Slicer 5.8: Summary, Highlights, and Changelog

[jcfr (Jean Christophe Fillion Robin (Kitware))]

Changelog: 5.8.0

• Core
  • Rendering & display
  • IO
  • Performances
  • Fixes
  • Application
  • Extension
  • CLI
  • Scripting
  • Internationalization/Localization
  • Installation
  • MRML
  • API Updates
  • Telemetry Support
  • Documentation
• Improved Modules
  • Data
  • DICOM
  • Endoscopy
  • Markups
  • Models
  • Reformat
  • SampleData
  • Segmentations
  • Segment Statistics
  • Sequences
  • Subject Hierarchy
  • Texts
  • Terminologies
  • Transforms
  • Volume Rendering
  • WebServer
• Infrastructure
  • Packaging
  • Testing
  • Continuous integration (CI)
  • Build system
  • Platform support
  • Dependencies
  • Custom Slicer application support
• Extensions
  • New
  • Updated
  • Removed

Core

Rendering & display

• Add clipping options to models, segmentation, and volume rendering (PR-7996, PR-8087)
• Allow disabling layer blend clipping to background in slice views (PR-7886)
• Add option to display shadows in 3D views (PR-7515)
• Allow setting ambient shadows intensity (PR-7822)
• Disable shadows in 3D views by default (PR-7583)
• Add option to display slice edges in 3D view (PR-8008)
• Re-enable display of interaction handles in VR (PR-7630)
• Allow reslicing of 32-bit integer images (PR-7292)
• Fix backface color on Slice nodes in 3D views (PR-8056)
• Standardize fit slice to volume behavior (PR-8063, PR-8076)
• Fix fit slice view if no background volume is selected (PR-7986)
• Fix interaction handle enable/disable not working in views (PR-8068)
• Fix slice view “More Options” opening by default (PR-8096)
• Ensure background SeriesTime corner annotation is displayed (PR-8122)

IO

• Show more details about scene changes on close or exit (PR-8000)
• Improve vtkMRMLVolumeArchetypeStorageNode for left-handed volumes (PR-7627)
• Improve ultrasound reading (PR-7649)
• Improve automatic detection of NIFTI displacement field transform files (PR-7967)
• Show warning if data loss occurs when saving to TIFF (PR-7655)
• Allow aliases for NRRD “type” header in postNRRD (PR-7664)
• Log more information when NRRD reading fails (PR-7700)
• Improve automatic detection of segmentation files (PR-7967)
• Reduce bundle temp directory length when saving scene MRB (PR-7899)
• Make minor fixes from 5D NRRD IO development (PR-7880)
• Fix reading of images that have a left-handed IJK coordinate system (PR-7746)
• Fix saving of NRRD files with certain filenames (PR-7616)
• Make automatic detection of segmentation files more robust (PR-7738)
• Make segmentation .seg.nrrd file reading more robust (PR-7738)
• Fix export of VTK unstructured grid (PR-7760)
• Fix reading of volume property (.vp) file (PR-7772)
• Fix tensor image reading (PR-7773)
• Fix saving with long node names (PR-8028)
• Fix loading and saving .mrb files with trailing space in filename (PR-8134)

Performances

• Update ITK to suppress irrelevant TIFF warnings (PR-8016)

Fixes

• Do not show warning popup on exit if camera node is changed (PR-8000)
• Re-introduce logging of unparsed arguments (to log file only) (PR-7943)
• Fix crash when module category name matches a module name (PR-7524)
• Fix Model DM crash when adding display node (PR-8131)
• Fix crash when hovering over interaction handles after scene load (PR-8067)
• Suppress “Populating font family aliases” warning on macOS (PR-8159)
• Remove unneeded display of ignored command line arguments (PR-7941)
• Remove “Active” prefix from some node selection comboboxes (PR-7985)

Application

• Display instantiated module name in splash screen (PR-7454)
• Allow dragging of splash window (PR-7527)
• Support dragging of the splash window just after clicking on it (PR-7532)
• Update Slicer.crt CA bundle (PR-7575, PR-7781, PR-7916, PR-8054)

Extension

• Support specifying contributor extension metadata with newlines (PR-7720)
• Switch extension index entry format from .s4ext to .json (PR-7709)
• Simplify Slicer version check in extensions (PR-7954)
• Add “tier” property to extensions catalog schema (PR-8066)
• Simplify extension manager build system (PR-7644)
• Fix loading of modules that depend on another extension (PR-7580)
• Fix extension schema ID (PR-7710)

