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=Welcome to the 3D Slicer Wiki pages!=
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__NOTOC__
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= Welcome to the 3D Slicer Wiki pages =
  
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{{:Documentation/Nightly/Slicer}}
  
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Welcome to the Slicer Wiki Home Page.
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 +
----
  
 
'''How to use this site:'''   
 
'''How to use this site:'''   
−
* 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 it organized and up to date.
+
* The [http://www.slicer.org Slicer Web pages] provide a guided tour to the application, training materials, and the development community.  New users should start there because we try to keep it organized and up to date.
 
* These wiki pages are more free-form, with notes and reference pages that help support developers and users across multiple sites.  You will find good information on the wiki, but it's possible that it's out of date or describes features that are still in the planning phase.
 
* These wiki pages are more free-form, with notes and reference pages that help support developers and users across multiple sites.  You will find good information on the wiki, but it's possible that it's out of date or describes features that are still in the planning phase.
  
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<gallery widths="200px" perrow="4">
 
−
Image:ExtractSubvolumeROI_gallery.png|[[Modules:ExtractSubvolumeROI-Documentation-3.5|ExtractSubvolumeROI is a new GUI module in Slicer 3.5]] that allows to extract and resample an arbitrary parallelepiped shaped region from a larger scalar image volume.
 
−
Image:Qt-KWW-Transforms-2009-11-24.png|Frame from a movie showing Qt Transforms module. See whole movie [http://www.youtube.com/watch?v=oJFSJWBUFEI on youtube] or download [[file:QSlicerTransformsModule.ogg]].
 
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Image:VolumeRenderingICPE.png|Volume rendering: Illustrative Context Preserving Exploration
 
−
Image:Dual 3D View.png|Multiple 3D rendering windows
 
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</gallery>
 
−
 
−
 
−
 
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More images at the [[Slicer3:VisualBlog| Slicer3 Visual Blog...]]
 
  
 
----
 
----
−
 
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'''From the Slicer 4 visual blog. For more, see [[Slicer4:VisualBlog| here]]'''
−
In a nutshell, Slicer3 is:
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<gallery widths="200px" perrow="5">
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* A cross-platform end user application for analyzing and visualizing medical images.
+
Image:SlicerProstate_Logo_1.0_128x128.png|[[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate extension]] has been released! Current functionality includes support of MRI-TRUS fusion and implementation of popular DWI MRI models for prostate cancer characterization
−
* A collection of Open Source libraries for developing and deploying new image computing technologies.
+
Image:2014-08-26-SlicerIGT-EMBC2014Tutorial.png | Pre-conference tutorial session [http://www.slicerigt.org/wp/embc-2014-tutorial/ Building image-guidance systems from open-source components] at IEEE EMBC in Chicago (August 26, 2014).  
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* Intended to replace the venerable Slicer2 (see [[Slicer3:Transition_from_Slicer2 |information on the transition]])
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Image:TCIABrowserLogo.png|The  [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser extension]] TCIABrowser gives you access to 18 collections of The Cancer Imaging Archive (http://cancerimagingarchive.net/), which contains a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs.
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* An algorithm development platform with a powerful new [[Slicer3:Execution_Model_Documentation| Execution Model]] to facilitate creation of new modules.
+
Image:ShapeModelSequenceBrowsing3dOnly.gif| The [[Documentation/Nightly/Extensions/MultidimData|Multidimensional data extension]] allows creating, editing, and visualizing multidimensional data sets in 3D Slicer. Browsing, replaying 4D volumes, reviewing deforming 3D models, replaying tracked ultrasound, tool navigation data in 3D, applying time-varying transforms are now all possible.
−
 
+
Image:UKFTractography_CC.jpg|[[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] is a module for computing tractography of DWI images using an unscented Kalman filter.  Because of its 2-tensor algorithm, it is able to model fiber crossings and capture many more fibers than a single tensor algorithm.
 +
</gallery>
 
----
 
----
  
−
==News==
+
<!-- See page http://www.slicer.org/slicerWiki/index.php/News -->
−
* December 2009
+
{{:News}}
−
** Lots of activity around the [[Slicer3:Developers:Projects:QtSlicer| Port of Slicer to Qt]]
 
−
** [http://www.na-mic.org/Wiki/index.php/Dec-2009-SlicerAIMBrainstorming New Annotation Tools are in the works]
 
−
* November 2009
 
−
**Seb Barre from Kitware has taken the lead in adding multiple camera support to Slicer 3. The work is currently focused on multiple cameras and multiple views, but only one scene. The nightly build contains a new module, called cameras. Jim Miller has added a new layout, called [[Image:Dual 3D View.png|thumb|200px|Dual 3D layout]].
 
