Slicer Wiki - User contributions [en]

Documentation/Nightly/Extensions/ArduinoController

2022-04-11T14:56:11Z

Pzaffino: /* Arduino Pedalboard */

<noinclude>{{documentation/versioncheck}}
</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/ArduinoController|ArduinoController]] 
Author: Paolo Zaffino, Magna Graecia University of Catanzaro - Italy 
Contributor1: Domenico Leuzzi, Magna Graecia University of Catanzaro - Italy 
Contributor2: Virgilio Sabatino, Magna Graecia University of Catanzaro - Italy 
Contributor3: Andras Lasso - PerkLab, Queen's 
Contributor4: Maria Francesca Spadea, Magna Graecia University of Catanzaro - Italy 
Contact: Paolo Zaffino, p.zaffino@unicz.it 
{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}

1. Arduino Connect: this module allows to connect Slicer and Arduino board. This will be use to build other modules and applications. The integration of the data coming from the board strongly relies on vtkMRMLScriptedModuleNode in order to notify to the entire system the arrival of a new data.

2. Arduino Motion Sensor: Module for 3D Slicer that allows to control the Slice View through gestures using an inexpensive motion sensor compatible with Arduino. (Module Icon made by Freepik from www.flaticon.com)

Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

If you use this extension please cite the following article:

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.
SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.
Bioengineering. 2020 Sep;7(3):109.

Journal link: https://www.mdpi.com/2306-5354/7/3/109


{{documentation/{{documentation/version}}/module-section|Use Cases}}

===Arduino Connect===
Users wants to connect, receive and transmit data from/to Arduino. Connection parameters can be set according to user environment.

A sender and a monitor/plotter of data coming from the board are also available without the need of writing code.

{|
|[[Image:ArduinoController_screenshot.png|thumb|340px|Arduino Connect module]]
|}

===Arduino Motion Sensor===
Users want to control the Slice View module by using gestures detected via dedicated Arduino sensor.

 {{documentation/{{documentation/version}}/module-section|Tutorials}}

===Arduino Connect===
1. Connect Arduino to the system (user has to take care of Arduino code side).
2. Click "Detect device(s)" button
3. Set port and other connection parameters according to PC environment
4. Click "Connect" button
5. Send receive data (via GUI and/or Python code)

===Arduino Motion Sensor===
1. Connect PAJ7620 to “Arduino”. To do this simply connect:

Vin to 3.3 V;

Gnd to Gnd;

SCL to SCL;

SDA to SDA.
2. Connect “Arduino” to the USB port of pc and and run “paj7620_9gestures” code on “arduino IDE”.

The code can be found here: “https://github.com/Seeed-Studio/Gesture_PAJ7620”.

3. Connect “Arduino” to “3D Slicer” using “Slicer Arduino Controller” extension.

4. “ArduinoMotionSensor” extension in “3D Slicer”, choose the desidered offset variation and press “Start Motion” button.

5. Use the gestures for controlling view settings by exploiting the following options:

“Left” = Select Previous View

“Right” = Select Next View

“Up” = Increase Offset

“Down” = Decrease Offset

“Forward” = Enable Full Screen

“Backward” = Disable Full Screen

===Arduino Pedalboard===

Module for 3D Slicer that allows to control the Slice View through a pedealboard connected via Arduino.

1. Connect buttons to Arduino as described in the figure below:

[[File:ArduinoPedalBoarad_schematic.png|500px]]

2. Load in Arduino board the code hosted into the folder "ArduinoCode/ArduinoPedalboard".

3. Connect “Arduino” to “3D Slicer” using “Slicer Arduino Controller” extension.

4. On “ArduinoPedalBoard” extension in “3D Slicer”, choose the desidered tasks and offset variation and press “Start” button.

5. Use the pedalboard for controlling view settings.

{{documentation/{{documentation/version}}/module-section|Panels and their use}}

Simple panel to connect Arduino and to interact with it.

{|
|
|[[Image:ArduinoController_UI_screenshot.png|thumb|280px|Arduino Connection Module UI]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.

SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.

Bioengineering. 2020 Sep;7(3):109.
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

Source code:
https://github.com/pzaffino/SlicerArduinoController


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

Documentation/Nightly/Extensions/ArduinoController

2022-04-11T14:55:16Z

Pzaffino: /* Arduino Pedalboard */

<noinclude>{{documentation/versioncheck}}
</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/ArduinoController|ArduinoController]] 
Author: Paolo Zaffino, Magna Graecia University of Catanzaro - Italy 
Contributor1: Domenico Leuzzi, Magna Graecia University of Catanzaro - Italy 
Contributor2: Virgilio Sabatino, Magna Graecia University of Catanzaro - Italy 
Contributor3: Andras Lasso - PerkLab, Queen's 
Contributor4: Maria Francesca Spadea, Magna Graecia University of Catanzaro - Italy 
Contact: Paolo Zaffino, p.zaffino@unicz.it 
{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}

1. Arduino Connect: this module allows to connect Slicer and Arduino board. This will be use to build other modules and applications. The integration of the data coming from the board strongly relies on vtkMRMLScriptedModuleNode in order to notify to the entire system the arrival of a new data.

2. Arduino Motion Sensor: Module for 3D Slicer that allows to control the Slice View through gestures using an inexpensive motion sensor compatible with Arduino. (Module Icon made by Freepik from www.flaticon.com)

Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

If you use this extension please cite the following article:

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.
SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.
Bioengineering. 2020 Sep;7(3):109.

Journal link: https://www.mdpi.com/2306-5354/7/3/109


{{documentation/{{documentation/version}}/module-section|Use Cases}}

===Arduino Connect===
Users wants to connect, receive and transmit data from/to Arduino. Connection parameters can be set according to user environment.

A sender and a monitor/plotter of data coming from the board are also available without the need of writing code.

{|
|[[Image:ArduinoController_screenshot.png|thumb|340px|Arduino Connect module]]
|}

===Arduino Motion Sensor===
Users want to control the Slice View module by using gestures detected via dedicated Arduino sensor.

 {{documentation/{{documentation/version}}/module-section|Tutorials}}

===Arduino Connect===
1. Connect Arduino to the system (user has to take care of Arduino code side).
2. Click "Detect device(s)" button
3. Set port and other connection parameters according to PC environment
4. Click "Connect" button
5. Send receive data (via GUI and/or Python code)

===Arduino Motion Sensor===
1. Connect PAJ7620 to “Arduino”. To do this simply connect:

Vin to 3.3 V;

Gnd to Gnd;

SCL to SCL;

SDA to SDA.
2. Connect “Arduino” to the USB port of pc and and run “paj7620_9gestures” code on “arduino IDE”.

The code can be found here: “https://github.com/Seeed-Studio/Gesture_PAJ7620”.

3. Connect “Arduino” to “3D Slicer” using “Slicer Arduino Controller” extension.

4. “ArduinoMotionSensor” extension in “3D Slicer”, choose the desidered offset variation and press “Start Motion” button.

5. Use the gestures for controlling view settings by exploiting the following options:

“Left” = Select Previous View

“Right” = Select Next View

“Up” = Increase Offset

“Down” = Decrease Offset

“Forward” = Enable Full Screen

“Backward” = Disable Full Screen

===Arduino Pedalboard===

Module for 3D Slicer that allows to control the Slice View through a pedealboard connected via Arduino.

1. Connect buttons to Arduino as described in the figure below:

[[File:ArduinoPedalBoarad_schematic.png]]

2. Load in Arduino board the code hosted into the folder "ArduinoCode/ArduinoPedalboard".

3. Connect “Arduino” to “3D Slicer” using “Slicer Arduino Controller” extension.

4. On “ArduinoPedalBoard” extension in “3D Slicer”, choose the desidered tasks and offset variation and press “Start” button.

5. Use the pedalboard for controlling view settings.

{{documentation/{{documentation/version}}/module-section|Panels and their use}}

Simple panel to connect Arduino and to interact with it.

{|
|
|[[Image:ArduinoController_UI_screenshot.png|thumb|280px|Arduino Connection Module UI]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.

SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.

Bioengineering. 2020 Sep;7(3):109.
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

Source code:
https://github.com/pzaffino/SlicerArduinoController


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

File:ArduinoPedalBoarad schematic.png

2022-04-11T14:54:30Z

Pzaffino:

Documentation/Nightly/Extensions/ArduinoController

2022-04-11T14:53:19Z

Pzaffino:

<noinclude>{{documentation/versioncheck}}
</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/ArduinoController|ArduinoController]] 
Author: Paolo Zaffino, Magna Graecia University of Catanzaro - Italy 
Contributor1: Domenico Leuzzi, Magna Graecia University of Catanzaro - Italy 
Contributor2: Virgilio Sabatino, Magna Graecia University of Catanzaro - Italy 
Contributor3: Andras Lasso - PerkLab, Queen's 
Contributor4: Maria Francesca Spadea, Magna Graecia University of Catanzaro - Italy 
Contact: Paolo Zaffino, p.zaffino@unicz.it 
{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}

1. Arduino Connect: this module allows to connect Slicer and Arduino board. This will be use to build other modules and applications. The integration of the data coming from the board strongly relies on vtkMRMLScriptedModuleNode in order to notify to the entire system the arrival of a new data.

2. Arduino Motion Sensor: Module for 3D Slicer that allows to control the Slice View through gestures using an inexpensive motion sensor compatible with Arduino. (Module Icon made by Freepik from www.flaticon.com)

Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

If you use this extension please cite the following article:

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.
SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.
Bioengineering. 2020 Sep;7(3):109.

Journal link: https://www.mdpi.com/2306-5354/7/3/109


{{documentation/{{documentation/version}}/module-section|Use Cases}}

===Arduino Connect===
Users wants to connect, receive and transmit data from/to Arduino. Connection parameters can be set according to user environment.

A sender and a monitor/plotter of data coming from the board are also available without the need of writing code.

{|
|[[Image:ArduinoController_screenshot.png|thumb|340px|Arduino Connect module]]
|}

===Arduino Motion Sensor===
Users want to control the Slice View module by using gestures detected via dedicated Arduino sensor.

 {{documentation/{{documentation/version}}/module-section|Tutorials}}

===Arduino Connect===
1. Connect Arduino to the system (user has to take care of Arduino code side).
2. Click "Detect device(s)" button
3. Set port and other connection parameters according to PC environment
4. Click "Connect" button
5. Send receive data (via GUI and/or Python code)

===Arduino Motion Sensor===
1. Connect PAJ7620 to “Arduino”. To do this simply connect:

Vin to 3.3 V;

Gnd to Gnd;

SCL to SCL;

SDA to SDA.
2. Connect “Arduino” to the USB port of pc and and run “paj7620_9gestures” code on “arduino IDE”.