CLI

• Disable compression for CLI output files (PR-7885)
• Report missing longflag in module description XML (PR-7779)
• Restore support for writing CLI output as .fcsv files (PR-7971)

Scripting

• Add parameter node GUI wrappings for certain CTK and other classes (PR-7918)
• Add methods for runTest upgrade (PR-7444)
• Fix support for registering parameterNodeWrapper plugins (PR-7480)
• Fix meta-object system registration of qSlicerIO::fileType return type (PR-7552)
• Support checking if IO registration from Python occurs with no registered IOs (PR-7553)
• Fix module reload of modules without reloadTestMenuButton (PR-8116)
• Fix QComboBoxToEnumConnector to avoid resetting default (PR-8116)

Internationalization/Localization

• Make translations in Python scripts more robust (PR-7611)
• Add translation for VolumeDisplayPresets.json (PR-7651)
• Only translate Python strings when necessary (PR-7813)
• Make more strings translatable (PR-7309)
• Fix translation in qMRMLThreeDViewCntrollerWidget (PR-7526)
• Mark translatable strings in Markups module (PR-7620)
• Mark translatable strings in ExtensionWizard module (PR-7698)
• Fix translation handle flickering when holding ALT; update Transforms module documentation to include interaction info (PR-7663)
• Fix translation of Python modules (PR-7909)
• Mark translatable strings in Reformat, Texts, and Transforms modules (PR-7817)

Installation

• Remove DMRIInstall module (PR-7662)

MRML

• Improve handling of invalid input in MRMLViewInteractorStyle classes (PR-7497)
• Register nodes in MRMLScene constructor deterministically (PR-8156)
• Check if a node is present in the scene before adding it (PR-8029)
• Fix incorrect vtkMRMLSliceDisplayNode XML attribute name (PR-8081)
• Fix folder display override for model nodes (PR-8083)
• Ensure MRB loading correctly reports loaded nodes (PR-8135)
• Fix issue with adding a new node after rename cancellation (PR-7598)
• Fix GetStorableNodesModifiedSinceRead for short text nodes (PR-8000)
• Fix vtkMRMLTextStorageNode::WriteDataInternal not throwing error (PR-8025)
• Fix creation of extra volume property storage nodes (PR-8029)
• Prevent making volume storage nodes modified after file save (PR-8029)

API Updates

• Add API to access SSAO rendering pass in 3D views (PR-7616)
• Improve vtkMRMLLayoutNode API (PR-7616)
• Migrate vtkSingleton to vtkAddon (PR-7849)

Telemetry Support

• Add API to log software usage events (PR-7855)

Documentation

• Switch highlighted social network to LinkedIn (PR-8023)
• Improve docstring of vtkMRMLViewInteractorStyle processing functions (PR-7498)
• Update installation and building instructions for ArchLinux (PR-7521)
• Update list of supported formats for Quantitative Reporting extension (PR-7557)
• Fix comment format, update variable names, and add missing closing bracket in script repository (PR-7615)
• Update FastModelAlign registration.md (PR-7669)
• Add Ubuntu 22.04 build instructions (PR-7689)
• Reorganize Ubuntu console example of required dev tools (PR-7692)
• Encourage trying preview release before reporting bugs (PR-7686)
• Update gui.md with an example of displaying a node in only some views (PR-7708)
• Improve segmentation DICOM export documentation (PR-7761)
• Match updated interface in SlicerSurfaceToolbox Dynamic Modeler (PR-7766)
• Clarify meaning of negative and positive sides of plane (PR-7769)
• Add documentation for 3D view CTRL + Left-click + drag (PR-7774)
• Update example of DICOM query/retrieve (PR-7802)
• Add plane creation example to markups.md (PR-7804)
• Add Python example for extracting a slice from a volume (PR-7808)
• Update Linux documentation (PR-7798)
• Add notes to SECURITY.md (PR-7818)
• Add notes on segment cross-sectional area measurement (PR-7863)
• Add script to query/retrieve DICOM with ctkDICOMScheduler (PR-7912)
• Add scriptedregistration.md with an example rigid registration (PR-7926)
• Remove outdated example and link to slicerio documentation (PR-7920)
• Improve slicer.util.pip_install documentation (PR-7959)
• Add example to compute distance of points from a plane (PR-7973)
• Update recommended screen resolution in documentation (PR-8010)
• Clarify doc of vtkMRMLMarkupsROINode::GetObjectToWorldMatrix (PR-8034)
• Clarify Qt 5.15.2 Windows binary install instructions (PR-8082)
• Update dicom.md (PR-8088)
• Fix “Edit on GitHub” link not appearing on ReadTheDocs (PR-8107)
• Set GitHub repository information for documentation generation (PR-8116, PR-8108)
• Improve slicer.util.getNode documentation (PR-8116)
• Update links to tutorials (PR-7910)

