Difference between revisions of "Documentation/4.3/Announcements"

From Slicer Wiki
Jump to: navigation, search
(Nightly -> 4.3)
 
 
(29 intermediate revisions by 8 users not shown)
Line 11: Line 11:
  
 
{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"
 
{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"
−
|[[#Introduction|Introduction ]]
+
|[[#Summary|Summary ]]
−
|[[#Our Philosophy| Our Philosophy ]]
+
|[[#What is 3D Slicer|What is 3D Slicer]]
−
|[[#Slicer Highlights|Slicer Highlights ]]
+
|[[#Slicer {{documentation/version}} Highlights|Slicer {{documentation/version}} Highlights]]
 
|[[#Slicer Extensions|Slicer Extensions]]
 
|[[#Slicer Extensions|Slicer Extensions]]
 
|[[#Other Improvements,  Additions & Documentation| Other Improvements,  Additions & Documentation]]
 
|[[#Other Improvements,  Additions & Documentation| Other Improvements,  Additions & Documentation]]
 
|}
 
|}
−
=Introduction=  
+
=Summary=  
  
 
The [http://www.slicer.org/pages/Acknowledgments community] of Slicer developers is proud to announce the release of '''Slicer {{documentation/version}}'''.
 
The [http://www.slicer.org/pages/Acknowledgments community] of Slicer developers is proud to announce the release of '''Slicer {{documentation/version}}'''.
  
−
*Slicer {{documentation/version}} introduces [...] and many tweaks and augmentations of the major changes introduced in Slicer {{documentation/version}}.
+
*Slicer {{documentation/version}} introduces  
 +
** a new App store, called the extension manager, for adding capabilities to Slicer. Close to 40 plug-ins are currently available.
 +
** close to 500 feature improvements and bug fixes lead to improved performance and stability.
 +
** augmentation of many modules.
 +
** improved workflows in registration and dMRI
 +
** the multivolume explorer allows interaction with time series and DCE data.
 +
** major improvements to the DICOM module
 +
** a new Markups module to streamline the use of fiducial lists
 +
 
  
 
*Click here to [http://download.slicer.org/ download] Slicer {{documentation/version}} for different platforms and find pointers to the source code, mailing lists and bug tracker.  
 
*Click here to [http://download.slicer.org/ download] Slicer {{documentation/version}} for different platforms and find pointers to the source code, mailing lists and bug tracker.  
−
*Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer4 are not fully tested.
+
*Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer are not fully tested.
−
*The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of courses for learning how to use Slicer4. The portfolio contains self-guided presentation and sample data sets.  
+
*The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of courses for learning how to use Slicer. The portfolio contains self-guided presentation and sample data sets.  
  
 
The main [http://www.slicer.org slicer.org] pages provide a guided tour to the application, training materials, and the development community.  New users should start there because we try to keep the pages organized and up to date.
 
The main [http://www.slicer.org slicer.org] pages provide a guided tour to the application, training materials, and the development community.  New users should start there because we try to keep the pages organized and up to date.
  
 +
<!--
 
Find out more about Slicer {{documentation/version}} in the webinar held on [...]:
 
Find out more about Slicer {{documentation/version}} in the webinar held on [...]:
  
 
[[Image:Webinar-Slicer-4.1.png|link=http://vimeo.com/41096643|400px|center]]
 
[[Image:Webinar-Slicer-4.1.png|link=http://vimeo.com/41096643|400px|center]]
 +
-->
  
−
=Our Philosophy=
+
=What is 3D Slicer=
 
Slicer is  a community platform created for the purpose of subject specific image analysis and visualization.  
 
Slicer is  a community platform created for the purpose of subject specific image analysis and visualization.  
  