The code can be found here: “https://github.com/Seeed-Studio/Gesture_PAJ7620”.

3. Connect “Arduino” to “3D Slicer” using “Slicer Arduino Controller” extension.

4. “ArduinoMotionSensor” extension in “3D Slicer”, choose the desidered offset variation and press “Start Motion” button.

5. Use the gestures for controlling view settings by exploiting the following options:

“Left” = Select Previous View

“Right” = Select Next View

“Up” = Increase Offset

“Down” = Decrease Offset

“Forward” = Enable Full Screen

“Backward” = Disable Full Screen

===Arduino Pedalboard===

Module for 3D Slicer that allows to control the Slice View through a pedealboard connected via Arduino.

1. Connect buttons to Arduino as described in the figure below:

2. Load in Arduino board the code hosted into the folder "ArduinoCode/ArduinoPedalboard".

3. Connect “Arduino” to “3D Slicer” using “Slicer Arduino Controller” extension.

4. On “ArduinoPedalBoard” extension in “3D Slicer”, choose the desidered tasks and offset variation and press “Start” button.

5. Use the pedalboard for controlling view settings.

{{documentation/{{documentation/version}}/module-section|Panels and their use}}

Simple panel to connect Arduino and to interact with it.

{|
|
|[[Image:ArduinoController_UI_screenshot.png|thumb|280px|Arduino Connection Module UI]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.

SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.

Bioengineering. 2020 Sep;7(3):109.
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

Source code:
https://github.com/pzaffino/SlicerArduinoController


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

Documentation/Nightly/Extensions/ArduinoController

2022-04-11T14:52:57Z

Pzaffino:

<noinclude>{{documentation/versioncheck}}
</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/ArduinoController|ArduinoController]] 
Author: Paolo Zaffino, Magna Graecia University of Catanzaro - Italy 
Contributor1: Domenico Leuzzi, Magna Graecia University of Catanzaro - Italy 
Contributor2: Virgilio Sabatino, Magna Graecia University of Catanzaro - Italy 
Contributor3: Andras Lasso - PerkLab, Queen's 
Contributor4: Maria Francesca Spadea, Magna Graecia University of Catanzaro - Italy 
Contact: Paolo Zaffino, p.zaffino@unicz.it 
{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}

1. Arduino Connect: this module allows to connect Slicer and Arduino board. This will be use to build other modules and applications. The integration of the data coming from the board strongly relies on vtkMRMLScriptedModuleNode in order to notify to the entire system the arrival of a new data.

2. Arduino Motion Sensor: Module for 3D Slicer that allows to control the Slice View through gestures using an inexpensive motion sensor compatible with Arduino. (Module Icon made by Freepik from www.flaticon.com)

Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

If you use this extension please cite the following article:

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.
SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.
Bioengineering. 2020 Sep;7(3):109.

Journal link: https://www.mdpi.com/2306-5354/7/3/109


{{documentation/{{documentation/version}}/module-section|Use Cases}}

===Arduino Connect===
Users wants to connect, receive and transmit data from/to Arduino. Connection parameters can be set according to user environment.

A sender and a monitor/plotter of data coming from the board are also available without the need of writing code.

{|
|[[Image:ArduinoController_screenshot.png|thumb|340px|Arduino Connect module]]
|}

===Arduino Motion Sensor===
Users want to control the Slice View module by using gestures detected via dedicated Arduino sensor.

 {{documentation/{{documentation/version}}/module-section|Tutorials}}

===Arduino Connect===
1. Connect Arduino to the system (user has to take care of Arduino code side).
2. Click "Detect device(s)" button
3. Set port and other connection parameters according to PC environment
4. Click "Connect" button
5. Send receive data (via GUI and/or Python code)

===Arduino Motion Sensor===
1. Connect PAJ7620 to “Arduino”. To do this simply connect:

Vin to 3.3 V;

Gnd to Gnd;

SCL to SCL;

SDA to SDA.
2. Connect “Arduino” to the USB port of pc and and run “paj7620_9gestures” code on “arduino IDE”.

The code can be found here: “https://github.com/Seeed-Studio/Gesture_PAJ7620”.

3. Connect “Arduino” to “3D Slicer” using “Slicer Arduino Controller” extension.

4. “ArduinoMotionSensor” extension in “3D Slicer”, choose the desidered offset variation and press “Start Motion” button.

5. Use the gestures for controlling view settings by exploiting the following options:

“Left” = Select Previous View

“Right” = Select Next View

“Up” = Increase Offset

“Down” = Decrease Offset

“Forward” = Enable Full Screen

“Backward” = Disable Full Screen

===Arduino Pedalboard===
Module for 3D Slicer that allows to control the Slice View through a pedealboard connected via Arduino.

1. Connect buttons to Arduino as described in the figure below:

2. Load in Arduino board the code hosted into the folder "ArduinoCode/ArduinoPedalboard".

3. Connect “Arduino” to “3D Slicer” using “Slicer Arduino Controller” extension.

4. On “ArduinoPedalBoard” extension in “3D Slicer”, choose the desidered tasks and offset variation and press “Start” button.

5. Use the pedalboard for controlling view settings.

{{documentation/{{documentation/version}}/module-section|Panels and their use}}

Simple panel to connect Arduino and to interact with it.

{|
|
|[[Image:ArduinoController_UI_screenshot.png|thumb|280px|Arduino Connection Module UI]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.

SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.

Bioengineering. 2020 Sep;7(3):109.
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

Source code:
https://github.com/pzaffino/SlicerArduinoController


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

Documentation/Nightly/Extensions/ArduinoController

2021-12-20T09:55:40Z

Pzaffino:

<noinclude>{{documentation/versioncheck}}
</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/ArduinoController|ArduinoController]] 
Author: Paolo Zaffino, Magna Graecia University of Catanzaro - Italy 
Contributor1: Domenico Leuzzi, Magna Graecia University of Catanzaro - Italy 
Contributor2: Virgilio Sabatino, Magna Graecia University of Catanzaro - Italy 
Contributor3: Andras Lasso - PerkLab, Queen's 
Contributor4: Maria Francesca Spadea, Magna Graecia University of Catanzaro - Italy 
Contact: Paolo Zaffino, p.zaffino@unicz.it 
{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}

1. Arduino Connect: this module allows to connect Slicer and Arduino board. This will be use to build other modules and applications. The integration of the data coming from the board strongly relies on vtkMRMLScriptedModuleNode in order to notify to the entire system the arrival of a new data.

2. Arduino Motion Sensor: Module for 3D Slicer that allows to control the Slice View through gestures using an inexpensive motion sensor compatible with Arduino. (Module Icon made by Freepik from www.flaticon.com)

Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

If you use this extension please cite the following article:

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.
SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.
Bioengineering. 2020 Sep;7(3):109.

Journal link: https://www.mdpi.com/2306-5354/7/3/109


{{documentation/{{documentation/version}}/module-section|Use Cases}}

===Arduino Connect===
Users wants to connect, receive and transmit data from/to Arduino. Connection parameters can be set according to user environment.

A sender and a monitor/plotter of data coming from the board are also available without the need of writing code.

{|
|[[Image:ArduinoController_screenshot.png|thumb|340px|Arduino Connect module]]
|}

===Arduino Motion Sensor===
Users want to control the Slice View module by using gestures detected via dedicated Arduino sensor.

 {{documentation/{{documentation/version}}/module-section|Tutorials}}

===Arduino Connect===
1. Connect Arduino to the system (user has to take care of Arduino code side).
2. Click "Detect device(s)" button
3. Set port and other connection parameters according to PC environment
4. Click "Connect" button
5. Send receive data (via GUI and/or Python code)

===Arduino Motion Sensor===
1. Connect PAJ7620 to “Arduino”. To do this simply connect:

Vin to 3.3 V;

Gnd to Gnd;

SCL to SCL;

SDA to SDA.
2. Connect “Arduino” to the USB port of pc and and run “paj7620_9gestures” code on “arduino IDE”.

The code can be found here: “https://github.com/Seeed-Studio/Gesture_PAJ7620”.

3. Connect “Arduino” to “3D Slicer” using “Slicer Arduino Controller” extension.

4. “ArduinoMotionSensor” extension in “3D Slicer”, choose the desidered offset variation and press “Start Motion” button.

5. Use the gestures for controlling view settings by exploiting the following options:

“Left” = Select Previous View

“Right” = Select Next View

“Up” = Increase Offset

“Down” = Decrease Offset

“Forward” = Enable Full Screen

“Backward” = Disable Full Screen

{{documentation/{{documentation/version}}/module-section|Panels and their use}}

Simple panel to connect Arduino and to interact with it.

{|
|
|[[Image:ArduinoController_UI_screenshot.png|thumb|280px|Arduino Connection Module UI]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.

SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.

Bioengineering. 2020 Sep;7(3):109.
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

Source code:
https://github.com/pzaffino/SlicerArduinoController


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

Documentation/Nightly/Extensions/ArduinoController

2021-12-20T09:55:06Z

Pzaffino:

<noinclude>{{documentation/versioncheck}}
</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/ArduinoController|ArduinoController]] 
Author: Paolo Zaffino, Magna Graecia University of Catanzaro - Italy 
Contributor1: Domenico Leuzzi, Magna Graecia University of Catanzaro - Italy 
Contributor2: Virgilio Sabatino, Magna Graecia University of Catanzaro - Italy 
Contributor3: Andras Lasso - PerkLab, Queen's 
Contributor4: Maria Francesca Spadea, Magna Graecia University of Catanzaro - Italy 
Contact: Paolo Zaffino, p.zaffino@unicz.it 
{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}

1. Arduino Connect: this module allows to connect Slicer and Arduino board. This will be use to build other modules and applications. The integration of the data coming from the board strongly relies on vtkMRMLScriptedModuleNode in order to notify to the entire system the arrival of a new data.

2. Arduino Motion Sensor: Module for 3D Slicer that allows to control the Slice View through gestures using an inexpensive motion sensor compatible with Arduino. (Module Icon made by Freepik from www.flaticon.com)

Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

If you use this extension please cite the following article:

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.
SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.
Bioengineering. 2020 Sep;7(3):109.