Improved Modules

Data

• Improve appearance of node information section in Data module (PR-7578)

DICOM

• Add visual DICOM browser (PR-7525, PR-7912, PR-7676, PR-7650, PR-7811, PR-7751)
• Add DICOM support for Multi-frame Grayscale Byte Secondary Capture Image (PR-7566)
• Add DICOM patcher rule to fix compressed ultrasound discolorization (PR-7656)
• Make characterset modifier DICOM patcher rule stronger (PR-7683)
• Add loadSuccess flag to loadable Qt and VTK DICOM classes (PR-8139)
• Fix context change at runtime in DICOM module (PR-7358)
• Fix error string format in DICOMScalarVolumePlugin and ImportItkSnapLabel (PR-7484)
• Prevent DICOM Browser popups on initial module entry (PR-7811)
• Force loading images from DICOM using right-handed coordinate system (PR-7858)
• Fix reading of multiple window/level presets in DICOMScalarVolumePlugin (PR-7922)
• Skip disabled plugins when loading DICOM by scripting (PR-7935)
• Fix regression for scans with negative spacing in DICOM (PR-7987)
• Fix hanging progress popup in DICOM browser (PR-8062)
• Add loadable warning in case of loading failure (PR-7163)

Endoscopy

• Use “Use this curve” instead of “Create flythrough path” for the button text (PR-7435)
• Simplify Endoscopy API related to quaternion (PR-7431)
• Improve Endoscopy module UI self-discovery (PR-7436)
• Fix rebuild of Endoscopy flythrough when modifying the input curve (PR-7433)
• Recompute EndoscopyLogic fields immediately instead of lazily (PR-7437)

Markups

• Fix crash in vtkPointLocator when markups curve polydata is empty (PR-7732)
• Fix issue preventing interaction with Markups curves (PR-8021)
• Fix incorrect plane interaction scale handles initialization (PR-8031)
• Hide angle markups when the line does not intersect with the slice (PR-7832)
• Add API to change screen scale factor (PR-7740)
• Skip creation of markups interaction widget in VR windows (PR-7612)
• Add Point(Start/End)InteractionEvent for Markups interaction handles (PR-8117)
• Fix crash in Markups widget when closing a scene (PR-7628)
• Fix markups handle scale not updating (PR-7675)
• Fix crash when deleting multiple markups in subject hierarchy (PR-7736)
• Fix warning messages when creating markups with no display nodes (PR-7747)
• Fix unnecessary confirmation popup after hovering over markups (PR-8000)
• Fix markups interaction handles not respecting visibility options (PR-7868)
• Fix reading of markup point position from integer values (PR-7928)
• Fix copying of markup measurements (PR-8012)
• Fix missing Markups ROI fill in some views (PR-8019)
• Remove explicit dependency of MarkupsROINode on JSON storage node (PR-8152)

Models

• Fix warnings when vtkMRMLModelNode has no mesh data (PR-7750)

Reformat

• Fix incorrect tooltip for “Rotate to Volume Reformat” button (PR-7787)
• Fix failing vtkMRMLCameraDisplayableManagerTest (PR-7853)

SampleData

• Add option to download sample data from a custom URL (PR-8133)
• Use specified filename as node name in SampleDataLogic.downloadFromSource (PR-8163)
• Do not require file type in sample data specification (PR-7479)
• Fix error handling in slicer.util.downloadFile (PR-7473)

Segmentations

• Add RemoveUnusedDisplayProperties to vtkMRMLSegmentationDisplayNode (PR-7784)
• Generate unique segment IDs using a random identifier (PR-7836)
• Introduce setting for using standard terminology in segments table (PR-8011)
• Allow hiding parts of the Segment Editor widget (PR-8116)
• Allow disabling histogram (2D views) interactions of ThresholdEffect (PR-7695)
• Simplify paint/erase diameter options for a more concise UI (PR-7278)
• Add SegmentationGeometryLogic API to set reference image geometry (PR-7607)
• Make SegmentsTableView functions available from Python (PR-7829)
• Change log level in Islands effect (PR-7848)
• Allow one draw effect point without preventing use in other slice offsets (PR-6997)
• Fix smoothing effect for all visible segments (PR-7483)
• Fix Mask volume effect node selector (PR-7478)
• Fix segment disappearing when sharing Segment Editor node between widgets (PR-7577)
• Fix loading of an empty segmentation (PR-7609)
• Fix issues caused by invalid Segmentation binary labelmap scalar types (PR-7605)
• Fix “Show 3D” button staying disabled (PR-7962)
• Fix visibility column in segment list (PR-8048)
• Fix segments not visible after thresholding (PR-8060)
• Fix name editing in Segment Editor (PR-8071)
• Fix output volume node selector in Mask Volume effect (PR-7939)