Line 43: Line 53:
 
There is no restriction on use, but permissions and compliance with rules are responsibility of users. For details on the license see [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl here]
 
There is no restriction on use, but permissions and compliance with rules are responsibility of users. For details on the license see [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl here]
  
−
=Slicer Highlights=
+
=Slicer {{documentation/version}} Highlights=
−
<gallery caption="New and Improved Modules" widths="250px" heights="150px" perrow="3">
+
<gallery caption="New and Improved Toolkits and Modules" widths="250px" heights="150px" perrow="3">
 
Image:ITK_logo.png|Moved from ITKv3 to ITKv4
 
Image:ITK_logo.png|Moved from ITKv3 to ITKv4
 
Image:SimpleITK_Logo.png|Added SimpleITK
 
Image:SimpleITK_Logo.png|Added SimpleITK
 
Image:CLIAutoRun.png|Added AutoRun mode for CLI modules to interactively search in parameter space and to create pipelines of filters. Watch the [https://vimeo.com/64813350  demo]!
 
Image:CLIAutoRun.png|Added AutoRun mode for CLI modules to interactively search in parameter space and to create pipelines of filters. Watch the [https://vimeo.com/64813350  demo]!
−
Image:Markups-GUI-Collapsed.png|The [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Markups Markups] module replaces Annotation fiducials.
+
Image:Markups-GUI-Collapsed.png|The [[Documentation/{{documentation/version}}/Modules/Markups|Markups]] module replaces Annotation fiducials.
 +
Image:RegLib_thumb.png| Slicer [[Documentation/{{documentation/version}}/Modules/BRAINSFit|image registration]] modules have been reimplemented using ITKv4, with streamlined interfaces and improved robustness. An updated [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary| Registration Library]] is showcasing examples with downloadable data and full step-by-step instructions.
 
</gallery>
 
</gallery>
  
−
=Slicer Extensions=
+
= Slicer Extensions =
−
<gallery caption="New and Improved Extensions" widths="250px" heights="150px" perrow="3">
+
 