−
 
 
−
* October 2009
 
−
** Test of [http://wiki.slicer.org/slicerWiki/index.php?title=Main_Page&useskin=chick mobile friendly wiki skin]
 
−
*September 2009
 
−
** [http://www.na-mic.org/Wiki/index.php/Sept-2009-SlicerWidgetsBrainstorm Serious work is beginning] on a [[Qt_in_Slicer3|Slicer3 port to Qt]]. 
 
−
** Attila Nagy and his colleagues created a [http://www.orl.szote.u-szeged.hu/~attila/presentations.html very nice set of presentations and animations] with slicer to illustrate 3D reconstruction as applied to otorhinolaryngology.  (See [[Nagy-videos-2009:Notes|Notes]]).
 
−
*August 2009
 
−
** New images in [[Slicer3:VisualBlog|the visual blog]] show integration of slicer and [http://www.bioimagesuite.org BioImageSuite].
 
−
* July 2009
 
−
** Several bug fixes are being rolled into a 3.4.1 patch release, expected for beginning of August
 
−
* June 2009
 
−
** [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week NA-MIC Summer Project Week] was a great success!
 
−
** New documentation is available, thanks to the [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009 Summer 2009 Tutorial Contest]
 
−
* May 2009
 
−
** [[Announcements:Slicer3.4|Slicer 3.4 release]]
 
−
** The [http://viewvc.slicer.org/branches/Slicer-3-4/ 3.4 release branch has been created in subversion]
 
−
** [http://tinyurl.com/cu9bzp A punch list of 3.4 bugs] is being maintained on the Mantis Bug Tracker.
 
−
* March 2009
 
−
** Development of slicer3.4 is still under way.  To check the status, go to the bug tracker and search for the tag "3.4 Targeted fix".  Our plan is to fix anything with that tag before branching the release.  http://na-mic.org/Mantis/main_page.php  The svn trunk for slicer3 is still in "feature freeze" mode, meaning that only fixes should be checked in.  Any new development should occur in svn branches for now.
 
−
** Developers, please be sure to apply the "3.4 Targeted fix" to anything you are working on for the release.
 
−
* January 2009
 
−
** A product release of Slicer 3.4 is scheduled for Feb/March
 
−
** There will be a code freeze on Feb 4, 2009
 
−
** Slicer3 and related research project were highlighted and demoed as part of the External Advisory Board meeting of the [http://nac.spl.harvard.edu Neuroimage Analysis Center].
 
−
* December 2008
 
−
** Andrew Farke posted [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-iv.html some excellent tutorials] on the use of 3D Slicer in paleontology research.
 
−
** A training course on [http://www.na-mic.org/Wiki/index.php/Events:RSNA2008 use of 3D Slicer by Radiologists] was held at [http://rsna2008.rsna.org/ RSNA] in Chicago.
 
−
** [http://www.ncigt.org NCIGT] is hosting a [http://www.na-mic.org/Wiki/index.php/2008_IGT_Project_Week Project Week] for developing Image Guided Therapy software that features many slicer projects.
 
−
* September 2008
 
−
** Andras Jakab won second place in [http://www.kitware.com/viscontest/medicalviswinner.html Kitware's medical image visualization contest!].  The image combines slice viewing, models, volume rendering, and tractography applied to a gamma knife neurooncology radiotherapy planning case.  Andras used slicer's registration tools to fuse CT and diffusion MR into a multimodal scene.
 
−
[[Image:Andras-Jakab-brainconnectivity.png|thumb|200px|Andras Jakab's award winning slicer image.]]
 
−
** [http://www.na-mic.org/Wiki/index.php/Miccai_2008_Tutorial A NA-MIC Workshop at MICCAI] addressed the creation of ITK-based command line modules for 3D Slicer.
 
−
** Slicer user Attila Nagy presented on Slicer3 for inner ear imaging ([http://www.orl.szote.u-szeged.hu/~attila/NagyA-2008-Miskolc.ppt Slides - Hungarian])
 
−
** Attila also provided patches to build Slicer3 and most of Slicer2 using the latest versions of Solaris and the optimized Sun C++ compilers.
 