Segment Statistics

• Add percentiles computation to Segment Statistics scalar volume plugin (PR-8037)

Sequences

• Recognize sequences generated by dcm2niix (PR-7871)
• Fix empty candidate node list in Sequences module (PR-7506)
• Increase minimum size of Sequences intensity plot (PR-7871)
• Fix saving of labelmap volume sequences (PR-7946)
• Make qMRMLSequenceBrowserPlayWidget shortcuts accessible from Python (PR-7715)
• Ensure selected item number in Sequence browser remains valid (PR-7458)
• Fix deletion of the last time point in a sequence (PR-7559)
• Fix warning when browsing a transform node sequence (PR-8116)

Subject Hierarchy

• Improve SubjectHierarchy API for UIDs (PR-7616)
• Fix loading of SubjectHierarchyPlugins at startup (PR-7477)
• Add SH options to control transform interaction handle type visibility (PR-7673)
• Fix subject hierarchy consolidation after loading a scene (PR-7616)
• Do not deselect items in SHTree::setCurrentItems before reselecting them (PR-7452)
• Fix subject hierarchy help button tooltip appearance in dark mode (PR-7906)

Texts

• Allow vtkMRMLTextStorageNode to store any text files (PR-7961)

Terminologies

• Improve terminology selector (PR-7691)
• Improve terminology selector speed (PR-7714)
• Make terminology code finding more robust (PR-8003)
• Add API for finding terminology from codes (PR-7735)
• Add methods for comparing terminologies (PR-7809)
• Improve terminology category selection (PR-7976)
• Add Python-wrappable methods for accessing anatomical regions (PR-7687)
• Fix condition for customization in qSlicerTerminologyItemDelegate (PR-8059)

Transforms

• Add interaction handle visualization for linear transform nodes (PR-7562, PR-7590)
• Improve interaction options in Transforms SH plugin and module widget (PR-7599)
• Add finer control of 2D interaction handle axis display (PR-7586)
• Add “jump to handle” action for interaction handles (PR-7595)
• Add “cancel” action for interaction handles (PR-7600)
• Add transform plugin in subject hierarchy tree view (PR-7997)
• Fix issue saving transform with a non-origin center of transformation (PR-7878)
• Fix editing of transform component values in spinbox (PR-7942)
• Resolve interaction handles rendering issues (PR-7903)

Volume Rendering

• Make volume rendering preset registration more robust (PR-7610)
• Fix volume rendering property always marked as modified (PR-8029)

WebServer

• Control the amount of console output from the Python web proxy (PR-7950)
• Add WebServer example scripts (PR-7841)
• Fix WebServer script repository formatting (PR-7843)
• Update HTTPS support and add WebXR demo as transform controller (PR-7568)
• Support returning results when executing Python from qSlicerWebWidget (PR-7624)
• Add missing OPTIONS request handler when CORS is enabled (PR-7998)

Infrastructure

Packaging

• Ensure packaging of the latest d3dcompiler_47.dll for SlicerVirtualReality (PR-7571)
• Ensure launcher scripts installed from wheels remain accessible (PR-7587)
• Include runtime libraries to ensure compatibility in SlicerExecutionModel (PR-8149)

Testing

• Fix vtkMRMLCameraDisplayableManagerTest1.mrml (PR-7517)
• Fix vtkMRMLTransformStorageNodeTest1 in debug mode (PR-8029)
• Fix py_SlicerRestoreSceneViewCrashIssue3445 test in debug mode (PR-8029)
• Fix qSlicerExtensionsManagerModelTest (PR-7584)
• Fix vtkMRMLVolumeArchetypeStorageNodeTest1.cxx (PR-7734)
• Fix MRMLDisplayableManagerCxxTests (PR-7734)
• Fix SampleData tests to align with revised file loading behavior (PR-8162)
• Fix self-tests by explicitly setting file loading parameters (PR-8164)