−
Image:QuickToolsLogo.png|[[Documentation/{{documentation/version}}/Extensions/ImageMaker|Image Maker]] to create volumes from scratch
+
<gallery caption="New and Improved Extensions" widths="250px" heights="150px" perrow="4">
 +
Image:AirwaySegmentation-ICON.png|[[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|Airway Segmentation]] to segment the airway from chest CT images.{{new}}
 +
Image:CMRTK-logo.png|[[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] to analyze cardiac LGE-MRI images. {{new}}
 +
Image:ChangeTracker logo.png|[[Documentation/{{documentation/version}}/Extensions/ChangeTracker| Change Tracker]] for quantification of the subtle changes in pathology.{{new}}
 +
Image:DataStoreIcon.png|[[Documentation/{{documentation/version}}/Extensions/DataStore|Data Store]] Allows to easily upload and download dataset files.{{new}}
 +
Image:DiceSimilarityCoefficient.png|[[Documentation/{{documentation/version}}/Extensions/DiceComputation|Dice Computation]] to calculate the Dice Similarity Coefficient (DSC) between multiple label map images.{{new}}
 +
Image:DTIAtlasBuilder.jpeg|[[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTI Atlas Builder]] to create an Atlas image as an average of several DTI images that will be registered.{{updated}}
 +
Image:DTIPrep.png|[[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTI Prep]].{{updated}}
 +
Image:DTIProcess-mj.png|[[Documentation/{{documentation/version}}/Extensions/DTIProcess| DTI Process]].{{updated}}
 +
Image:ErodeDilateLabelIcon.png|[[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|Erode/Dilate Label]] to perform binary erosion and dilation on a specified label.{{new}}
 +
Image:FacetedVisualizer.png|[[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|Faceted Visualizer]] to create flexible visualizations using Slicer by combining a 3D digital atlas and 3D scene models with an ontology.{{updated}}
 +
Image:FiberViewerLight.png|[[Documentation/{{documentation/version}}/Extensions/FiberViewerLight| Fiber Viewer Light]] to create fiber clusters based on methods such as Length, Gravity, Hausdorff, or Mean Distribution and Normalized Cut.{{updated}}
 +
Image:IASEM.png|[[Documentation/{{documentation/version}}/Extensions/IASEM| IASEM]] to segmentation and process of IASEM Electron Microscopy images.{{new}}
 +
Image:QuickToolsLogo.png|[[Documentation/{{documentation/version}}/Extensions/ImageMaker|Image Maker]] to create volumes from scratch. {{new}}
 +
Image:LAScarSegmenter.png|[[Documentation/{{documentation/version}}/Extensions/LAScarSegmenter|LA Scar Segmenter]] to perform segmentation of the left atrial scarring tissue from MR images. {{new}}
 +
Image:LASegmenter.png|[[Documentation/{{documentation/version}}/Extensions/LASegmenter|LA Segmenter]] to perform segmentation of the left atrium from MR images.{{new}}
 +
Image:LongitudinalPETCTLogo.png|[[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT| Longitudinal PET/CT]] to provide a user friendly Slicer interface for quantification of DICOM PET/CT image data.{{updated}
 +
Image:MatlabBridgeLogo.png|[[Documentation/{{documentation/version}}/Extensions/MatlabBridge| Matlab Bridge]] to allow running Matlab functions directly in 3D Slicer.{{new}}
 +
Image:ModelClipIcon.png|[[Documentation/{{documentation/version}}/Extensions/ModelClip| Model Clip]] to set osteotomy trajectory with multiple planes, and clip the model with just one click.{{new}}
 +
Image:PathPlannerIcon.png|[[Documentation/{{documentation/version}}/Extensions/PathPlanner| Path Planner]]to facilitate the creation of trajectory.{{new}}
 +
Image:PkModeling.png|[[Documentation/{{documentation/version}}/Extensions/PkModeling| Pk Modeling]] to calculate quantitative parameters from Dynamic Contrast Enhanced DCE-MRI images.{{new}}
 +
Image:PlusRemoteLogo.png|[[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] to send commands through OpenIGTLink Remote to PLUS.{{new}}
 +
Image:Portplacement_icon.png|[[Documentation/{{documentation/version}}/Extensions/PortPlacement| Port Placement]]to assists in the planning of surgical port placement in laparoscopic procedures.{{new}}
 +
Image:ReportingLogo.png|[[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] to create image annotations/markup that are stored in a structured form.{{updated}}
 +
Image:SkullStripper.png|[[Documentation/{{documentation/version}}/Extensions/SkullStripper|Skull Stripper]] to register an atlas image to the patient data.{{updated}}
 +
Image:SlicerIGTLogo.png|[[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] to use all the advanced features of 3D Slicer for real-time navigation.{{new}}
 +
Image:SlicerRT Logo 2.0 128x128.png|[[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] is a tool for powerful radiotherapy research. {{updated}}
 +
Image:SlicerToKiwiExporterLogo.png|[[Documentation/{{documentation/version}}/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]] to provide an easy way to export [[Documentation/{{documentation/version}}/Modules/Models|models]] into a [http://www.kiwiviewer.org/ KiwiViewer].{{new}}
 +
Image:SobolevSegmenter.png|[[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|Sobolev Segmenter]] implements Sobolev inner product based active contour, using the Chan-Vese energy functional.{{updated}}
 +
Image:SwissSkullStripper.png|[[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|Swiss Skull Stripper]] to register an atlas image to the patient data.{{new}}
 +
Image:TrackerStabilizer.png|[[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|Tracker Stabilizer]] to output a filtered transform node based on an tracker input (transform node).{{new}}
 +
Image:TransformVisualizerLogo.png|[[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] to visualize any transform (linear transform, B-spline deformable transform, any other non-linear transform) or vector volume.{{new}}
 +
Image:TubeTK-scaled.png|[[Documentation/{{documentation/version}}/Extensions/TubeTK| TubeTK]] is an open-source toolkit for the segmentation, registration, and analysis of tubes and surfaces in images.{{updated}}
 +
Image:UKFTractography.png|[[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKF Tractography]] a framework which uses an unscented Kalman filter for performing tractography.{{updated}}
 +
Image:VisuaLine.png|[[Documentation/{{documentation/version}}/Extensions/VisuaLine|VisuaLine]] to display lines in Slicer.{{updated}}
 +
Image:WindowLevelEffectLogo.png|[[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|Window/Level Effect]] to adjust window/level for volumes using mouse and/or region of interest.{{new}}
 +
Image:XNATSlicerIcon.jpg|[[Documentation/{{documentation/version}}/Extensions/XNATSlicer| XNAT Slicer]] Secure GUI-based IO with any XNAT server.{{new}}
 +
Image:PerkTutorLogo.png|[[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] for training in image-guided needle interventions.{{new}}
 +
 