Journal link: https://www.mdpi.com/2306-5354/7/3/109


{{documentation/{{documentation/version}}/module-section|Use Cases}}

=== Arduino Connect ===
Users wants to connect, receive and transmit data from/to Arduino. Connection parameters can be set according to user environment.

A sender and a monitor/plotter of data coming from the board are also available without the need of writing code.

{|
|[[Image:ArduinoController_screenshot.png|thumb|340px|Arduino Connect module]]
|}

=== Arduino Motion Sensor ===
Users want to control the Slice View module by using gestures detected via dedicated Arduino sensor.
 {{documentation/{{documentation/version}}/module-section|Tutorials}}

=== Arduino Connect ===
1. Connect Arduino to the system (user has to take care of Arduino code side).
2. Click "Detect device(s)" button
3. Set port and other connection parameters according to PC environment
4. Click "Connect" button
5. Send receive data (via GUI and/or Python code)

=== Arduino Motion Sensor ===
1. Connect PAJ7620 to “Arduino”. To do this simply connect:

Vin to 3.3 V;

Gnd to Gnd;

SCL to SCL;

SDA to SDA.
2. Connect “Arduino” to the USB port of pc and and run “paj7620_9gestures” code on “arduino IDE”.

The code can be found here: “https://github.com/Seeed-Studio/Gesture_PAJ7620”.

3. Connect “Arduino” to “3D Slicer” using “Slicer Arduino Controller” extension.

4. “ArduinoMotionSensor” extension in “3D Slicer”, choose the desidered offset variation and press “Start Motion” button.

5. Use the gestures for controlling view settings by exploiting the following options:

“Left” = Select Previous View

“Right” = Select Next View

“Up” = Increase Offset

“Down” = Decrease Offset

“Forward” = Enable Full Screen

“Backward” = Disable Full Screen

{{documentation/{{documentation/version}}/module-section|Panels and their use}}

Simple panel to connect Arduino and to interact with it.

{|
|
|[[Image:ArduinoController_UI_screenshot.png|thumb|280px|Arduino Connection Module UI]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.

SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.

Bioengineering. 2020 Sep;7(3):109.
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

Source code:
https://github.com/pzaffino/SlicerArduinoController


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

Documentation/Nightly/Extensions/ArduinoController

2021-12-20T09:50:00Z

Pzaffino:

<noinclude>{{documentation/versioncheck}}
</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/ArduinoController|ArduinoController]] 
Author: Paolo Zaffino, Magna Graecia University of Catanzaro - Italy 
Contributor1: Domenico Leuzzi, Magna Graecia University of Catanzaro - Italy 
Contributor2: Virgilio Sabatino, Magna Graecia University of Catanzaro - Italy 
Contributor3: Andras Lasso - PerkLab, Queen's 
Contributor4: Maria Francesca Spadea, Magna Graecia University of Catanzaro - Italy 
Contact: Paolo Zaffino, p.zaffino@unicz.it 
{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}

1. Arduino Connect: this module allows to connect Slicer and Arduino board. This will be use to build other modules and applications. The integration of the data coming from the board strongly relies on vtkMRMLScriptedModuleNode in order to notify to the entire system the arrival of a new data.

2. Arduino Motion Sensor: Module for 3D Slicer that allows to control the Slice View through gestures using an inexpensive motion sensor compatible with Arduino. (Module Icon made by Freepik from www.flaticon.com)

Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

If you use this extension please cite the following article:

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.
SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.
Bioengineering. 2020 Sep;7(3):109.

Journal link: https://www.mdpi.com/2306-5354/7/3/109


{{documentation/{{documentation/version}}/module-section|Use Cases}}

=== Arduino Connect ===
Users wants to connect, receive and transmit data from/to Arduino. Connection parameters can be set according to user environment.

A sender and a monitor/plotter of data coming from the board are also available without the need of writing code.

{|
|[[Image:ArduinoController_screenshot.png|thumb|340px|Arduino Connect module]]
|}

=== Arduino Motion Sensor ===
Users want to control the Slice View module by using gestures detected via dedicated Arduino sensor.
 {{documentation/{{documentation/version}}/module-section|Tutorials}}

=== Arduino Connect ===
1. Connect Arduino to the system (user has to take care of Arduino code side).
2. Click "Detect device(s)" button
3. Set port and other connection parameters according to PC environment
4. Click "Connect" button
5. Send receive data (via GUI and/or Python code)

=== Arduino Motion Sensor ===
aa
{{documentation/{{documentation/version}}/module-section|Panels and their use}}

Simple panel to connect Arduino and to interact with it.

{|
|
|[[Image:ArduinoController_UI_screenshot.png|thumb|280px|Arduino Connection Module UI]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.

SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.

Bioengineering. 2020 Sep;7(3):109.
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

Source code:
https://github.com/pzaffino/SlicerArduinoController


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

Documentation/Nightly/Extensions/ArduinoController

2021-12-20T09:46:21Z

Pzaffino:

<noinclude>{{documentation/versioncheck}}
</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/ArduinoController|ArduinoController]] 
Author: Paolo Zaffino, Magna Graecia University of Catanzaro - Italy 
Contributor1: Domenico Leuzzi, Magna Graecia University of Catanzaro - Italy 
Contributor2: Virgilio Sabatino, Magna Graecia University of Catanzaro - Italy 
Contributor3: Andras Lasso - PerkLab, Queen's 
Contributor4: Maria Francesca Spadea, Magna Graecia University of Catanzaro - Italy 
Contact: Paolo Zaffino, p.zaffino@unicz.it 
{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}

1. Arduino Connect: this module allows to connect Slicer and Arduino board. This will be use to build other modules and applications. The integration of the data coming from the board strongly relies on vtkMRMLScriptedModuleNode in order to notify to the entire system the arrival of a new data.

2. Arduino Motion Sensor: Module for 3D Slicer that allows to control the Slice View through gestures using an inexpensive motion sensor compatible with Arduino. (Module Icon made by Freepik from www.flaticon.com)

Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

If you use this extension please cite the following article:

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.
SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.
Bioengineering. 2020 Sep;7(3):109.

Journal link: https://www.mdpi.com/2306-5354/7/3/109


{{documentation/{{documentation/version}}/module-section|Use Cases}}

Users wants to connect, receive and transmit data from/to Arduino. Connection parameters can be set according to user environment.

A sender and a monitor/plotter of data coming from the board are also available without the need of writing code.

{|
|[[Image:ArduinoController_screenshot.png|thumb|340px|Arduino Connect module]]
|}

{{documentation/{{documentation/version}}/module-section|Tutorials}}

1. Connect Arduino to the system (user has to take care of Arduino code side).
2. Click "Detect device(s)" button
3. Set port and other connection parameters according to PC environment
4. Click "Connect" button
5. Send receive data (via GUI and/or Python code)


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

Simple panel to connect Arduino and to interact with it.

{|
|
|[[Image:ArduinoController_UI_screenshot.png|thumb|280px|Arduino Connection Module UI]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}

Zaffino P, Merola A, Leuzzi D, Sabatino V, Cosentino C, Spadea MF.

SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.

Bioengineering. 2020 Sep;7(3):109.
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
Full documentation and examples available at:
https://pzaffino.github.io/SlicerArduinoController/index

Source code:
https://github.com/pzaffino/SlicerArduinoController


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

Documentation/Nightly/Extensions/DensityLungSegmentation

2021-09-14T13:14:19Z

Pzaffino:

Documentation/Nightly/Extensions/DensityLungSegmentation

2021-09-11T14:36:10Z

Pzaffino:

Documentation/Nightly/Extensions/DensityLungSegmentation

2021-09-11T14:34:37Z

Pzaffino:

Documentation/Nightly/Extensions/DensityLungSegmentation

2021-09-11T14:18:08Z

Pzaffino:

