Difference between revisions of "AHM2010:NA-MIC Kit Update"
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| + | Back to [[AHM_2010#Agenda|AHM 2010]] | ||
==Goals== | ==Goals== | ||
Information about NA-MIC Kit component developments over the past year so that developers will have an idea of what new features are available for their use. | Information about NA-MIC Kit component developments over the past year so that developers will have an idea of what new features are available for their use. | ||
=== ITK === | === ITK === | ||
| + | |||
| + | * [http://www.itk.org/Wiki/ITK_10th_Anniversary_Activities ITK turned 10 years old!] | ||
| + | * Slicer currently uses [http://www.kitware.com/news/home/browse/ITK?2009_09_16&ITK+3.16+Released ITK 3.16] | ||
| + | * [http://www.insight-journal.org/browse/publication/149 Label image classes], [http://hdl.handle.net/1926/584 Label map classes], Label map morphology | ||
| + | * [http://hdl.handle.net/10380/3055 Region based Level Sets] | ||
| + | * Improvements in Streaming large images | ||
| + | * QuadEdgeMesh spherical registration | ||
| + | ** Rigid (in NAMIC Sandbox) | ||
| + | ** Deformable (Diffeomorphic Demons) (in NAMIC Sandbox) | ||
| + | ** Improvements in the QuadEdgeMesh filter class (in ITK to support the two above). | ||
| + | * Pixel coordinates consistency | ||
| + | * Multi-threaded registration framework (fixes) | ||
| + | ** multi-threaded metrics | ||
| + | ** thread-safe transforms | ||
| + | * Hessian-based shape descriptors | ||
| + | * Fractal dimensions | ||
| + | * [http://hdl.handle.net/1926/585 FFT based image reconstruction] | ||
=== VTK === | === VTK === | ||
| + | * VTK 5.4 released | ||
| + | * vtkWidgets | ||
| + | * [http://www.vtk.org/Wiki/VTK/ARB VTK ARB] formed | ||
| + | * [http://vtk.uservoice.com/pages/31508-general User Voice] added to gather community feedback | ||
| + | * [http://www.midasjournal.org/?journal=35 VTK Journal] | ||
| + | * [http://www.vtkedge.org/ VTK Edge] will be consolidated into VTK | ||
| + | * In progress: | ||
| + | ** [http://blog.cryos.net/archives/236-VTK-New-2D-API,-Canvas-and-Charting-Features.html VTK 2D Charting] | ||
| + | ** Informatics | ||
| + | ** Examples makeover | ||
| + | ** git mirror of VTK | ||
=== Teem === | === Teem === | ||
| + | * [http://teem.sf.net Teem] 1.11 Soon to be Released | ||
| + | ** release branch being used in slicer3 nightly builds | ||
| + | ** Many improvements and new features described in the [http://sourceforge.net/mailarchive/forum.php?thread_name=9FE12D1D-D52B-40F6-B793-D8AA9D2124CB%40uchicago.edu&forum_name=teem-users Teem 1.11 Change Log Message] | ||
| + | * Python wrappers (auto-generated by ctypeslib) now included in teem/python/ctypes; used previously for [[Two-tensor tractography in Slicer using Python and Teem]] | ||
| + | * The tenGage kind (for doing convolution-based measurements in tensor fields) now includes direct computation of the fiber curving (tenGageFiberCurving) and fiber dispersion (tenGageFiberDispersion) indices used in [[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH) | ||
| + | * New [http://people.cs.uchicago.edu/~glk/ssp/ scale space partices] functionality, with applications to lung airway segmentation and white matter skeletonization from DTI | ||
| + | * New applications of scale-space particles for COPD with Raul San Jose (see http://www.airwayinspector.org/) | ||
| + | * New functionality from Thomas Schultz to implement fast crease surface extraction (see his recent TVCG paper [[http://www.ci.uchicago.edu/~schultz/papers/schultz-crease-2008.pdf]]) | ||
=== XNAT === | === XNAT === | ||
| + | |||
| + | * [http://groups.google.com/group/xnat_discussion/browse_thread/thread/f46581afed629a5c XNAT 1.4 RC3] available | ||
| + | ** More robust QC modeling via xnat:qcManualAssessorData. | ||
| + | ** New 'columns' variable for REST based listings. | ||
| + | ** LDAP support. | ||
| + | ** Improved memory footprint and efficiency. | ||
| + | ** Refactored Search UI in the listing engine. | ||
| + | ** Prebuilt XNAT images using VMWare and Virtualbox | ||
| + | * [http://code.google.com/p/xnatfs/ xnatfs] provides WebDav access to XNAT instances | ||
=== GWE === | === GWE === | ||
| + | |||
| + | * Interactive experiments' results browser. | ||
| + | * CSV and generated commands dumps and preview. | ||
| + | * Support for LSF and Lava cluster DRMs. | ||
| + | * Ability to override auto-discovered DRMs with configured ones. | ||
| + | * Ability to override default database installation location. | ||
| + | * Function to extract experiments' parameters from text files. | ||
| + | * Operations to delete, pause and resume experiments. | ||
| + | * Recommended to watch: [http://www.youtube.com/watch?v=yXdRks5Wu5Q 5 minutes demo video]. | ||
=== BatchMake === | === BatchMake === | ||
| + | * Improvement in the integration of grid computing using condor. | ||
| + | * Semi-Automatic conversion of Slicer modules for batch processing | ||
| + | * Parameter exploration is now possible | ||
| + | * Execution of algorithms are faster | ||
=== CMake/CPack/CTest/CDash === | === CMake/CPack/CTest/CDash === | ||
| + | * parallel ctest (ctest -j) | ||
