Difference between revisions of "Documentation/Nightly/Modules/CornerAnnotation"

From Slicer Wiki
Jump to: navigation, search
 
(52 intermediate revisions by the same user not shown)
Line 8: Line 8:
 
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
 
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
 
{{documentation/{{documentation/version}}/module-introduction-row}}
 
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is supported by NA-MIC, NCIGT, Slicer Community, and Shiga University of Medical Science in Japan.
+
This work is supported by Shiga University of Medical Science (SUMS) in Japan, NA-MIC, NCIGT, and Slicer Community.
 
<!-- This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br> -->
 
<!-- This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br> -->
  
Author: Atsushi Yamada, Shiga University of Medical Science (SUMS), Japan<br>
+
Author: Atsushi Yamada (SUMS)<br>
Contributors: Junichi Tokuda (Brigham and Women's Hospital), Koichiro Murakami (SUMS), Shigeyuki Naka (SUMS), Tohru Tani (SUMS)<br>
+
Contributors: Junichi Tokuda (BWH), Koichiro Murakami (BWH, SUMS), Soichiro Tani (SUMS), Shigeyuki Naka (SUMS), Tohru Tani (SUMS)<br>
 
Contact: Atsushi Yamada, <email>ayamada@belle.shiga-med.ac.jp</email><br>
 
Contact: Atsushi Yamada, <email>ayamada@belle.shiga-med.ac.jp</email><br>
 +
License: [http://www.slicer.org/pages/LicenseText Slicer License]
 +
 
{{documentation/{{documentation/version}}/module-introduction-row}}
 
{{documentation/{{documentation/version}}/module-introduction-row}}
 
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
 
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:SumsLogo2014.jpg|Shiga University of Medical Science, Japan
+
|Image:SumsLogo2014.jpg|Shiga University of Medical Science (SUMS) in Japan
 
|{{collaborator|logo|namic}}|NA-MIC
 
|{{collaborator|logo|namic}}|NA-MIC
 
|{{collaborator|logo|ncigt}}|NCIGT
 
|{{collaborator|logo|ncigt}}|NCIGT
Line 25: Line 27:
 
{{documentation/{{documentation/version}}/module-section|Module Description}}
 
{{documentation/{{documentation/version}}/module-section|Module Description}}
 
{|
 
{|
|[[File:PercutaneousPathDesignerView1.png|360x240px]]
+
|[[File:CA-1.png|460x640px]]
|[[File:PercutaneousPathDesignerView2.png|360x240px]]
 
|[[File:PercutaneousPathDesignerView3.png|360x240px]]
 
 
|}
 
|}
 +
 
{|
 
{|
|[[File:PercutaneousPathDesignerView4.png|360x240px]]
+
|[[File:CA-UI3.png|460x760px]]
|[[File:PercutaneousPathDesignerView8.png|360x240px]]
 
|[[File:PercutaneousPathDesignerView9.png|360x240px]]
 
 
|}
 
|}
 +
The CornerAnnottion module is a Slicer4 module designed to display annotations, time count, node elements on each panels (3D, Red, Yellow and Green views, respectively) on the Slicer user interface.
 +
You can edit annotations, display panels, font style, color, and opacity, respectively.
  
PercutaneousPathDesigner is a Slicer4 module designed to display bundles of needle path candidates to avoid blood vessels, bones and specific anatomies and create the path from the bundle.
 
The bundles of path candidates is calculated based on a target point, a skin model and an obstacle model.
 
After the calculation, you can obtain possible trajectories to avoid the obstacles as bundles of path candidates.
 
This bundle expression may help you grasp safety paths easily. 
 
Furthermore, it is possible to evaluate the each path on the bundles based on the length and the trajectory comparing with the longest path and the shortest path.
 
The location of the skin entry point of each path can be modified by extending and shrinking the path.
 
The target point and the skin entry point you modified on the selected path could be output as a MarkupsFiducial List.
 
You can clean up the models generated from this module.       
 
 
<!--
 
<!--
 
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.
 