Documentation/Nightly/ModuleExtensionListing/Extensions by name

2021-09-11T14:16:33Z

Pzaffino: /* Extensions by name */

__NOTOC__
* [[#Extensions_by_name|Extensions by name]]
= Extensions by name =
83 extensions:
* [http://www.nitrc.org/projects/abc ABC]
* [[Documentation/Nightly/Extensions/AirwaySegmentation|AirwaySegmentation]]
* [[Documentation/Nightly/Extensions/AnomalousFilters|AnomalousFilters]]
* [[Documentation/Nightly/Extensions/ArduinoController|ArduinoController]]
* [[Documentation/Nightly/Extensions/BoneTextureExtension|BoneTextureExtension]]
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit]
* [http://brainsia.github.io/CardiacAgatstonMeasures/ CardiacAgatstonMeasures]
* [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|CarreraSlice]]
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC_3D_I2MConversion]]
* [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]]
* [http://www.chestimagingplatform.org Chest_Imaging_Platform]
* [[Documentation/Nightly/Extensions/CleaverExtension|CleaverExtension]]
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]
* [[Documentation/Nightly/Extensions/CornerAnnotation|CornerAnnotation]]
* [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]]
* [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]]
* [[Documentation/Nightly/Extensions/DCMQI|DCMQI]]
* [[Documentation/Nightly/Extensions/DebuggingTools|DebuggingTools]]
* [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]]
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]]
* [[Documentation/Nightly/Extensions/DiceComputation|DiceComputation]]
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]
* [[Documentation/Nightly/Extensions/EasyClip|EasyClip]]
* [[Documentation/4.3/Modules/FastGrowCut|FastGrowCutEffect]]
* [[Documentation/Nightly/Modules/FilmDosimetry|FilmDosimetryAnalysis]]
* [[Documentation/Nightly/Modules/GelDosimetry|GelDosimetryAnalysis]]
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment]
* [[Documentation/Nightly/Extensions/GyroGuide|GyroGuide]]
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]
* [[Documentation/Nightly/Extensions/iGyne|iGyne]]
* [[Documentation/Nightly/Extensions/ImageCompare|ImageCompare]]
* [[Documentation/Nightly/Extensions/ImageMaker|ImageMaker]]
* [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]]
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScarSegmenter]]
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|LongitudinalPETCT]]
* [[Documentation/Nightly/Extensions/DensityLungSegmentation|DensityLungSegmentation]]
* [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]]
* [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]]
* [https://github.com/SlicerIGT/MarkupsToModel MarkupsToModel]
* [[Documentation/Nightly/Extensions/MeshStatistics|MeshStatistics]]
* [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]]
* [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]]
* [[Documentation/Nightly/Extensions/mpReview|mpReview]]
* [[Documentation/Nightly/Extensions/MultiLevelRegistration|MultiLevelRegistration]]
* [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]]
* [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]]
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCVExample]]
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|PercutaneousApproachAnalysis]]
* [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]]
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]]
* [[Documentation/Nightly/Extensions/PETDICOM|PETDICOMExtension]]
* [[Documentation/Nightly/Extensions/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]]
* [http://gti-fing.github.io/SlicerPetSpectAnalysis PetSpectAnalysis]
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]]
* [[Documentation/Nightly/Extensions/PickAndPaint|PickAndPaintExtension]]
* [[Documentation/Nightly/Extensions/PkModeling|PkModeling]]
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]
* [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]]
* [[Documentation/Nightly/Extensions/Radiomics|Radiomics]]
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]]
* [[Documentation/Nightly/Extensions/ResectionPlanner|ResectionPlanner]]
* [[Documentation/Nightly/Extensions/ROBEXBrainExtraction|ROBEXBrainExtraction]]
* [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]]
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]
* [[Documentation/Nightly/Extensions/SegmentationWizard|SegmentationWizard]]
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects]
* [https://github.com/SlicerRt/SegmentRegistration SegmentRegistration]
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]
* [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]]
* [[Documentation/Nightly/Extensions/ShapeVariationAnalyzer|ShapeVariationAnalyzer]]
* [[Documentation/Nightly/Extensions/SkullStripper|SkullStripper]]
* [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]]
* [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]]
* [https://github.com/lassoan/SlicerElastix SlicerElastix]
* [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]]
* [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]]
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound]
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]
* [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]]
* [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]]
* [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]]
* [https://github.com/moselhy/SequenceRegistration SlicerSequenceRegistration]
* [[Documentation/Nightly/Extensions/SlicerVirtualReality|SlicerVirtualReality]]
* [https://github.com/SlicerIGT/SlicerSoundControl SoundControl]
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|SlicerToKiwiExporter]]
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]]
* [https://github.com/Tomnl/Slicer-Wasp Wasp]
* [[Documentation/Nightly/Extensions/SobolevSegmenter|SobolevSegmenter]]
* [http://www.nitrc.org/projects/spharm-pdm SPHARM-PDM]
* [[Documentation/Nightly/Extensions/SwissSkullStripper|SwissSkullStripper]]
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]
* [[Documentation/Nightly/Extensions/TrackerStabilizer|TrackerStabilizer]]
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]
* [[Documentation/Nightly/Extensions/VirtualFractureReconstruction|VirtualFractureReconstruction]]
* [http://slicer.vmtk.org/ VMTK]
* [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]]
* [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]]
* [[Documentation/Nightly/Extensions/XNATSlicer|XNATSlicer]]
__NOTOC__

Documentation/Nightly/Extensions/DensityLungSegmentation

2021-09-11T14:12:16Z

Pzaffino: Pzaffino moved page Documentation/Nightly/Extensions/LungDensitySegmentation to Documentation/Nightly/Extensions/DensityLungSegmentation

Documentation/Nightly/Extensions/LungDensitySegmentation

2021-09-11T14:12:16Z

Pzaffino: Pzaffino moved page Documentation/Nightly/Extensions/LungDensitySegmentation to Documentation/Nightly/Extensions/DensityLungSegmentation

#REDIRECT [[Documentation/Nightly/Extensions/DensityLungSegmentation]]

Documentation/Nightly/Extensions/DensityLungSegmentation

2021-09-10T13:14:00Z

Pzaffino:

Documentation/Nightly/Extensions/DensityLungSegmentation

2021-09-10T10:58:01Z

Pzaffino:

Documentation/Nightly/Extensions/DensityLungSegmentation

2021-09-10T10:57:29Z

Pzaffino:

Documentation/Nightly

2021-08-31T15:00:39Z

Pzaffino: /* Segmentation */

<noinclude>{{documentation/versioncheck}}
</noinclude>
__NOTOC__

{{documentation/versionlist}}

{| border="0" align="center" width="100%" cellspacing="7" cellpadding="2" valign="top"
|-
! width="33%" |
! |
! width="33%" |
! |
! width="33%" |
|-
| valign="top" |
----
Where to start ?
----

* [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/getting_started.html Getting started]

:Quick overview about Slicer

*[[Documentation/{{documentation/version}}/Training|Training pages]]

:Information on how to use Slicer {{documentation/version}}

*[[Documentation/{{documentation/version}}/FAQ|FAQ]]

:Set of common questions/answers

*[https://discourse.slicer.org Discussion Forum]

:The most effective way to get help from the community


----
How to
----

*[[Documentation/{{documentation/version}}/Report a problem|Report a problem]] / [[Documentation/{{documentation/version}}/Create_a_feature_request|Create a feature request]]{{new}}

----
{{:{{FULLPAGENAME}}/SlicerApplication}}

| bgcolor="#CCCCCC" |
| valign="top" |
----
Modules
----

{| width="100%" cellspacing="7" cellpadding="2"

|- style="vertical-align:top; border-style:hidden;"

| width="5%" |
 

| width="45%" |
[[Image:SlicerAnnotationsV2-Small.png|32px]] [[{{FULLPAGENAME}}/Modules/Annotations|Annotations]]
 

[[Image:DataIcon.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/data.html Data]
 

[[Image:DataStoreIcon_128.png|32px]] [[{{FULLPAGENAME}}/Modules/DataStore|Data Store]]
 

[[Image:DICOM.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM]
 

[[Image:Editor.png|32px]] [[{{FULLPAGENAME}}/Modules/Editor|Editor]]
 

[[Image:Markups.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/markups.html Markups]
 

[[Image:SlicerModels-Small.png|32px]] [[{{FULLPAGENAME}}/Modules/Models|Models]]
 

[[Image:SceneViews.png|32px]] [[{{FULLPAGENAME}}/Modules/SceneViews|Scene Views]]
 

[[Image:Segmentations.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmentations.html Segmentations]
 

[[Image:SegmentEditor.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor]
 

[[Image:Transforms.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/transforms.html Transforms]
 

[[Image:ViewControllersIcon.png|32px]] [[{{FULLPAGENAME}}/Modules/ViewControllers|View Controllers]]
 

[[Image:VolumeRendering.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumerendering.html Volume Rendering]
 

[[Image:SlicerVolume-Small.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumes.html Volumes]
 

[[Image:Welcome.png|32px]] [[{{FULLPAGENAME}}/Modules/Welcome|Welcome to Slicer]]
 

| width="50%" |

{{:{{FULLPAGENAME}}/ModuleExtensionListing/TOC}}

|}


| bgcolor="#CCCCCC" |
| valign="top" |
----
Developers Corner
----

*[[Documentation/Nightly/Developers | Information for Software Developers]]{{updated}}

:Source code, contribute patch, develop modules


----
Miscellaneous
----


*[[Documentation/{{documentation/version}}/HowTo|Documentation guidelines]]

:Slicer user documentation principle and guidelines

*[[Slicer4:VisualBlog|Visual blog]]

:Set of screenshots showing Slicer in action.

*[[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]

:Platform specific issues and considerations

*[[Documentation/{{documentation/version}}/Announcements|Announcements]] & [[Documentation/{{documentation/version}}/Acknowledgments|Acknowledgments]]

*[[Documentation/Nightly/Registration/RegistrationLibrary|Registration Library]]

:Real-life example cases of using the Slicer registration tools, incl. datasets and step-by-step instructions to follow and try yourself.

----
Documentation in other languages
----
{{:{{FULLPAGENAME}}/Lang/ES}}

|}



{| border="0" align="center" width="100%" cellspacing="7" cellpadding="2" valign="top"

|- style="vertical-align:top; border-style:hidden;"

|

{{:{{FULLPAGENAME}}/ModuleExtensionListing/Extensions_by_name}}

|
 
 
=Modules by category=

==Converters==

*[[Documentation/Nightly/Modules/CropVolume|Crop Volume]] (loadable)
*[[Documentation/Nightly/Modules/OrientScalarVolume|Orient Scalar Volume]] (cli)
*[[Documentation/Nightly/Modules/VectorToScalarVolume|Vector To Scalar Volume]] (scripted)
*[[Documentation/Nightly/Modules/CreateDICOMSeries|Create DICOM Series]] (cli)

==Diffusion==

*[[Documentation/Nightly/Modules/DMRIInstall|DMRI Install]] (scripted)


===Diffusion Data Conversion===

*DWI Convert (cli)


===Diffusion Weighted Images===

*BRAINS DWI Cleanup (cli)


===Import and Export===

*DWI Convert (cli)


===Utilities===

*BRAINS DWI Cleanup (cli)
*[[Documentation/Nightly/Modules/ResampleDTIVolume|Resample DTI Volume]] (cli)
*[[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|Resample Scalar Vector DWI Volume]] (cli)


==Endoscopy==

*[[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] (scripted)


==Filter==

*IslandRemoval (cli)


==Filtering==

*[[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4 ITK Bias Field Correction]] (cli)
*[[Documentation/Nightly/Modules/ImageLabelCombine|Image Label Combine]] (cli)
*[[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (cli)
*[[Documentation/Nightly/Modules/CheckerBoardFilter|Checker Board Filter]] (cli)
*[[Documentation/Nightly/Modules/ExtractSkeleton|Extract Skeleton]] (cli)
*[[Documentation/Nightly/Modules/SimpleFilters|Simple Filters]] (scripted)
*[[Documentation/Nightly/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (cli)
*[[Documentation/Nightly/Modules/HistogramMatching|Histogram Matching]] (cli)


===Arithmetic===

*[[Documentation/Nightly/Modules/MultiplyScalarVolumes|Multiply Scalar Volumes]] (cli)
*[[Documentation/Nightly/Modules/AddScalarVolumes|Add Scalar Volumes]] (cli)
*[[Documentation/Nightly/Modules/MaskScalarVolume|Mask Scalar Volume]] (cli)
*[[Documentation/Nightly/Modules/SubtractScalarVolumes|Subtract Scalar Volumes]] (cli)
*[[Documentation/Nightly/Modules/CastScalarVolume|Cast Scalar Volume]] (cli)


===Denoising===

*[[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (cli)
*[[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|Gradient Anisotropic Diffusion]] (cli)
*[[Documentation/Nightly/Modules/MedianImageFilter|Median Image Filter]] (cli)
*[[Documentation/Nightly/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (cli)


===Morphology===

*[[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (cli)
*[[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (cli)


==IGT==

*[[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLink IF]] (loadable)


