|[[Image:GUIPanelErodeLabel.PNG|thumb|280px|The GUI panel for BinaryErodeOperations Module after LabelBinaryImages Module]]
|}

As seen above, the first figure shows the GUI panel if the user implements BinaryThresholding Module before erosion, whereas the second one shows the GUI panel of BinaryErodeOperations module in the case of using LabelBinaryImages module before erosion.

==DEVELOPMENT==

===Dependencies===

The BinaryErodeOperations Module uses four ITK classes. One of them is for binary erosion, which is called itkBinaryErodeImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryErodeImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for erosion the ball structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of erosion depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after erosion. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of ball structuring element. Therefore, ball structuring element was used in BinaryErodeOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive. The difference between the performance of structuring elements can be seen in ''Screen shots'' section.

In addition to the problems, I encountered with a problem when I used binary labeled image as an input to BinaryErodeOperations Module. The problem is that I could not create a label map by using Editor Module in Slicer 3. The reason may be due to the output I have after LabelBinaryImages Module. The inside pixel is 1 and the outside pixel is 0 for the binary labeled images. The erosion worked well these images but at the end of the erosion, I could not define two different labels by using Editor Module. Therefore, without having different labels, I could not continue on dilation because in dilation my aim is to see different labeled images touched each other but not overwritten after several steps. However, the failure in creating labels is the reason of not using the binary labeled images for my project. The detailed information is given in the section of ''the Problems'' in [[Slicer3:Module:LabelBinaryImages-Documentation|LabelBinaryImages]].

===Screen shots===

{|
|[[Image:Erode.png|thumb|280px|Binary Erode Iterations]]
|[[Image:AfterLabelChange.PNG|thumb|280px|Creating two different labels after erosion processes]]
|[[Image:AfterModelMaker.PNG|thumb|280px|Creating 3D model of separated and different labeled binary images by using Model Maker Module]]
|[[Image:Erosion1.png|thumb|300px|The results of erosion;neighborhood, ball, cross in order]]
|}

Although the first figure shows four steps in erosion, it took 7 steps in order to make them totally separate. The ball structuring element with radius 5 was used in erosion process.
The last figure shows the different results by using three different structuring elements:neighborhood, ball, cross in order. It can be observed that the shape is better when ball structuring element is used compared to cases of using either neighborhood or cross structuring element.

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Arcitecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]

Slicer3:Module:BinaryErodeOperations-Documentation

2008-08-27T20:25:18Z

Bikekilic: /* Screen shots */

==Binary Erode Operations==

{|
|+
| __TOC__
|}

==GENERAL INFORMATION==

===Module Type&Category===

This module is for performing erosion on binary images. The type of this module is CLI and is in the category of Segmentation of Slicer 3.

===Authors, Collaborators & Contact===

* Author: Bike Kilic, MSc student in Northeastern University
* Contact: kilicbike@gmail.com

===Module Description===

This module aims to perform erosion method in order to make the two different objects separate in a given image. After separating them, the next step will be creating a label map and changing the labels to specify different regions.

This method uses a structuring element in order to cover the object border with given foreground value. It shrinks the object with this structuring element. For this project, the structuring element is ball structuring element with a radius size which is defined by the user.

For example, the results given in ''Screen shots'' part, the structuring element is ball structuring element with radius 5. It took 7 iterations in order to get the desired output before creating different labels.

The input of this module is the output of the BinaryThresholding( or LabelBinaryImages) module at the beginning. For the following iterations, the input is the eroded binary image from the previous iteration.

==USAGE==

===Quick Tour of Features and Use===

{|
|[[Image:GUIPanelErode.PNG|thumb|280px|The GUI panel for BinaryErodeOperations Module after binary thresholding]]
|[[Image:GUIPanelErodeLabel.PNG|thumb|280px|The GUI panel for BinaryErodeOperations Module after LabelBinaryImages Module]]
|}

As seen above, the first figure shows the GUI panel if the user implements BinaryThresholding Module before erosion, whereas the second one shows the GUI panel of BinaryErodeOperations module in the case of using LabelBinaryImages module before erosion.