−
* August 2008
 
−
**[http://www.na-mic.org/Wiki/index.php/Events:August_2008_NCBC_AHM  August 14, 2008: NCBC 2008 Science Fair "Three ways of using the NA-MIC Kit" ]
 
−
**[http://www.na-mic.org/Wiki/index.php/Events:NCI_Workshop_August_2008 August 15, 2008: NCI Workshop - August 15, 2008 ]
 
−
[[Image:NITRC logo Listed.jpg|thumb|200px|http://www.nitrc.org/projects/slicer/]]
 
−
* July 2008
 
−
** [http://www.airwayinspector.org Airway Inspector] is a powerful tool for lung image analysis build on slicer2.  A port to slicer3 is getting under way in the next few weeks and is expected to take about 6 months.
 
−
** Slicer and the NA-MIC software environment were presented as part of the [https://www.ipam.ucla.edu/schedule.aspx?pc=mbi2008 UCLA Institute for Pure and Applied Mathematics Summer School on Mathematics and Brain Imaging].
 
−
** A [http://www.na-mic.org/Wiki/index.php/2008_July_Slicer_IGT_VV_Link_Session_II very productive working meeting] between researchers at BWH and Yale resulted in successful connection of Slicer3 to the BrainLab commercial image guided neurosurgery system.
 
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* June 2008
 
−
** [http://www.na-mic.org/Wiki/index.php/2008_June_Workshop_Germany June 16-17, 2008: Training Event in Germany]
 
−
** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week June 23-27, 2008, Summer Project Week]
 
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* May 2008
 
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**[[Announcements:Slicer3.2|Slicer 3.2 release]]
 
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**Slicer3 included in review paper on  [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2039808 "Rapid Development of Medical Imaging Tools with Open Source Libraries"]
 
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* April 2008
 
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**[http://www.ohloh.net/p/3376/factoids Slicer rated in the top 2% of project teams in Ohloh]
 
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**[[Slicer3:Slicer3_Workshop_UNC_Chapel_Hill_2008| April 14, 2008: Slicer 3 User and Developer Workshop, UNC Chapel Hill]]
 
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* March 2008
 
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**A new [http://en.wikipedia.org/wiki/3DSlicer 3D Slicer Wikipedia entry] has been created.
 
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* Feb 2008
 
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**February 20th, 2008, [[Slicer3:Spring-2008-User-Training| Spring 2008 Slicer3 User Training Workshop ]] in the SPL at 1249 Boylston St. Boston.
 
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* Jan 2008
 
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**[[tutorialwishlist|Wishlist for tutorials]]
 
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**Lots of Slicer development activity as part of '''[http://www.na-mic.org/Wiki/index.php/AHM_2008  NA-MIC All Hands Meeting] and [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week Winter Project Week]
 
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* December 2007
 
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**A three-day retreat for [http://www.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming  Slicer in Image Guided Therapy] was held in Boston.
 
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* November 2007
 
−
** New builds are now available for [http://www.slicer.org/DownloadSlicer.php/Snapshots/linux-x86_64/Slicer3-3.0.2007-11-21-linux-x86_64.sh Linux 64], [http://www.slicer.org/DownloadSlicer.php/Snapshots/linux-x86/Slicer3-3.0.2007-11-21-linux-x86.sh Linux 32], [http://www.slicer.org/DownloadSlicer.php/Snapshots/win32/Slicer3-3.0.2007-11-19-win32.exe Windows], [http://www.slicer.org/DownloadSlicer.php/Snapshots/darwin-ppc/Slicer3-3.0.2007-11-19-darwin-ppc.sh Darwin PPC], and [http://www.slicer.org/DownloadSlicer.php/Snapshots/darwin-x86/Slicer3-3.0.2007-11-19-darwin-x86.sh Darwin x86]
 
−
* June 2007
 
−
** Lots of Slicer3 work at [http://wiki.na-mic.org/Wiki/index.php/Engineering:Programming_Events the Project Weeks]
 
−
* March 2007
 
−
** New Image Guided Therapy (IGT) functionality for tracking surgical instruments added by developers working at the [http://www.ncigt.org National Center for IGT].
 
−
* February 2007
 
−
** Feb 7-8, 2007. [[Slicer3:MiniRetreat February 7-8, 2007| Slicer3 Mini-Retreat, Boston]]
 
−
** Resulted in the implementation of a [[Slicer3::Python | Python interface]] to Slicer3.
 
  
−
* January 2007
 
−
** Slicer3 developers are getting together in Salt Lake City for a "programming half-week" as part of the [http://wiki.na-mic.org/Wiki/index.php/AHM_2007 NA-MIC All-Hands Meeting]
 
−
** [[Slicer3:Developers#Information_for_Developers| Lots of new developer documentation added!]]
 