| + | * cpack | ||
| + | * conversion to cmake in-progress | ||
| + | * linkage between CTest and MIDAS in progress | ||
| + | ** Host large datasets for algorithm validation and performance testing | ||
| + | *** Demonstrated using RegisterImages | ||
=== 3D Slicer === | === 3D Slicer === | ||
| + | * List of new modules and features (TBD) | ||
| + | ** See here for a list of [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#List_of_Modules_new_to_3.5 modules new to 3.5]. | ||
| + | * 3.4/3.4.1 release information | ||
| + | * Extension Architecture and Extension Modules | ||
| + | * ARRA Supplement Projects | ||
| + | * Qt Port (lead in to Julien's 8:30 session) | ||
| + | ** Co-existence of KWWidgets and Qt | ||
| + | ** Creation of a subset of the needed Qt widgets | ||
| + | ** Full port in Qt of first modules | ||
| + | ** Design of the core architecture in Qt (plugin mechanism, Command line modules, widget libraries...) | ||
| + | ** Tutorials for the slicer developer community to port modules | ||
| + | ** [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/Gallery Gallery] and [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/Tutorials Tutorials] | ||
| + | * More info on the [https://www.slicer.org/wiki/Main_Page#News Slicer wiki News Page] | ||
| + | * multi-camera view in Slicer (endoscopy application) | ||
=== Other Topics === | === Other Topics === | ||
* [http://Commontk.org Common Toolkit] | * [http://Commontk.org Common Toolkit] | ||
Latest revision as of 17:10, 10 July 2017
Home < AHM2010:NA-MIC Kit UpdateBack to AHM 2010
Contents
Goals
Information about NA-MIC Kit component developments over the past year so that developers will have an idea of what new features are available for their use.
ITK
- ITK turned 10 years old!
- Slicer currently uses ITK 3.16
- Label image classes, Label map classes, Label map morphology
- Region based Level Sets
- Improvements in Streaming large images
- QuadEdgeMesh spherical registration
- Rigid (in NAMIC Sandbox)
- Deformable (Diffeomorphic Demons) (in NAMIC Sandbox)
- Improvements in the QuadEdgeMesh filter class (in ITK to support the two above).
- Pixel coordinates consistency
- Multi-threaded registration framework (fixes)
- multi-threaded metrics
- thread-safe transforms
- Hessian-based shape descriptors
- Fractal dimensions
- FFT based image reconstruction
VTK
- VTK 5.4 released
- vtkWidgets
- VTK ARB formed
- User Voice added to gather community feedback
- VTK Journal
- VTK Edge will be consolidated into VTK
- In progress:
- VTK 2D Charting
- Informatics
- Examples makeover
- git mirror of VTK
Teem
- Teem 1.11 Soon to be Released
- release branch being used in slicer3 nightly builds
- Many improvements and new features described in the Teem 1.11 Change Log Message
- Python wrappers (auto-generated by ctypeslib) now included in teem/python/ctypes; used previously for Two-tensor tractography in Slicer using Python and Teem
- The tenGage kind (for doing convolution-based measurements in tensor fields) now includes direct computation of the fiber curving (tenGageFiberCurving) and fiber dispersion (tenGageFiberDispersion) indices used in Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev BWH)
- New scale space partices functionality, with applications to lung airway segmentation and white matter skeletonization from DTI
- New applications of scale-space particles for COPD with Raul San Jose (see http://www.airwayinspector.org/)
- New functionality from Thomas Schultz to implement fast crease surface extraction (see his recent TVCG paper [[1]])
XNAT
- XNAT 1.4 RC3 available
- More robust QC modeling via xnat:qcManualAssessorData.
- New 'columns' variable for REST based listings.
- LDAP support.
- Improved memory footprint and efficiency.
- Refactored Search UI in the listing engine.
- Prebuilt XNAT images using VMWare and Virtualbox
- xnatfs provides WebDav access to XNAT instances
GWE
- Interactive experiments' results browser.
- CSV and generated commands dumps and preview.
- Support for LSF and Lava cluster DRMs.
- Ability to override auto-discovered DRMs with configured ones.
- Ability to override default database installation location.
- Function to extract experiments' parameters from text files.
- Operations to delete, pause and resume experiments.
- Recommended to watch: 5 minutes demo video.
BatchMake
- Improvement in the integration of grid computing using condor.
- Semi-Automatic conversion of Slicer modules for batch processing
- Parameter exploration is now possible
- Execution of algorithms are faster
CMake/CPack/CTest/CDash
- parallel ctest (ctest -j)
- cpack
- conversion to cmake in-progress
- linkage between CTest and MIDAS in progress
- Host large datasets for algorithm validation and performance testing
- Demonstrated using RegisterImages
- Host large datasets for algorithm validation and performance testing
3D Slicer
- List of new modules and features (TBD)
- See here for a list of modules new to 3.5.
- 3.4/3.4.1 release information
- Extension Architecture and Extension Modules
- ARRA Supplement Projects
- Qt Port (lead in to Julien's 8:30 session)
- More info on the Slicer wiki News Page
- multi-camera view in Slicer (endoscopy application)