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.
Line 52: Line 45:
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
{{documentation/{{documentation/version}}/module-section|Use Cases}}
+
{{documentation/{{documentation/version}}/module-section|Use Cases}}  
PercutaneousPathDesigner is a useful tool for planning needle insertion.
+
{|
Percutaneous thermal ablations including radio frequency, microwave and cryotherapy requires needle trajectories to avoid blood vessels, bones and specific anatomies to reach probes to target around tumors.
+
|[[File:CornerAnnotationModuleSS.png|460x760px]]
Needle biopsy also requires safety path to gather multiple tissue.
+
|}
For these cases, this module can help to obtain the path candidates based on the target point, a segmented model of the avoidable region and another segmented model which represents skin entry surface.  
+
 
 
+
The CornerAnnotation module allows to display any texts you create at any corners on your Slicer viewers. Furthermore, you can also display a timer count and elements of transform matrixes you set.
 +
Therefore, you can use this module, for example, to alert a surgeon to an ablation time and to indicate the tip of the tracker for quantitative assessment attractively in image guided therapy.  
 +
We hope this module can help 3D Slicer to be used as a navigation system.      
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
Line 66: Line 61:
 
{{documentation/{{documentation/version}}/module-section|Panels and their use}}
 
{{documentation/{{documentation/version}}/module-section|Panels and their use}}
 
{|
 
{|
|[[Image:PercutaneousPathDesignerPanel4.png|thumb|400px|{{documentation/modulename}} Parameters panel ]]
+
|[[File:CA-UI1.png|460x640px]]
 
|}
 
|}
 
+
* Annotations panel
* Parameters panel
+
** This module allows to create four annotations: Left Bottom, Left Upper, Right Bottom and Right Upper. Each Enable button display each text you created.
** Target Point requires MarkupsFiducial List created in Markups Module which has only one markup.
+
**Text format
** Output Fiducial List requires MarkupsFiducial List created in Markups Module which has no markups.  
+
***@n: start a new line
** Skin Model requires a model which represents a skin, that is, a surface on the needle tips.
+
***@t: display timer
*** Opacity Slider can change the opacity parameter of the Skin Model selected.
+
***[3-10]: Element(1,0) of Node3
** Obstacle Model requires a model which represents obstacles needle paths should avoid.
 
*** Opacity Slider can change the opacity parameter for the Obstacle Model selected.
 
** Create Paths button starts creating path candidates from target point to the skin model to avoid the obstacle model.
 
 
 
 
{|
 
{|
|[[Image:PercutaneousPathDesignerPanel2.png|thumb|400px|{{documentation/modulename}} Outcomes panel ]]
+
|[[File:CA-UI2.png|460x660px]]
 
|}
 
|}
 
* Outcomes panel
 
** All Paths (Yellow) check button displays all path candidates shown as the yellow bundles of lines. 
 
*** Opacity Slider can change the opacity parameter for the yellow bundles.
 
** The Longest Path (Green) check button displays the longest path as the green line.
 
** The Shortest Path (Blue) check button displays the shortest path as the blue line.
 
** The Path Candidate (Red) check button displays the one of the yellow bundles as the red line.
 
*** Path Candidate (No.) Slider can select the line from the yellow bundles.
 
*** Point Candidate on the Path Slider can extend and shrink the selected red line from the skin entry point.
 
*** Create Point on the Path button writes the entry position to the Output Fiducial List you set in the Parameters panel. 
 
 
{|
 
|[[Image:PercutaneousPathDesignerPanel3.png|thumb|400px|{{documentation/modulename}} Configurations panel ]]
 
|}
 
 
 
* Configurations panel
 
* Configurations panel
** Delete Paths button erases the all models created by this module.
+
**Display Panels check boxes can enable annotations you created to display on 3D, Red, Yellow, and Green views respectively.
 +
**Font Family selector can change font style.
 +
**Font color selector can change font color.
 +
**Font opacity slider bar can change opacity for displayed annotations.
 +
**Font Style
 +
***Bold, Italic, Shadow checkboxes can change the font style of the annotations.
 +
***Size slider bar can change font size.
 +
**Timer
 +
***Start button can start the timer.
 +
***Stop button can stop the timer count.
 +
***Reset button can reset the timer count.
 +
***Description
 +
****You can display timer count by typing "@t" in the annotation texts.
 +
**Node selectors
 +
***There are four node selector. You can select Transform Node you created by using Transform module.
 +
***Description
 +
****You can display the transform element (0,2) of Node1 by typing "[1-02]" in the annotation texts. 
 +
****You can display the transform element (0,1) of Node2 by typing "[2-01]" in the annotation texts. 
  