−
** Slicer3 beta released
 
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** [http://na-mic.org/Mantis/main_page.php New bug tracker installed]
 
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* December 2006
 
−
** There was a big meltdown of the na-mic.org server in December, and some things were lost including wiki history, slicer3 bug tracker and doxygen, and some of the older download files.  Please bear with us as we pick ourselves up and carry on.
 
−
* November 2006
 
−
** [[Slicer3_Alpha_builds| Slicer3 Alpha builds]] available for Linux (32 and 64 bit) and windows!
 
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* October 2006
 
−
** Slicer3 development version shown at the [http://www.nbirn.net/press/current/ahm2006.shtm BIRN All Hands Meeting] as the platform for the BIRN Query Atlas Project and overall visualization issue in BIRN. See [[Media:BIRNFIPS2Slicer3-2006-10-24.ppt| these slides for more information]].
 
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* September 2006:
 
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** [http://wiki.na-mic.org/Wiki/index.php/2006_September_Slicer3_Update Development meeting at BWH September 19, 20.]
 
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* July, 2006:
 
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** There was active development of Slicer3 at and around the [http://wiki.na-mic.org/Wiki/index.php/2006_Programming/Project_Week_MIT NA-MIC Programming/Project week].
 
−
** New Slicer3 wiki page organization is under way. Please send feedback to the [mailto:slicer-devel@massmail.spl.harvard.edu slicer-developers mailing list].
 
 
<br>
 
<br>
 
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<br>
 
<br>
−
*[[Editing Guide:Getting Started|Wiki Editing Guide]]
 
  
−
=== For Wiki Administration ===
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=For Wiki Administration=
  
 +
* [[Editing Guide:Getting Started|Wiki Editing Guide]]
 +
* [[Documentation/Nightly/WikiCheatSheet|WikiCheatSheet]]
 
* [[Special:Userlogin|Create user account]]
 
* [[Special:Userlogin|Create user account]]
 
* [[Special:Listusers|Users List]]
 
* [[Special:Listusers|Users List]]
−
* Authorized users can commit edited web pages through [https://www.slicer.org/slicerWikiWeb/ slicer's wiki2web interface]
+
* https://www.slicer.org/index.html can be updated by submitting a Pull Request to https://github.com/Slicer/slicer.org. Wiki web pages are updated on-wiki by registered users.

Latest revision as of 13:57, 27 November 2019

Welcome to the 3D Slicer Wiki pages

3D Slicer is:

  • A software platform for the analysis (including registration and interactive segmentation) and visualization (including volume rendering) of medical images and for research in image guided therapy.
  • A free, open source software available on multiple operating systems: Linux, MacOSX and Windows
  • Extensible, with powerful plug-in capabilities for adding algorithms and applications.

Features include:

  • Multi organ: from head to toe.
  • Support for multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy.
  • Bidirectional interface for devices.

There is no restriction on use, but Slicer is not approved for clinical use and intended for research. Permissions and compliance with applicable rules are the responsibility of the user. For details on the license see here


How to use this site:

  • The Slicer Web pages provide a guided tour to the application, training materials, and the development community. New users should start there because we try to keep it organized and up to date.
  • These wiki pages are more free-form, with notes and reference pages that help support developers and users across multiple sites. You will find good information on the wiki, but it's possible that it's out of date or describes features that are still in the planning phase.


From the Slicer 4 visual blog. For more, see here

  • SlicerProstate extension has been released! Current functionality includes support of MRI-TRUS fusion and implementation of popular DWI MRI models for prostate cancer characterization

  • Pre-conference tutorial session Building image-guidance systems from open-source components at IEEE EMBC in Chicago (August 26, 2014).

  • The TCIABrowser extension TCIABrowser gives you access to 18 collections of The Cancer Imaging Archive (http://cancerimagingarchive.net/), which contains a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs.

  • The Multidimensional data extension allows creating, editing, and visualizing multidimensional data sets in 3D Slicer. Browsing, replaying 4D volumes, reviewing deforming 3D models, replaying tracked ultrasound, tool navigation data in 3D, applying time-varying transforms are now all possible.

  • UKFTractography is a module for computing tractography of DWI images using an unscented Kalman filter. Because of its 2-tensor algorithm, it is able to model fiber crossings and capture many more fibers than a single tensor algorithm.


For the latest Slicer news, visit the community forum:

https://discourse.slicer.org

To learn how the Slicer community transitioned away from mailing lists. See below

News

2018 and beyond

2017

April

  • Thanks to the stewardship of Isaiah Norton and the kindness of the Discourse organization, Slicer forum is graciously hosted under the condition we keep the word "discourse" in the URL: https://discourse.slicer.org
  • A group of Slicer community members have extensively discussed the advantages of an updated forum software, and developed a consensus at the 24th Project Week that we test Discourse as a new home for questions and discussion by users and developers of Slicer and any extension/topical communities who are interested.