==DEVELOPMENT==

===Dependencies===

The BinaryErodeOperations Module uses four ITK classes. One of them is for binary erosion, which is called itkBinaryErodeImageFilter [http://www.itk.org/Doxygen/html/classitk_1_1BinaryErodeImageFilter.html]. Three of ITK classes which are included are used to create structuring elements. For ball structuring element, itkBinaryBallStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryBallStructuringElement.html]; for cross structuring element itkBinaryCrossStructuringElement[http://www.itk.org/Doxygen/html/classitk_1_1BinaryCrossStructuringElement.html] and for neighborhood structuring element itkNeighborhood[http://www.itk.org/Doxygen/html/classitk_1_1Neighborhood.html] are added.

In this project, for erosion the ball structuring element has been chosen.

===The Problems===

In this module, the problems were stemmed from the choices of structuring element, the radius size of them. The performance of erosion depends on the properties of structuring element. The reason is that sometimes the shape of the binary image can not be preserved after erosion. For instance, the spheres data I used became had like a square shape if I used other structuring elements instead of ball structuring element. Therefore, ball structuring element was used in BinaryErodeOperations Module. However, if user wants to try others, the default value for structuring element should be changed from the code file. I could not also do it interactive. The difference between the performance of structuring elements can be seen in ''Screen shots'' section.

In addition to the problems, I encountered with a problem when I used binary labeled image as an input to BinaryErodeOperations Module. The problem is that I could not create a label map by using Editor Module in Slicer 3. The reason may be due to the output I have after LabelBinaryImages Module. The inside pixel is 1 and the outside pixel is 0 for the binary labeled images. The erosion worked well these images but at the end of the erosion, I could not define two different labels by using Editor Module. Therefore, without having different labels, I could not continue on dilation because in dilation my aim is to see different labeled images touched each other but not overwritten after several steps. However, the failure in creating labels is the reason of not using the binary labeled images for my project. The detailed information is given in the section of ''the Problems'' in [[Slicer3:Module:LabelBinaryImages-Documentation|LabelBinaryImages]].

===Screen shots===

{|
|[[Image:Erode.png|thumb|280px|Binary Erode Iterations]]
|[[Image:AfterLabelChange.PNG|thumb|280px|Creating two different labels after erosion processes]]
|[[Image:AfterModelMaker.PNG|thumb|280px|Creating 3D model of separated and different labeled binary images by using Model Maker Module]]
|[[Image:Erosion1.png|thumb|300px|The results of erosion;neighborhood, ball, cross in order]]
|}

Although the first figure shows four steps in erosion, it took 7 steps in order to make them totally separate. The ball structuring element with radius 5 was used in erosion process.
The last figure shows the different results by using three different structuring elements:neighborhood, ball, cross in order.

==MORE INFORMATION==

===Future work===

In this module, what we should improve is using effective structuring element. ITK has four different structuring elements which I have tried three of. A structuring element which stores an information of the shape of the whole image may be effective in this goal. On the other hand, if the data is noisy, any smoothing or enhancement method should be performed before erosion.

===References===

#Gu L., Seminar Series on Advanced Medical Image Processing, ''Mathematical Morphology(1)'', 2002.
#Ibanez L.,ITK Architecture, ''ITK Basic Filters'', 2006.
#Ibanez L.,ITK Arcitecture, ''ITK Segmentation Methods'', 2000.
#Ibanez L., Schroeder W.,Ng L. & Cates J., The ITK Software Guide Second Edition Updated for ITK Version 2.4, 2005.
#Lehmann G., Binary Morphological closing and opening image filters, 2006.
#Lehmann G., Improving features and performance of binary erode and dilate filters, 2006.
#Vleeschouwer C., Morphology, 2007.[http://www.tele.ucl.ac.be/~devlees/]