==Informatics==

*[[Documentation/Nightly/Modules/SEG2NRRD|SEG 2 NRRD]] (cli)
*[[Documentation/Nightly/Modules/Tables|Tables]] (loadable)
*[[Documentation/Nightly/Modules/Data|Data]] (loadable)
*DumpSEGFrame (cli)
*[[Documentation/Nightly/Modules/Terminologies|Terminologies]] (loadable)
*[[Documentation/Nightly/Modules/Units|Units]] (loadable)
*[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM] (scripted)
*[[Documentation/Nightly/Modules/SampleData|Sample Data]] (scripted)
*[[Documentation/Nightly/Modules/Colors|Colors]] (loadable)
*[[Documentation/Nightly/Modules/Annotations|Annotations]] (loadable)
*[[Documentation/Nightly/Modules/Markups|Markups]] (loadable)


===Converters===

*[[Documentation/Nightly/Modules/EncodeSEG|Encode SEG]] (cli)


==Legacy==

===Converters===

*[[Documentation/Nightly/Modules/BSplineToDeformationField|BSpline To Deformation Field]] (cli)


===Filtering===

*[[Documentation/Nightly/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (cli)
*[[Documentation/Nightly/Modules/ResampleScalarVolume|Resample Scalar Volume]] (cli)


===Registration===

*Test Grid Transform Registration (cli)
*[[Documentation/Nightly/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] (cli)

==MultiVolume Support==

*[[Documentation/Nightly/Modules/MultiVolumeImporter|MultiVolume Importer]] (scripted)
*[[Documentation/Nightly/Modules/MultiVolumeExplorer|MultiVolume Explorer]] (loadable)


==Quantification==

*[[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (cli)
*SegmentStatistics (scripted)
*[[Documentation/Nightly/Modules/LabelStatistics|Label Statistics]] (scripted)
*BRAINSLabelStats (cli)
*[[Documentation/Nightly/Modules/DataProbe|Data Probe]] (scripted)


==Registration==

*[[Documentation/Nightly/Modules/Transforms|Transforms]] (loadable)
*BRAINSResize (cli)
*PerformMetricTest (cli)
*[[Documentation/Nightly/Modules/LandmarkRegistration|Landmark Registration]] (scripted)
*[[Documentation/Nightly/Modules/BRAINSResample|BRAINS Resample]] (cli)
*[[Documentation/Nightly/Modules/BRAINSFit|General registration (BRAINS)]] (cli)


===Specialized===

*[[Documentation/Nightly/Modules/ACPCTransform|AC-PC Transform]] (cli)
*[[Documentation/Nightly/Modules/FiducialRegistration|Fiducial Registration]] (cli)
*[[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINS Demon Warp]] (cli)
*[[Documentation/Nightly/Modules/Reformat|Reformat]] (loadable)
*VBRAINSDemonWarp (cli)


==Segmentation==

*[[Documentation/Nightly/Modules/Segmentations|Segmentations]] (loadable)
*[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor] (scripted)
*[[Documentation/Nightly/Modules/Editor|Editor]] (scripted)
*[[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (cli)
*[[Documentation/Nightly/Modules/EMSegment|EMSegment]] (loadable)

*EMSegmentQuick (loadable)


===Specialized===

*BRAINS ROI Auto (cli)
*[[Documentation/Nightly/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (cli)
*EMSegment CommandLine (cli)



==Surface Models==

*[[Documentation/Nightly/Modules/SurfaceToolbox|Surface Toolbox]] (scripted)
*[[Documentation/Nightly/Modules/GrayscaleModelMaker|Grayscale Model Maker]] (cli)
*[[Documentation/Nightly/Modules/ModelMaker|Model Maker]] (cli)
*[[Documentation/Nightly/Modules/ModelToLabelMap|Model To LabelMap]] (cli)
*[[Documentation/Nightly/Modules/MergeModels|Merge Models]] (cli)
*[[Documentation/Nightly/Modules/LabelMapSmoothing|LabelMap Smoothing]] (cli)
*[[Documentation/Nightly/Modules/ProbeVolumeWithModel|Probe Volume With Model]] (cli)


==Utilities==

*[[Documentation/Nightly/Modules/ScreenCapture|Screen Capture]] (scripted)
*[[Documentation/Nightly/Modules/DataStore|Data Store]] (loadable)
*[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicompatcher.html DICOM Patcher] (scripted)
*BRAINS Strip Rotation (cli)
*EMSegment Transform To New Format (cli)


===BRAINS===

*BRAINS Transform Convert (cli)


==Wizards==

*[[Documentation/Nightly/Modules/CompareVolumes|Compare Volumes]] (scripted)


==Developer Tools==

*[[Documentation/Nightly/Modules/Cameras|Cameras]] (loadable)
*[[Documentation/Nightly/Modules/ExecutionModelTour|Execution Model Tour]] (cli)
*[[Documentation/Nightly/Modules/ExtensionWizard|Extension Wizard]] (scripted)
*[[Documentation/Nightly/Modules/EventBroker|Event Broker]]
*Double Arrays (loadable)


===DICOM Plugins===

*DICOMParametricMapPlugin
*DicomUltrasoundPlugin
*DICOMSegmentationPlugin
*DICOMSlicerDataBundlePlugin
*DICOMTID1500Plugin
*[[Documentation/Nightly/Modules/DICOMPETSUVPlugin|DICOMPETSUVPlugin]]
*DICOMScalarVolumePlugin
*DICOMDiffusionVolumePlugin
*DICOMLongitudinalPETCTPlugin
*DicomSroImportPlugin
*[[Documentation/Nightly/Modules/DICOMRWVMPlugin|DICOMRWVMPlugin]]
*DicomRtImportExportPlugin
*MultiVolumeImporterPlugin

|}

Documentation/Nightly

2021-08-31T14:59:46Z

Pzaffino: /* Segmentation */

<noinclude>{{documentation/versioncheck}}
</noinclude>
__NOTOC__

{{documentation/versionlist}}

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|-
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----
Where to start ?
----

* [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/getting_started.html Getting started]

:Quick overview about Slicer

*[[Documentation/{{documentation/version}}/Training|Training pages]]

:Information on how to use Slicer {{documentation/version}}

*[[Documentation/{{documentation/version}}/FAQ|FAQ]]

:Set of common questions/answers

*[https://discourse.slicer.org Discussion Forum]

:The most effective way to get help from the community


----
How to
----

*[[Documentation/{{documentation/version}}/Report a problem|Report a problem]] / [[Documentation/{{documentation/version}}/Create_a_feature_request|Create a feature request]]{{new}}

----
{{:{{FULLPAGENAME}}/SlicerApplication}}

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----
Modules
----

{| width="100%" cellspacing="7" cellpadding="2"

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[[Image:SlicerAnnotationsV2-Small.png|32px]] [[{{FULLPAGENAME}}/Modules/Annotations|Annotations]]
 

[[Image:DataIcon.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/data.html Data]
 

[[Image:DataStoreIcon_128.png|32px]] [[{{FULLPAGENAME}}/Modules/DataStore|Data Store]]
 

[[Image:DICOM.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM]
 

[[Image:Editor.png|32px]] [[{{FULLPAGENAME}}/Modules/Editor|Editor]]
 

[[Image:Markups.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/markups.html Markups]
 

[[Image:SlicerModels-Small.png|32px]] [[{{FULLPAGENAME}}/Modules/Models|Models]]
 

[[Image:SceneViews.png|32px]] [[{{FULLPAGENAME}}/Modules/SceneViews|Scene Views]]
 

[[Image:Segmentations.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmentations.html Segmentations]
 

[[Image:SegmentEditor.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor]
 

[[Image:Transforms.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/transforms.html Transforms]
 

[[Image:ViewControllersIcon.png|32px]] [[{{FULLPAGENAME}}/Modules/ViewControllers|View Controllers]]
 

[[Image:VolumeRendering.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumerendering.html Volume Rendering]
 

[[Image:SlicerVolume-Small.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumes.html Volumes]
 

[[Image:Welcome.png|32px]] [[{{FULLPAGENAME}}/Modules/Welcome|Welcome to Slicer]]
 

| width="50%" |

{{:{{FULLPAGENAME}}/ModuleExtensionListing/TOC}}

|}


| bgcolor="#CCCCCC" |
| valign="top" |
----
Developers Corner
----

*[[Documentation/Nightly/Developers | Information for Software Developers]]{{updated}}

:Source code, contribute patch, develop modules


----
Miscellaneous
----


*[[Documentation/{{documentation/version}}/HowTo|Documentation guidelines]]

:Slicer user documentation principle and guidelines

*[[Slicer4:VisualBlog|Visual blog]]

:Set of screenshots showing Slicer in action.

*[[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]

:Platform specific issues and considerations

*[[Documentation/{{documentation/version}}/Announcements|Announcements]] & [[Documentation/{{documentation/version}}/Acknowledgments|Acknowledgments]]

*[[Documentation/Nightly/Registration/RegistrationLibrary|Registration Library]]

:Real-life example cases of using the Slicer registration tools, incl. datasets and step-by-step instructions to follow and try yourself.