January

2016

November

  • Slicer 4.6.2 released!

July

  • Discussion about a new user manual page. See here

2015

November

  • 17: Slicer 4.5 has been released. See the announcement for more information.

August

  • Release schedule for Slicer 4.5 established. RSNA 2015 is target date for the release.
  • 17: Ron Kikinis presented the state of 3D Slicer to BISTI, Natcher Building, NIH, Bethesda, MD (download here, ~78MB).

2014

December

  • Slicer 4.4 has been released. See the announcement for more information.

April

2013

Be sure to check out the NA-MIC Wiki Events page for updated information about tutorials, workshops, and other community events!

Also the Slicer Publication Database has a list of Slicer-related papers and datasets.

November

September

  • Slicer 4.3 has been released. See the announcement for more information.

March

2012

November

  • Slicer 4.2 has been released. See the announcement for more information.

July

April

January

2011

November

  • Slicer 4.0 released in November 2011.

  • Over 200 attendees at training events in two 90 minute training sessions.

August

  • Slicer3 development trunk (and nightly builds) have changed over to Tcl 8.5 and cmake 2.8.5 in order to address some issues with ubuntu 11.04.
  • Plans are in place to release slicer4 at RSNA 2011 (end of November). Developers are actively working on making that a usable and feature rich release.

March

  • Slicer3.6.3 Patch Released on March 4th, 2011.

February

  • A very productive CTK Hackfest made significant progress on new dicom interoperability features that will be a key part of slicer4.

January

2010

October

  • Our friends and colleagues at UFP in Barcelona, Spain have released version 1.2 of the Gimias application. This new version includes an interface so that Gimias can discover and execute slicer command line modules to operate on data loaded in Gimias.

September

  • The first alpha versions of Slicer4 (the Qt version) are starting to become available. Contact the slicer-devel list if you want access to a binary installer for testing.
  • A video has been nominated for official slicer bug fixing anthem ;)

August

July

June

  • Slicer 3.6 Released in June 2010.

May

  • first (05/17) and second (05/25) release candidates for Slicer 3.6

April

March

January

2009

December

November

  • Seb Barre from Kitware has taken the lead in adding multiple cameras support to Slicer 3. The work is currently focused on multiple cameras and multiple views, but only one scene. The nightly build contains a new module, called cameras. Jim Miller has added a new layout, called Dual 3D Layout.

    • Dual 3D layout.

    October

    September

    August

    July

    • Several bug fixes are being rolled into a 3.4.1 patch release, expected for beginning of August.

    June

    May

    March

    • Development of slicer3.4 is still under way. To check the status, go to the bug tracker and search for the tag "3.4 Targeted fix". Our plan is to fix anything with that tag before branching the release. http://na-mic.org/Mantis/main_page.php The svn trunk for slicer3 is still in "feature freeze" mode, meaning that only fixes should be checked in. Any new development should occur in svn branches for now.
    • Developers, please be sure to apply the "3.4 Targeted fix" to anything you are working on for the release.

    January

    • A product release of Slicer 3.4 is scheduled for Feb/March
    • There will be a code freeze on Feb 4, 2009
    • Slicer3 and related research project were highlighted and demoed as part of the External Advisory Board meeting of the Neuroimage Analysis Center.

    2008

    December

    September

    • Andras Jakab won second place in Kitware's medical image visualization contest!. The image combines slice viewing, models, volume rendering, and tractography applied to a gamma knife neurooncology radiotherapy planning case. Andras used slicer's registration tools to fuse CT and diffusion MR into a multimodal scene.

    • Andras Jakab's award winning slicer image.

    • A NA-MIC Workshop at MICCAI addressed the creation of ITK-based command line modules for 3D Slicer.
    • Slicer user Attila Nagy presented on Slicer3 for inner ear imaging (Slides - Hungarian)
    • Attila also provided patches to build Slicer3 and most of Slicer2 using the latest versions of Solaris and the optimized Sun C++ compilers.

    August

    July

    June

    May

    April

    March

    February

    January

    2007

    December

    November

    June

    March

    February

    January

    2006

    December

    • There was a big meltdown of the na-mic.org server in December, and some things were lost including wiki history, slicer3 bug tracker and doxygen, and some of the older download files. Please bear with us as we pick ourselves up and carry on.

    November

    October

    September

    July



    For Wiki Administration

    Retrieved from "https://www.slicer.org/w/index.php?title=Main_Page&oldid=62645"