 
<!--
 
<!--
Line 109: Line 102:
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|References}}
 
{{documentation/{{documentation/version}}/module-section|References}}
*[http://www.na-mic.org/Wiki/index.php/2014_Project_Week:PercutaneousApproachAnalysis Percutaneous Approach Analysis project in 2014 Winter Project Week ]
+
*[https://github.com/ayamada0614/CornerAnnotation Github source code repository]
*[https://github.com/ayamada0614/PercutaneousPathDesigner Source code repository]
+
*Transform module
 +
*[http://openigtlink.org/ OpenIGTLinkIF module]
 +
 
 +
<!-- ---------------------------- -->
 +
{{documentation/{{documentation/version}}/module-section|Logo}}
 +
{|
 +
|[[File:CornerAnnotationIcon.png|128x128px]]
 +
|}
 +
 
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->

Latest revision as of 08:35, 3 December 2014

Home < Documentation < Nightly < Modules < CornerAnnotation

For the stable Slicer documentation, visit the 4.10 page.

Introduction and Acknowledgements

This work is supported by Shiga University of Medical Science (SUMS) in Japan, NA-MIC, NCIGT, and Slicer Community.

Author: Atsushi Yamada (SUMS)
Contributors: Junichi Tokuda (BWH), Koichiro Murakami (BWH, SUMS), Soichiro Tani (SUMS), Shigeyuki Naka (SUMS), Tohru Tani (SUMS)
Contact: Atsushi Yamada, <email>ayamada@belle.shiga-med.ac.jp</email>
License: Slicer License

Shiga University of Medical Science (SUMS) in Japan  
NA-MIC  
NCIGT  

Module Description

CA-1.png
CA-UI3.png

The CornerAnnottion module is a Slicer4 module designed to display annotations, time count, node elements on each panels (3D, Red, Yellow and Green views, respectively) on the Slicer user interface. You can edit annotations, display panels, font style, color, and opacity, respectively.


Use Cases

CornerAnnotationModuleSS.png

The CornerAnnotation module allows to display any texts you create at any corners on your Slicer viewers. Furthermore, you can also display a timer count and elements of transform matrixes you set. Therefore, you can use this module, for example, to alert a surgeon to an ablation time and to indicate the tip of the tracker for quantitative assessment attractively in image guided therapy. We hope this module can help 3D Slicer to be used as a navigation system.

Tutorials

N/A

Panels and their use

CA-UI1.png
  • Annotations panel
    • This module allows to create four annotations: Left Bottom, Left Upper, Right Bottom and Right Upper. Each Enable button display each text you created.
    • Text format
      • @n: start a new line
      • @t: display timer
      • [3-10]: Element(1,0) of Node3
CA-UI2.png
  • Configurations panel
    • Display Panels check boxes can enable annotations you created to display on 3D, Red, Yellow, and Green views respectively.
    • Font Family selector can change font style.
    • Font color selector can change font color.
    • Font opacity slider bar can change opacity for displayed annotations.
    • Font Style
      • Bold, Italic, Shadow checkboxes can change the font style of the annotations.
      • Size slider bar can change font size.
    • Timer
      • Start button can start the timer.
      • Stop button can stop the timer count.
      • Reset button can reset the timer count.
      • Description
        • You can display timer count by typing "@t" in the annotation texts.
    • Node selectors
      • There are four node selector. You can select Transform Node you created by using Transform module.
      • Description
        • You can display the transform element (0,2) of Node1 by typing "[1-02]" in the annotation texts.
        • You can display the transform element (0,1) of Node2 by typing "[2-01]" in the annotation texts.


Similar Modules

N/A

References

CornerAnnotationIcon.png


Information for Developers