----
Documentation in other languages
----
{{:{{FULLPAGENAME}}/Lang/ES}}

|}



{| border="0" align="center" width="100%" cellspacing="7" cellpadding="2" valign="top"

|- style="vertical-align:top; border-style:hidden;"

|

{{:{{FULLPAGENAME}}/ModuleExtensionListing/Extensions_by_name}}

|
 
 
=Modules by category=

==Converters==

*[[Documentation/Nightly/Modules/CropVolume|Crop Volume]] (loadable)
*[[Documentation/Nightly/Modules/OrientScalarVolume|Orient Scalar Volume]] (cli)
*[[Documentation/Nightly/Modules/VectorToScalarVolume|Vector To Scalar Volume]] (scripted)
*[[Documentation/Nightly/Modules/CreateDICOMSeries|Create DICOM Series]] (cli)

==Diffusion==

*[[Documentation/Nightly/Modules/DMRIInstall|DMRI Install]] (scripted)


===Diffusion Data Conversion===

*DWI Convert (cli)


===Diffusion Weighted Images===

*BRAINS DWI Cleanup (cli)


===Import and Export===

*DWI Convert (cli)


===Utilities===

*BRAINS DWI Cleanup (cli)
*[[Documentation/Nightly/Modules/ResampleDTIVolume|Resample DTI Volume]] (cli)
*[[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|Resample Scalar Vector DWI Volume]] (cli)


==Endoscopy==

*[[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] (scripted)


==Filter==

*IslandRemoval (cli)


==Filtering==

*[[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4 ITK Bias Field Correction]] (cli)
*[[Documentation/Nightly/Modules/ImageLabelCombine|Image Label Combine]] (cli)
*[[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (cli)
*[[Documentation/Nightly/Modules/CheckerBoardFilter|Checker Board Filter]] (cli)
*[[Documentation/Nightly/Modules/ExtractSkeleton|Extract Skeleton]] (cli)
*[[Documentation/Nightly/Modules/SimpleFilters|Simple Filters]] (scripted)
*[[Documentation/Nightly/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (cli)
*[[Documentation/Nightly/Modules/HistogramMatching|Histogram Matching]] (cli)


===Arithmetic===

*[[Documentation/Nightly/Modules/MultiplyScalarVolumes|Multiply Scalar Volumes]] (cli)
*[[Documentation/Nightly/Modules/AddScalarVolumes|Add Scalar Volumes]] (cli)
*[[Documentation/Nightly/Modules/MaskScalarVolume|Mask Scalar Volume]] (cli)
*[[Documentation/Nightly/Modules/SubtractScalarVolumes|Subtract Scalar Volumes]] (cli)
*[[Documentation/Nightly/Modules/CastScalarVolume|Cast Scalar Volume]] (cli)


===Denoising===

*[[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (cli)
*[[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|Gradient Anisotropic Diffusion]] (cli)
*[[Documentation/Nightly/Modules/MedianImageFilter|Median Image Filter]] (cli)
*[[Documentation/Nightly/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (cli)


===Morphology===

*[[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (cli)
*[[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (cli)


==IGT==

*[[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLink IF]] (loadable)


==Informatics==

*[[Documentation/Nightly/Modules/SEG2NRRD|SEG 2 NRRD]] (cli)
*[[Documentation/Nightly/Modules/Tables|Tables]] (loadable)
*[[Documentation/Nightly/Modules/Data|Data]] (loadable)
*DumpSEGFrame (cli)
*[[Documentation/Nightly/Modules/Terminologies|Terminologies]] (loadable)
*[[Documentation/Nightly/Modules/Units|Units]] (loadable)
*[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM] (scripted)
*[[Documentation/Nightly/Modules/SampleData|Sample Data]] (scripted)
*[[Documentation/Nightly/Modules/Colors|Colors]] (loadable)
*[[Documentation/Nightly/Modules/Annotations|Annotations]] (loadable)
*[[Documentation/Nightly/Modules/Markups|Markups]] (loadable)


===Converters===

*[[Documentation/Nightly/Modules/EncodeSEG|Encode SEG]] (cli)


==Legacy==

===Converters===

*[[Documentation/Nightly/Modules/BSplineToDeformationField|BSpline To Deformation Field]] (cli)


===Filtering===

*[[Documentation/Nightly/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (cli)
*[[Documentation/Nightly/Modules/ResampleScalarVolume|Resample Scalar Volume]] (cli)


===Registration===

*Test Grid Transform Registration (cli)
*[[Documentation/Nightly/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] (cli)

==MultiVolume Support==

*[[Documentation/Nightly/Modules/MultiVolumeImporter|MultiVolume Importer]] (scripted)
*[[Documentation/Nightly/Modules/MultiVolumeExplorer|MultiVolume Explorer]] (loadable)


==Quantification==

*[[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (cli)
*SegmentStatistics (scripted)
*[[Documentation/Nightly/Modules/LabelStatistics|Label Statistics]] (scripted)
*BRAINSLabelStats (cli)
*[[Documentation/Nightly/Modules/DataProbe|Data Probe]] (scripted)


==Registration==

*[[Documentation/Nightly/Modules/Transforms|Transforms]] (loadable)
*BRAINSResize (cli)
*PerformMetricTest (cli)
*[[Documentation/Nightly/Modules/LandmarkRegistration|Landmark Registration]] (scripted)
*[[Documentation/Nightly/Modules/BRAINSResample|BRAINS Resample]] (cli)
*[[Documentation/Nightly/Modules/BRAINSFit|General registration (BRAINS)]] (cli)


===Specialized===

*[[Documentation/Nightly/Modules/ACPCTransform|AC-PC Transform]] (cli)
*[[Documentation/Nightly/Modules/FiducialRegistration|Fiducial Registration]] (cli)
*[[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINS Demon Warp]] (cli)
*[[Documentation/Nightly/Modules/Reformat|Reformat]] (loadable)
*VBRAINSDemonWarp (cli)


==Segmentation==

*[[Documentation/Nightly/Modules/Segmentations|Segmentations]] (loadable)
*[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor] (scripted)
*[[Documentation/Nightly/Modules/Editor|Editor]] (scripted)
*[[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (cli)
*[[Documentation/Nightly/Modules/EMSegment|EMSegment]] (loadable)
*[[Documentation/Nightly/Modules/LungDensitySegmentation|Lung Density Segmentation]] (scripted)

*EMSegmentQuick (loadable)


===Specialized===

*BRAINS ROI Auto (cli)
*[[Documentation/Nightly/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (cli)
*EMSegment CommandLine (cli)



==Surface Models==

*[[Documentation/Nightly/Modules/SurfaceToolbox|Surface Toolbox]] (scripted)
*[[Documentation/Nightly/Modules/GrayscaleModelMaker|Grayscale Model Maker]] (cli)
*[[Documentation/Nightly/Modules/ModelMaker|Model Maker]] (cli)
*[[Documentation/Nightly/Modules/ModelToLabelMap|Model To LabelMap]] (cli)
*[[Documentation/Nightly/Modules/MergeModels|Merge Models]] (cli)
*[[Documentation/Nightly/Modules/LabelMapSmoothing|LabelMap Smoothing]] (cli)
*[[Documentation/Nightly/Modules/ProbeVolumeWithModel|Probe Volume With Model]] (cli)


==Utilities==

*[[Documentation/Nightly/Modules/ScreenCapture|Screen Capture]] (scripted)
*[[Documentation/Nightly/Modules/DataStore|Data Store]] (loadable)
*[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicompatcher.html DICOM Patcher] (scripted)
*BRAINS Strip Rotation (cli)
*EMSegment Transform To New Format (cli)


===BRAINS===

*BRAINS Transform Convert (cli)


==Wizards==

*[[Documentation/Nightly/Modules/CompareVolumes|Compare Volumes]] (scripted)


==Developer Tools==

*[[Documentation/Nightly/Modules/Cameras|Cameras]] (loadable)
*[[Documentation/Nightly/Modules/ExecutionModelTour|Execution Model Tour]] (cli)
*[[Documentation/Nightly/Modules/ExtensionWizard|Extension Wizard]] (scripted)
*[[Documentation/Nightly/Modules/EventBroker|Event Broker]]
*Double Arrays (loadable)


===DICOM Plugins===

*DICOMParametricMapPlugin
*DicomUltrasoundPlugin
*DICOMSegmentationPlugin
*DICOMSlicerDataBundlePlugin
*DICOMTID1500Plugin
*[[Documentation/Nightly/Modules/DICOMPETSUVPlugin|DICOMPETSUVPlugin]]
*DICOMScalarVolumePlugin
*DICOMDiffusionVolumePlugin
*DICOMLongitudinalPETCTPlugin
*DicomSroImportPlugin
*[[Documentation/Nightly/Modules/DICOMRWVMPlugin|DICOMRWVMPlugin]]
*DicomRtImportExportPlugin
*MultiVolumeImporterPlugin

|}

Documentation/Nightly/ModuleExtensionListing/Extensions by name

2021-08-31T14:48:35Z

Pzaffino: /* Extensions by name */

__NOTOC__
* [[#Extensions_by_name|Extensions by name]]
= Extensions by name =
83 extensions:
* [http://www.nitrc.org/projects/abc ABC]
* [[Documentation/Nightly/Extensions/AirwaySegmentation|AirwaySegmentation]]
* [[Documentation/Nightly/Extensions/AnomalousFilters|AnomalousFilters]]
* [[Documentation/Nightly/Extensions/ArduinoController|ArduinoController]]
* [[Documentation/Nightly/Extensions/BoneTextureExtension|BoneTextureExtension]]
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit]
* [http://brainsia.github.io/CardiacAgatstonMeasures/ CardiacAgatstonMeasures]
* [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|CarreraSlice]]
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC_3D_I2MConversion]]
* [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]]
* [http://www.chestimagingplatform.org Chest_Imaging_Platform]
* [[Documentation/Nightly/Extensions/CleaverExtension|CleaverExtension]]
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]
* [[Documentation/Nightly/Extensions/CornerAnnotation|CornerAnnotation]]
* [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]]
* [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]]
* [[Documentation/Nightly/Extensions/DCMQI|DCMQI]]
* [[Documentation/Nightly/Extensions/DebuggingTools|DebuggingTools]]
* [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]]
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]]
* [[Documentation/Nightly/Extensions/DiceComputation|DiceComputation]]
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]
* [[Documentation/Nightly/Extensions/EasyClip|EasyClip]]
* [[Documentation/4.3/Modules/FastGrowCut|FastGrowCutEffect]]
* [[Documentation/Nightly/Modules/FilmDosimetry|FilmDosimetryAnalysis]]
* [[Documentation/Nightly/Modules/GelDosimetry|GelDosimetryAnalysis]]
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment]
* [[Documentation/Nightly/Extensions/GyroGuide|GyroGuide]]
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]
* [[Documentation/Nightly/Extensions/iGyne|iGyne]]
* [[Documentation/Nightly/Extensions/ImageCompare|ImageCompare]]
* [[Documentation/Nightly/Extensions/ImageMaker|ImageMaker]]
* [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]]
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScarSegmenter]]
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|LongitudinalPETCT]]
* [[Documentation/Nightly/Extensions/LungDensitySegmentation|LungDensitySegmentation]]
* [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]]
* [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]]
* [https://github.com/SlicerIGT/MarkupsToModel MarkupsToModel]
* [[Documentation/Nightly/Extensions/MeshStatistics|MeshStatistics]]
* [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]]
* [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]]
* [[Documentation/Nightly/Extensions/mpReview|mpReview]]
* [[Documentation/Nightly/Extensions/MultiLevelRegistration|MultiLevelRegistration]]
* [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]]
* [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]]
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCVExample]]
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|PercutaneousApproachAnalysis]]
* [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]]
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]]
* [[Documentation/Nightly/Extensions/PETDICOM|PETDICOMExtension]]
* [[Documentation/Nightly/Extensions/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]]
* [http://gti-fing.github.io/SlicerPetSpectAnalysis PetSpectAnalysis]
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]]
* [[Documentation/Nightly/Extensions/PickAndPaint|PickAndPaintExtension]]
* [[Documentation/Nightly/Extensions/PkModeling|PkModeling]]
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]
* [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]]
* [[Documentation/Nightly/Extensions/Radiomics|Radiomics]]
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]]
* [[Documentation/Nightly/Extensions/ResectionPlanner|ResectionPlanner]]
* [[Documentation/Nightly/Extensions/ROBEXBrainExtraction|ROBEXBrainExtraction]]
* [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]]
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]
* [[Documentation/Nightly/Extensions/SegmentationWizard|SegmentationWizard]]
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects]
* [https://github.com/SlicerRt/SegmentRegistration SegmentRegistration]
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]
* [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]]
* [[Documentation/Nightly/Extensions/ShapeVariationAnalyzer|ShapeVariationAnalyzer]]
* [[Documentation/Nightly/Extensions/SkullStripper|SkullStripper]]
* [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]]
* [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]]
* [https://github.com/lassoan/SlicerElastix SlicerElastix]
* [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]]
* [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]]
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound]
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]
* [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]]
* [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]]
* [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]]
* [https://github.com/moselhy/SequenceRegistration SlicerSequenceRegistration]
* [[Documentation/Nightly/Extensions/SlicerVirtualReality|SlicerVirtualReality]]
* [https://github.com/SlicerIGT/SlicerSoundControl SoundControl]
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|SlicerToKiwiExporter]]
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]]
* [https://github.com/Tomnl/Slicer-Wasp Wasp]
* [[Documentation/Nightly/Extensions/SobolevSegmenter|SobolevSegmenter]]
* [http://www.nitrc.org/projects/spharm-pdm SPHARM-PDM]
* [[Documentation/Nightly/Extensions/SwissSkullStripper|SwissSkullStripper]]
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]
* [[Documentation/Nightly/Extensions/TrackerStabilizer|TrackerStabilizer]]
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]
* [[Documentation/Nightly/Extensions/VirtualFractureReconstruction|VirtualFractureReconstruction]]
* [http://slicer.vmtk.org/ VMTK]
* [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]]
* [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]]
* [[Documentation/Nightly/Extensions/XNATSlicer|XNATSlicer]]
__NOTOC__