Continuous integration (CI)

• Add GitHub workflow for keeping pre-commit configuration up to date (PR-7636)
• Add GitHub workflow to update the nightly-main branch daily (PR-7953)
• Skip “CI (Build)” workflow if only SuperBuild changes on nightly-main (PR-7945)
• Speed up doxygen generation by enabling parallel build (PR-8138)
• Add GitHub workflow to trigger Doxygen build and publish (PR-8144)
• Fix GitHub workflow for daily updates to nightly-main branch (PR-7955)
• Fix GitHub workflow authentication for “Update Preview Branch” (PR-7965)
• Update .gitignore to ensure changes to .github files are reported (PR-7635)
• Add support for codespell 2.3.0 and fix identified typos (PR-7762)
• Add support for codespell 2.4.0 and fix identified typos (PR-8158)
• Fix source files and update pre-commit setting to run additional hooks (PR-7647)
• Update “commit-message” workflow to use dedicated GitHub action (PR-7925)
• Fix manual trigger of Doxygen build/publish through GitHub UI (PR-8146)
• Fix pull request description generated by pre-commit-autoupdate workflow (PR-7688)
• Fix workflow file link in pre-commit-autoupdate workflow (PR-7690)
• Fix version extraction in pre-commit-autoupdate workflow (PR-7755)

Build system

• Update acceptable VS2022 MSVC version for TBB install (PR-7833)
• Remove obsolete WebKit-specific integration code from qSlicerWebWidget (PR-7625)
• Drop support for MSVC toolset v141 (Visual Studio 2017) (PR-7989)
• Enable OpenSSL support in DCMTK build (PR-8106)
• Fix generation of additional launcher settings for list-based settings (PR-7485)
• Re-generate additional launcher settings if they are updated (PR-7486)
• Ensure full path ID for macOS libraries installed for fixup (PR-7537)
• Prefer clearing CMAKE_INSTALL_NAME_TOOL on a per-project basis (PR-7540)
• Fix ITK’s threading-related method name deprecation warnings (PR-7400)
• Fix extension build to ensure build dependency directories are passed (PR-7712)
• Remove redundant call in vtkITKMorphologicalContourInterpolator (PR-7723)
• Resolve deprecated warning in MRML testing macro for std::string (PR-8041)
• Replace vtkStdString with std::string (PR-8042)

Platform support

• Add support for configuring _manylinux module (PR-8168)
• Update minimum required CMAKE_OSX_DEPLOYMENT_TARGET to 13.0 (PR-7990)
• Fix fatal error not reported for MSVC + TBB compatibility (PR-7834)

Dependencies

CTK:

• Update CTK DICOM Database version from 0.7.0 to 0.8.0 (PR-7472)
• Update CTK (PR-7544, PR-7558, PR-7964)
• Add removePatient/Series/Study signals to DICOM database (PR-7549)
• Backport PythonQt fixes & restore script compilation to .pyc (PR-7561)
• Fix Qt designer crash at startup (PR-7585)

DCMTK:

• Update DCMTK from 3.6.6 to 3.6.8 (PR-8018)
• Backport fixes for CVE-2022-2119 and CVE-2022-2120 (PR-8017)

ITK:

• Update ITK to 5.4.0 (PR-7771)
• Fix HDF5 symbol clash when importing ITK wheel (PR-7838)

libarchive:

• Fix libarchive build error with Clang 16 (PR-8097)

VTK:

• Backport selected Rendering, OpenVR, and OpenXR patches (PR-7487)
• Backport VR, OpenVR, and OpenXR improvements (PR-7514, PR-7516)
• Backport OpenXR-SDK improvements for streamlined integration (PR-7529)
• Backport support for Holographic.Remoting.OpenXr >= 2.9.3 (PR-7534)
• Backport fix for OpenVR gesture recognition (PR-7503)
• Backport vtkSSAOPass fixes (PR-7554)
• Backport vtkSSAOPass intensity adjustment feature (PR-7820)
• Fix preprocessor expression in vtkOpenGLRenderWindow (PR-7505)
• Backport deprecation macro update (PR-7508)

Other Dependencies:

• Update FindVcvars for future MSVC versions (PR-7815)
• Update LandmarkRegistration in SuperBuild.cmake (PR-7977)
• Update Python packages to latest (PR-7597, PR-7776)
• Update SimpleITK to fix missing use of custom namespace (PR-7812)
• Update SlicerSurfaceToolbox to include dynamic modeler extrude tool (PR-8145)

Custom Slicer application support

Slicer Application

• Improve and customize URI argument handling for custom applications (PR-7938)
• Support customizing interaction widget event translation (PR-8101)
• Fix sitkUtils without MRMLIDImageIO (PR-7940)

Build-System

• Support reuse of “commit-message” GitHub workflow (PR-7898)
• Update “pre-commit” workflow to support reuse from private projects (PR-7900)
• Fix collision of main project source dir with extension of same name (PR-7724)

Extensions

Listed below are extensions added, removed or updated since the 5.6 release.