 +
<!-- You could user either {{new}} or {{updated}} macros.
 +
 
 
</gallery>
 
</gallery>
  
Line 60: Line 111:
 
Image:SlicerModels-Large.svg|Added advanced controls for the [[Documentation/{{documentation/version}}/Modules/Models|model display representation]]
 
Image:SlicerModels-Large.svg|Added advanced controls for the [[Documentation/{{documentation/version}}/Modules/Models|model display representation]]
 
Image:SlicerModels-Large.svg|Depth peeling option for translucent surface models in [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D views]]
 
Image:SlicerModels-Large.svg|Depth peeling option for translucent surface models in [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D views]]
 +
 +
Image:Fiber select.PNG|Added [[Documentation/{{documentation/version}}/Modules/FiberBundleLabelSelect|fiber selection based on label map module]]
 +
 +
Image:TractographyDisplayModule.PNG|Added individual fiber editing option in [[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display module]]
 +
 
Image:SlicerVolume-Large.svg|Added read/write support for [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat|MRC files]]
 
Image:SlicerVolume-Large.svg|Added read/write support for [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat|MRC files]]
 
Image:ctkDoubleSpinBox.gif|Improved support for image precision.
 
Image:ctkDoubleSpinBox.gif|Improved support for image precision.
Line 65: Line 121:
 
</gallery>
 
</gallery>
  
−
= Looking at the Code Changes =
+
= For Developers: Looking at the Code Changes =
  
 
From a git checkout you can easily see the all the commits since the time of the 4.4.2 release:
 
From a git checkout you can easily see the all the commits since the time of the 4.4.2 release:

Latest revision as of 23:30, 4 October 2013

Home < Documentation < 4.3 < Announcements


For the latest Slicer documentation, visit the read-the-docs.




4.3


Summary What is 3D Slicer Slicer 4.3 Highlights Slicer Extensions Other Improvements, Additions & Documentation

Summary

The community of Slicer developers is proud to announce the release of Slicer 4.3.

  • Slicer 4.3 introduces
    • a new App store, called the extension manager, for adding capabilities to Slicer. Close to 40 plug-ins are currently available.
    • close to 500 feature improvements and bug fixes lead to improved performance and stability.
    • augmentation of many modules.
    • improved workflows in registration and dMRI
    • the multivolume explorer allows interaction with time series and DCE data.
    • major improvements to the DICOM module
    • a new Markups module to streamline the use of fiducial lists


  • Click here to download Slicer 4.3 for different platforms and find pointers to the source code, mailing lists and bug tracker.
  • Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer are not fully tested.
  • The Slicer Training page provides a series of courses for learning how to use Slicer. The portfolio contains self-guided presentation and sample data sets.

The main slicer.org pages provide a guided tour to the application, training materials, and the development community. New users should start there because we try to keep the pages organized and up to date.


What is 3D Slicer

Slicer is a community platform created for the purpose of subject specific image analysis and visualization.

  • Multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy
  • Multi organ from head to toe
  • Bidirectional interface for devices
  • Expandable and interfaced to multiple toolkits

There is no restriction on use, but permissions and compliance with rules are responsibility of users. For details on the license see here

Slicer 4.3 Highlights

  • New and Improved Toolkits and Modules

  • Moved from ITKv3 to ITKv4

  • Added SimpleITK

  • Added AutoRun mode for CLI modules to interactively search in parameter space and to create pipelines of filters. Watch the demo!

  • The Markups module replaces Annotation fiducials.

  • Slicer image registration modules have been reimplemented using ITKv4, with streamlined interfaces and improved robustness. An updated Registration Library is showcasing examples with downloadable data and full step-by-step instructions.