Documentation/Nightly/Extensions/DensityLungSegmentation

2021-08-31T13:35:45Z

Pzaffino:

File:LungDensitySegmentation UI.png

2021-08-31T13:34:55Z

Pzaffino:

Documentation/Nightly/Extensions/DensityLungSegmentation

2021-08-31T13:33:28Z

Pzaffino:

Documentation/Nightly/Extensions/DensityLungSegmentation

2021-08-31T13:32:49Z

Pzaffino:

File:LungDensitySegmentation screenshot.png

2021-08-31T13:31:24Z

Pzaffino:

Documentation/Nightly/Extensions/DensityLungSegmentation

2021-08-31T13:17:34Z

Pzaffino: Created page with "<noinclude>{{documentation/versioncheck}} </noinclude>  {{documentation/{{documentation/version}}/module-header}} <!-- -------------------..."

Documentation/Nightly/Extensions/ArduinoController

2020-09-28T10:21:00Z

Pzaffino:

Documentation/Nightly/Extensions/ArduinoController

2020-09-28T10:19:51Z

Pzaffino:

Documentation/Nightly/Extensions/ArduinoController

2020-08-27T16:47:01Z

Pzaffino:

Documentation/Nightly/Extensions/ArduinoController

2020-08-27T16:45:29Z

Pzaffino:

Documentation/Nightly/Extensions/ArduinoController

2020-08-27T16:44:37Z

Pzaffino:

Documentation/Nightly/Extensions/ArduinoController

2020-08-27T16:42:52Z

Pzaffino:

Documentation/Nightly/Extensions/ArduinoController

2020-08-27T16:41:45Z

Pzaffino:

Documentation/Nightly/Extensions/ArduinoController

2020-08-27T16:39:49Z

Pzaffino:

Documentation/Nightly/Extensions/ArduinoController

2020-08-27T16:39:34Z

Pzaffino:

Documentation/Nightly/Extensions/ArduinoController

2020-08-27T16:38:38Z

Pzaffino:

Documentation/Nightly/Extensions/ArduinoController

2020-08-27T16:38:07Z

Pzaffino:

Documentation/Nightly/Extensions/ArduinoController

2020-08-27T16:37:27Z

Pzaffino:

File:ArduinoController UI screenshot.png

2020-08-27T16:29:46Z

Pzaffino: Pzaffino uploaded a new version of File:ArduinoController UI screenshot.png

File:ArduinoController screenshot.png

2020-08-27T16:25:40Z

Pzaffino: Pzaffino uploaded a new version of File:ArduinoController screenshot.png

User:Pzaffino

2020-06-05T20:50:38Z

Pzaffino: /* '''Paolo Zaffino''' */

='''Paolo Zaffino'''=
[[File:Paolo Zaffino.jpg|thumb]]
Paolo Zaffino received both his master’s degree cum laude (2011) in Biomedical Engineering and his PhD degree (2015) in Bioengineering from Magna Graecia University of Catanzaro (Italy).

After 4 years (September 2015 - July 2019) as a PostDoc fellow and contractor Professor at the same University, since August 2019 he is assistant professor of Biomedical Engineering.

During his PhD he was also a visiting fellow at Massachusetts General Hospital, – Harvard Medical School in Boston (USA). His main topics of interest are in the field of medical image processing,

exploiting machine and deep learning techniques, for clinical applications in diagnosis, radiotherapy and image guided surgery.

He attended several international conferences and workshops about these topics. His current international collaborations include Harvard Medical School, (Boston, USA), German Cancer Center –DKFZ (Heidelberg, Germany), University Medical Center Groningen - UMCG (Groningen, Netherlands) and University for Health Sciences, Medical Informatics and Technology - UMIT (Hall in Tirol, Austria).

He is a member of the National Alliance for Medical Image Computing (NAMIC) and of European Association for Cancer Research (EACR), where he was awarded with a travel grant for pursuing his research collaboration with UMCG.

Paolo joined NAMIC community in 2013 and, in 2017, served as local organizing committee for the 25th Slicer Project Week, held in Catanzaro, Italy.

 

=== Links: ===

* [https://scholar.google.it/citations?user=lOvu6lAAAAAJ&hl=it&oi=ao Google scholar]
* [https://www.researchgate.net/profile/Paolo_Zaffino Research gate]
* [https://orcid.org/0000-0002-0219-0157 ORCID]
* [https://github.com/pzaffino GitHub]
* [http://dmsc.unicz.it/personale/docente/paolozaffino University webpage]

User:Pzaffino

2020-06-05T20:49:25Z

Pzaffino:

='''Paolo Zaffino'''=
[[File:Paolo Zaffino.jpg|thumb]]
Paolo Zaffino received both his master’s degree cum laude (2011) in Biomedical Engineering and his PhD degree (2015) in Bioengineering from Magna Graecia University of Catanzaro (Italy).

After 4 years (September 2015 - July 2019) as a PostDoc fellow and contractor Professor at the same University, since August 2019 he is assistant professor of Biomedical Engineering.

During his PhD he was also a visiting fellow at Massachusetts General Hospital, – Harvard Medical School in Boston (USA). His main topics of interest are in the field of medical image processing,

exploiting machine and deep learning techniques, for clinical applications in diagnosis, radiotherapy and image guided surgery.

He attended several international conferences and workshops about these topics. His current international collaborations include Harvard Medical School, (Boston, USA), German Cancer Center –DKFZ (Heidelberg, Germany), University Medical Center Groningen - UMCG (Groningen, Netherlands) and University for Health Sciences, Medical Informatics and Technology - UMIT (Hall in Tirol, Austria).

He is a member of the National Alliance for Medical Image Computing (NAMIC) and of European Association for Cancer Research (EACR), where he was awarded with a travel grant for pursuing his research collaboration with UMCG.

Paolo joined NAMIC community in 2013 and, in 2017, served as local organizing committee for the 25th Slicer Project Week, held in Catanzaro, Italy.

 

=== Links: ===

* [https://scholar.google.it/citations?user=lOvu6lAAAAAJ&hl=it&oi=ao Google scholar]
* [https://www.researchgate.net/profile/Paolo_Zaffino Research gate]
* [https://orcid.org/0000-0002-0219-0157 ORCID]
* [https://github.com/pzaffino Git-Hub]
* [http://dmsc.unicz.it/personale/docente/paolozaffino University webpage]

User:Pzaffino

2020-06-05T20:39:18Z

Pzaffino:

=Paolo Zaffino=
 
[[File:Paolo Zaffino.jpg|thumb]]
Paolo Zaffino received both his master’s degree cum laude (2011) in Biomedical Engineering and his PhD degree (2015) in Bioengineering from Magna Graecia University of Catanzaro (Italy).

After 4 years (September 2015 - July 2019) as a PostDoc fellow and contractor Professor at the same University, since August 2019 he is assistant professor of Biomedical Engineering.

During his PhD he was also a visiting fellow at Massachusetts General Hospital, – Harvard Medical School in Boston (USA). His main topics of interest are in the field of medical image processing,

exploiting machine and deep learning techniques, for clinical applications in diagnosis, radiotherapy and image guided surgery.

He attended several international conferences and workshops about these topics. His current international collaborations include Harvard Medical School, (Boston, USA), German Cancer Center –DKFZ (Heidelberg, Germany), University Medical Center Groningen - UMCG (Groningen, Netherlands) and University for Health Sciences, Medical Informatics and Technology - UMIT (Hall in Tirol, Austria).

He is a member of the National Alliance for Medical Image Computing (NAMIC) and of European Association for Cancer Research (EACR), where he was awarded with a travel grant for pursuing his research collaboration with UMCG.

Paolo joined NAMIC community in 2013 and, in 2017, served as local organizing committee for the 25th Slicer Project Week, held in Catanzaro, Italy.

User:Pzaffino

2020-06-05T20:38:27Z

Pzaffino:

=Paolo Zaffino=
 
[[File:Paolo Zaffino.jpg|thumb]]
Paolo Zaffino received both his master’s degree cum laude (2011) in Biomedical Engineering and his PhD degree (2015) in Bioengineering from Magna Graecia University of Catanzaro (Italy).