The Slicer extensions manager enables Slicer users to install more than 190 extensions written and contributed by their peers from around the world.

New

• ConnectToSupervisely: Extension designed to organize and manage the work of labeling teams on the Supervisely computer vision platform.

• DTI-ALPS: Calculate the diffusion tensor image analysis along the perivascular space

• FractionalMyocardialMass: Computation of fractional myocardial mass (FMM) and myocardial mass at risk (MMAR).

• ImageAugmenter is a MONAI- and PyTorch-based medical image augmentation tool for 3D Slicer. Inspired by the AugmentedDataLoader, it applies a range of transformations to each image, expanding the training dataset for deep learning models with minimal coding effort.

  

• LesionSimulator: Provides a toolkit for Multiple Sclerosis lesion simulation in multimodal MRI images, such as T1, T2, T2-FLAIR and DTI scalar maps.

• LesionSpotlight: Provides modern T2-FLAIR MRI segmentation and enhancement methods that highlight abnormal white matter voxels, enabling increased contrast and segmentation of hyperintense Multiple Sclerosis lesions.

• MassVision: End-to-end AI solution for Mass Spectrometry Imaging (MSI) data, enabling targeted and non-targeted visualization, histopathology-driven co-localization, dataset curation with spatial and spectral guidance, multi-slide data alignment and denoising, AI model training and validation, and whole-slide AI deployment.

• MorphoDepot: use GitHub infrastructure to manage multi-person segmentation projects.

• MusculoskeletalAnalysis: Analyzes 3D musculoskeletal images and generates reports.

• Photogrammetry: Preprocess (mask) large collections of photographs which then can be processed to construct 3D models with texture.

  

• ScriptEditor: A script editor. It allows auto complete, text highlighting and saving of the python scripts as text nodes into the scene. To execute a code, highlight in the editor, hit copy and then manually paste it into the python console.

• SegmentationVerification: Enables quick review and verification of AI segmentation results by inspecting each segment (mask or label).

• SegmentHumanBody: Integrate the SegmentAnyBone developed by Mazurowski Lab.

  

• SlicerCineTrack: Visual verification of target tracking results. The extension enables target tracking visualization by replaying cine 2D images and overlays the outline of the Region of interest (ROI) using a displacement data file.

• SlicerDiffusionComplexityMap: Image processing technique using the principle of diffusion distribution evaluation regarding the LMC complexity measure

• SlicerMOOSE: MOOSE (Multi-organ objective segmentation) is a data-centric AI solution that generates multilabel organ segmentations to facilitate systemic TB whole-person research.

• SlicerNeuropacs: Receive and analyze diffusion MRI data from patients aged 40 years and older presenting with Parkinson’s disease (PD) symptoms.

• SlicerSOFA: Integrate mechanical simulations with 3D Slicer. This extension integrates the SOFA Framework in 3D Slicer to facilitate the development and execution of mechanical simulations involving 3D meshes, medical-image volumes and interaction with 3D Slicer markups. Currently, the extension enables the use of the SOFA API in python and provides its own SlicerSOFA API (optional) to set up a simulation and transfer data between 3D Slicer objects and SOFA objects

• SlicerTractParcellation: Automatic parcellation of white matter tractography using White matter analysis (WMA) method and O’Donnell Research Group (ORG) atlas.

  

• TutorialMaker: Streamline the creation of 3D Slicer tutorials in multiple languages.

• Ultrasound: Provide modules to process ultrasound video data.

• UniGradICON: A Foundation Model for Medical Image Registration. The extension provides a Slicer interface for the model, allowing users to perform image registration tasks using the models.

Updated

All the existing extensions have been maintained and updated to account for API and build environment changes.

Removed

Between Slicer 5.6 and Slicer 5.8, the extensions iGyne and SlicerOpenCV were removed.

List of archived extensions is documented at Slicer/ExtensionsIndex/ARCHIVE/README.md.