Slicer Extensions

  • New and Improved Extensions

  • Airway Segmentation to segment the airway from chest CT images.  NEW

  • Cardiac MRI Toolkit to analyze cardiac LGE-MRI images.   NEW

  • Change Tracker for quantification of the subtle changes in pathology.  NEW

  • Data Store Allows to easily upload and download dataset files.  NEW

  • Dice Computation to calculate the Dice Similarity Coefficient (DSC) between multiple label map images.  NEW

  • DTI Atlas Builder to create an Atlas image as an average of several DTI images that will be registered.  UPDATED

  • DTI Prep.  UPDATED

  • DTI Process.  UPDATED

  • Erode/Dilate Label to perform binary erosion and dilation on a specified label.  NEW

  • Faceted Visualizer to create flexible visualizations using Slicer by combining a 3D digital atlas and 3D scene models with an ontology.  UPDATED

  • Fiber Viewer Light to create fiber clusters based on methods such as Length, Gravity, Hausdorff, or Mean Distribution and Normalized Cut.  UPDATED

  • IASEM to segmentation and process of IASEM Electron Microscopy images.  NEW

  • Image Maker to create volumes from scratch.   NEW

  • LA Scar Segmenter to perform segmentation of the left atrial scarring tissue from MR images.   NEW

  • LA Segmenter to perform segmentation of the left atrium from MR images.  NEW

  • Longitudinal PET/CT to provide a user friendly Slicer interface for quantification of DICOM PET/CT image data.{{updated}

  • Matlab Bridge to allow running Matlab functions directly in 3D Slicer.  NEW

  • Model Clip to set osteotomy trajectory with multiple planes, and clip the model with just one click.  NEW

  • Path Plannerto facilitate the creation of trajectory.  NEW

  • Pk Modeling to calculate quantitative parameters from Dynamic Contrast Enhanced DCE-MRI images.  NEW

  • Plus Remote to send commands through OpenIGTLink Remote to PLUS.  NEW

  • Port Placementto assists in the planning of surgical port placement in laparoscopic procedures.  NEW

  • Reporting to create image annotations/markup that are stored in a structured form.  UPDATED

  • Skull Stripper to register an atlas image to the patient data.  UPDATED

  • SlicerIGT to use all the advanced features of 3D Slicer for real-time navigation.  NEW

  • SlicerRT is a tool for powerful radiotherapy research.   UPDATED

  • Slicer To Kiwi Exporter to provide an easy way to export models into a KiwiViewer.  NEW

  • Sobolev Segmenter implements Sobolev inner product based active contour, using the Chan-Vese energy functional.  UPDATED

  • Swiss Skull Stripper to register an atlas image to the patient data.  NEW

  • Tracker Stabilizer to output a filtered transform node based on an tracker input (transform node).  NEW

  • Transform Visualizer to visualize any transform (linear transform, B-spline deformable transform, any other non-linear transform) or vector volume.  NEW

  • TubeTK is an open-source toolkit for the segmentation, registration, and analysis of tubes and surfaces in images.  UPDATED

  • UKF Tractography a framework which uses an unscented Kalman filter for performing tractography.  UPDATED

  • VisuaLine to display lines in Slicer.  UPDATED

  • Window/Level Effect to adjust window/level for volumes using mouse and/or region of interest.  NEW

  • XNAT Slicer Secure GUI-based IO with any XNAT server.  NEW

  • PerkTutor for training in image-guided needle interventions.  NEW

Other Improvements, Additions & Documentation

For Developers: Looking at the Code Changes

From a git checkout you can easily see the all the commits since the time of the 4.4.2 release: 

git log --since="Sat Dec 8 03:32:53 2012"

To see a summary of your own commits, you could use something like: 

git log --since="Sat Dec 8 03:32:53 2012"  --oneline --author=pieper

see the git log man page for more options.

Commit stats and full changelog

Related Projects

Retrieved from "https://www.slicer.org/w/index.php?title=Documentation/4.3/Announcements&oldid=36170"