After 4 years (September 2015 - July 2019) as a PostDoc fellow and contractor Professor at the same University, since August 2019 he is assistant professor of Biomedical Engineering.

During his PhD he was also a visiting fellow at Massachusetts General Hospital, – Harvard Medical School in Boston (USA). His main topics of interest are in the field of medical image processing,

exploiting machine and deep learning techniques, for clinical applications in diagnosis, radiotherapy and image guided surgery.

He attended several international conferences and workshops about these topics. His current international collaborations include Harvard Medical School, (Boston, USA), German Cancer Center –DKFZ (Heidelberg, Germany),

University Medical Center Groningen - UMCG (Groningen, Netherlands) and University for Health Sciences, Medical Informatics and Technology - UMIT (Hall in Tirol, Austria).

He is a member of the National Alliance for Medical Image Computing (NAMIC) and of European Association for Cancer Research (EACR), where he was awarded with a travel grant for pursuing his research collaboration with UMCG.

Paolo joined NAMIC community in 2013 and, in 2017, served as local organizing committee for the 25th Slicer Project Week, held in Catanzaro, Italy.

File:Paolo Zaffino.jpg

2020-06-05T20:37:42Z

Pzaffino:

Paolo Zaffino

User:Pzaffino

2020-06-05T20:36:10Z

Pzaffino:

=Paolo Zaffino=
Paolo Zaffino received both his master’s degree cum laude (2011) in Biomedical Engineering and his PhD degree (2015) in Bioengineering from Magna Graecia University of Catanzaro (Italy).

After 4 years (September 2015 - July 2019) as a PostDoc fellow and contractor Professor at the same University, since August 2019 he is assistant professor of Biomedical Engineering.

During his PhD he was also a visiting fellow at Massachusetts General Hospital, – Harvard Medical School in Boston (USA). His main topics of interest are in the field of medical image processing,

exploiting machine and deep learning techniques, for clinical applications in diagnosis, radiotherapy and image guided surgery.

He attended several international conferences and workshops about these topics. His current international collaborations include Harvard Medical School, (Boston, USA), German Cancer Center –DKFZ (Heidelberg, Germany),

University Medical Center Groningen - UMCG (Groningen, Netherlands) and University for Health Sciences, Medical Informatics and Technology - UMIT (Hall in Tirol, Austria).

He is a member of the National Alliance for Medical Image Computing (NAMIC) and of European Association for Cancer Research (EACR), where he was awarded with a travel grant for pursuing his research collaboration with UMCG.

Paolo joined NAMIC community in 2013 and, in 2017, served as local organizing committee for the 25th Slicer Project Week, held in Catanzaro, Italy.

User:Pzaffino

2020-06-05T20:31:26Z

Pzaffino:

= Paolo Zaffino =
My name is Paolo Zaffino, I am a biomedical engineer and I work as an assistant professor a Magna Graecia University, Catanzaro, Italy.
I got my PhD in 2015.
I joined namic community in 2013.
I work on image registration, image segmentation, and deep learning solutions for medical applications, in particualr for radiotherapy.

Documentation/Nightly/ModuleExtensionListing/Extensions by category

2020-02-05T13:47:01Z

Pzaffino: /* Developer Tools */

__NOTOC__
* [[#Extensions_by_category|Extensions by category]]
= Extensions by category =
33 categories:
* [[#Extensions_by_category_Astronomy|Astronomy]]
* [[#Extensions_by_category_Cardiac|Cardiac]]
* [[#Extensions_by_category_Cardiac_MRI_toolkit|Cardiac MRI toolkit]]
* [[#Extensions_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
* [[#Extensions_by_category_Converters|Converters]]
* [[#Extensions_by_category_Developer_Tools|Developer Tools]]
* [[#Extensions_by_category_DICOM|DICOM]]
* [[#Extensions_by_category_Diffusion|Diffusion]]
* [[#Extensions_by_category_Digital_Pathology|Digital Pathology]]
* [[#Extensions_by_category_Editor_Effects|Editor Effects]]
* [[#Extensions_by_category_Examples|Examples]]
* [[#Extensions_by_category_Exporter|Exporter]]
* [[#Extensions_by_category_Filtering|Filtering]]
* [[#Extensions_by_category_IGT|IGT]]
* [[#Extensions_by_category_Informatics|Informatics]]
* [[#Extensions_by_category_Libraries|Libraries]]
* [[#Extensions_by_category_Machine_Learning|Machine Learning]]
* [[#Extensions_by_category_Mesh_Generation|Mesh Generation]]
* [[#Extensions_by_category_Microscopy|Microscopy]]
* [[#Extensions_by_category_Nuclear_Medicine|Nuclear Medicine]]
* [[#Extensions_by_category_Quantification|Quantification]]
* [[#Extensions_by_category_Radiotherapy|Radiotherapy]]
* [[#Extensions_by_category_Registration|Registration]]
* [[#Extensions_by_category_Remote|Remote]]
* [[#Extensions_by_category_Scoliosis|Scoliosis]]
* [[#Extensions_by_category_Segmentation|Segmentation]]
* [[#Extensions_by_category_Sequences|Sequences]]
* [[#Extensions_by_category_Shape_Analysis|Shape Analysis]]
* [[#Extensions_by_category_Tractography|Tractography]]
* [[#Extensions_by_category_Training|Training]]
* [[#Extensions_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Extensions_by_category_Virtual_Reality|Virtual Reality]]
* [[#Extensions_by_category_Web_System_Tools|Web System Tools]]
* [[#Extensions_by_category_Wizards|Wizards]]

== Astronomy ==
* [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]]

== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]]
* [http://brainsia.github.io/CardiacAgatstonMeasures/ CardiacAgatstonMeasures]

== Cardiac MRI toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit]

== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org Chest_Imaging_Platform]

== Converters ==
* [[Documentation/Nightly/Extensions/PETDICOM|PETDICOMExtension]]

== Developer Tools ==
* [[Documentation/Nightly/Extensions/ArduinoController|ArduinoController]]
* [https://github.com/gregsharp/Slicer-CUDAProbe CUDA Probe]
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]]
* [[Documentation/Nightly/Extensions/DebuggingTools|DebuggingTools]]
* [[Documentation/Nightly/Extensions/ImageMaker|ImageMaker]]
* [[Documentation/Nightly/Extensions/MatlabBridge|MatlabBridge]]


== DICOM ==
* [[Documentation/Nightly/Extensions/DCMQI|DCMQI]]

== Diffusion ==
* [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]]
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]]

== Digital Pathology ==
* [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]]

== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]]

== Examples ==
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCVExample]]

== Exporter ==
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|SlicerToKiwiExporter]]

== Filtering ==
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound]

== IGT ==
* [[Documentation/Nightly/Extensions/GyroGuide|GyroGuide]]
* [[Documentation/Nightly/Extensions/TrackerStabilizer|TrackerStabilizer]]
* [[Documentation/Nightly/Extensions/CornerAnnotation|CornerAnnotation]]
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]]
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|PercutaneousApproachAnalysis]]
* [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]]
* [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]]
* [[Documentation/Nightly/Extensions/iGyne|iGyne]]
* [[Documentation/Nightly/Extensions/ResectionPlanner|ResectionPlanner]]

== Informatics ==
* [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]]
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|LongitudinalPETCT]]
* [[Documentation/Nightly/Extensions/mpReview|mpReview]]
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]
* [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]]
* [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]]

== Libraries ==
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]

== Machine Learning ==
* [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]]


== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC_3D_I2MConversion]]
* [[Documentation/Nightly/Extensions/CleaverExtension|CleaverExtension]]

== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]

== Nuclear Medicine ==
* [http://gti-fing.github.io/SlicerPetSpectAnalysis PetSpectAnalysis]

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]
* [[Documentation/Nightly/Extensions/ImageCompare|ImageCompare]]
* [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]]
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]
* [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]]
* [[Documentation/Nightly/Extensions/DiceComputation|DiceComputation]]
* [[Documentation/Nightly/Extensions/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]]
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]]
* [[Documentation/Nightly/Extensions/PkModeling|PkModeling]]
* [[Documentation/Nightly/Extensions/ShapeVariationAnalyzer|ShapeVariationAnalyzer]]


== Radiotherapy ==
* [[Documentation/Nightly/Modules/FilmDosimetry|FilmDosimetryAnalysis]]
* [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]]
* [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]]
* [[Documentation/Nightly/Modules/GelDosimetry|GelDosimetryAnalysis]]

== Registration ==
* [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]]
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]
* [[Documentation/Nightly/Extensions/MultiLevelRegistration|MultiLevelRegistration]]


== Remote ==
* [[Documentation/Nightly/Extensions/XNATSlicer|XNATSlicer]]

== Scoliosis ==
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]

== Segmentation ==
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment]
* [http://www.nitrc.org/projects/abc ABC]
* [[Documentation/Nightly/Extensions/ROBEXBrainExtraction|ROBEXBrainExtraction]]
* [[Documentation/Nightly/Extensions/SwissSkullStripper|SwissSkullStripper]]
* [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|CarreraSlice]]
* [[Documentation/Nightly/Extensions/SkullStripper|SkullStripper]]
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]]
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScarSegmenter]]
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects]
* [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]]
* [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]]
* [https://github.com/Tomnl/Slicer-Wasp Wasp]
* [[Documentation/Nightly/Extensions/AirwaySegmentation|AirwaySegmentation]]
* [[Documentation/Nightly/Extensions/SobolevSegmenter|SobolevSegmenter]]
* [[Documentation/4.3/Modules/FastGrowCut|FastGrowCutEffect]]
* [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]]

== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]

== Shape Analysis ==
* [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]]
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]
* [[Documentation/Nightly/Extensions/EasyClip|EasyClip]]
* [[Documentation/Nightly/Extensions/PickAndPaint|PickAndPaintExtension]]
* [[Documentation/Nightly/Extensions/MeshStatistics|MeshStatisticsExtension]]
* [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/SpharmPdm SPHARM-PDM]
* [[Documentation/Nightly/Extensions/SkeletalRepresentation|SkeletalRepresentation]]


== Tractography ==
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]

== Training ==
* [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]]

== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ VMTK]


==Virtual Reality==
* [[Documentation/Nightly/Extensions/SlicerVirtualReality|SlicerVirtualReality]]


== Web System Tools ==
* [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]]

== Wizards ==
* [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]]
__NOTOC__