Slicer 5.0: Summary, Highlights and Changelog

[Sam_Horvath (Sam Horvath (Kitware))]

Changelog

• Core
  • Application
  • Extension
  • Scripting
  • Internationalization/Localization
  • Installation
  • IO
  • Rendering and display
  • Registration
• New Modules
  • Text
  • Sequences
  • Lights
• Improved Modules
  • Markups
  • DICOM
  • Models
  • Segmentations
• Infrastructure
  • Build system
  • Platform support
  • Dependencies
• Extensions
  • New
  • Updated
  • Removed

Core

Application

• Revamped module finder!
• Improved touch screen and trackpad support

Extension

• New feature: Automatic update of extensions

Scripting

• Slicer now uses Python 3!
• Slicer’s python is now binary-compatible with pypi packages
• Users can install most packages using slicer.util.pip_install

Installation

• Slicer installation is now fully portable
• User-space install on Windows

Internationalization/Localization

• Improved support for utf-8 character strings

IO

• Compressed video support
• Export nodes from data module

Rendering & Display

• New support for basic physically based rendering (PBR)
• Interactive Slice Intersections
• Updated Color Scalar Bar
• Volume display presets
• Improved RGB volume rendering
• View maximization
• 3D view tilt lock
• Surface rendering with ambient shadows
• Improved curved planar reformat
• New lightbox image mode in Screen Capture
• 3D view watermark
• Improved window/level management

Registration

• Partial Surface Registration Videotutorial

New Modules

Text

• Texts module

Sequences

• Sequences module moved into Slicer core

Lights

• Lights module to customize lighting in 3D view

• Lights module enables Surface rendering with ambient shadows:

  Without ambient-shadows	With ambient-shadows

Improved Modules

Markups

• New, better widget infrastructure
• New line, curve, angle markups, and more
• Markups UI improvements
• Markups pluggable infrastructure - easily create new markups types in other modules

DICOM

• New DICOMWeb features
• Reworked DICOM browser to make it more responsive and display more relevant information. Additionally, the browser is now embedded in the layout rather than as a popup window.
• New GE Invenia ABUS plugin

Models

• Revamp of Models module with improved model hierarchies
• Boolean mesh operations
• New mesh decimation methods
• Dynamic Modeler - many new mesh operations
  • Select by Points
• Models are saved in LPS coordinate system by default

Segmentations

• New vertical toolbar layout
• Apply operations to all segments support
• Compute cross section area of segments
• New statistics added
• Histogram based thresholding
• Shared label maps
• Search and filter segments in table
• Introduction of new segment editor effects
  • Split volume
  • Local threshold
  • Create solid segments
  • Text engrave/emboss
  • Smoothing brush

Infrastructure

Build System

• Embrace C++11 for coding style
• Remove last remnants of TCL support. See details in dependencies

Platform Support

• Support for building on newer Mac OSX (10.15+) and newer Linux builds (Ubuntu 18.04+)

Dependencies

• Python wheels integration

  • Most recent python packages (at the time of the release) are installed using PyPI (Python Package Index) wheels. Relevant SHA256 hashes are specified for each supported platforms.

  • Re-organization of python external projects as External_python-<project>.cmake and External_python-<project>-requirements.cmake

  • Introduction of maintenance script python_package_updater.py to update external python project files with the latest package version along with corresponding download hashes.

• Updated dependencies

  Update	from	to
  DCMTK	v3.6.3_20180621 commontk/DCMTK@22f253424	DCMTK-3.6.6_20210115 commontk/DCMTK@0f9bf4d9e	See release announcements on the DCMTK forum.
  curl	7.34	7.70
  CTK	6cd82aab5	ec816cbb7	See list of commits.
  ITK	4.13.1 87f5d83f1	5.3rc03 46a71c744	See release notes for 4.13, 5.0, 5.1, 5.1.1, 5.1.2, 5.2.0, 5.2.1, 5.3rc01, 5.3rc02 and 5.3rc03.
  LibArchive	3.3.3 Slicer/LibArchive@0737ce706	3.6.1 libarchive/libarchive@6c3301111
  OpenSSL	1.0.2n (unix) 1.0.1h (windows)	1.1.1g
  qRestAPI	ddc0cfcc2	ea5e85a1e	Add support for Girder API. See list of commits
  SimpleITK	1.1.0 Slicer/SimpleITK@e52c9ab04	2.2rc3 SimpleITK/SimpleITK@ffd48e274	See release notes for 1.1.0, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.2.4, 2.0.0, 2.0.1, 2.0.2, 2.1.0, 2.1.1, 2.2rc1, 2.2rc2 and 2.2rc3
  TBB	2018_20171205oss	2021.5.0	See PR-5105 2018_20171205oss → 2019_20191006oss, PR-6405 2019_20191006oss → 2021.5.0 and oneTBB releases notes.
  VTK	8.2.0 Slicer/VTK@31dc6a08b	9.1.20220125 Slicer/VTK@bccd2b8f7	See release notes for 8.2 , and for 9.0 and 9.1. Include backports of selected rendering improvements and OpenXR Holographic Remoting support PR-6433.

• New dependencies

  	version
  LibFFI	v3.4.2 python-cmake-buildsystem/libffi@libffi-cmake-buildsystem-v3.4.2-2021-06-28-f9ea416	Introduced in PR-6026 to support building against Python 3.9.10. Our fork python-cmake-buildsystem/libffi provides support for building using CMake.
  LZMA	5.2.5	Introduced in PR-5194 to support use of lzma python module.
  sqlite	3.30.1

• Updated build-time dependencies

  Update	from	to
  PCRE	8.38	8.44	Used to generate SimpleITK Python wrappers.
  Swig	3.0.10	4.0.2	Used to generate SimpleITK Python wrappers.

• Removed dependencies

  • Removed support for building TCL compatibility layers and associated tk, tcl and incrTcl external projects.
  • Removed NUMPY and SciPy external projects now installed as python wheels.

Extensions

Listed below are extensions added, removed or updated since the 4.10.2 release.

The Slicer extensions manager enables Slicer users to install more than 150 extensions written and contributed by their peers from around the world.

New

• Segmentation
  • RVXLiverSegmentation
  • DensityLungSegmentation
  • SegmentGeometry
  • Breast DCE-MRI FTV
  • TITAN
  • T1_ECVMapping
  • BrainVolumeRefinement
• Infrastructure / Utilities
  • SlicerBatchAnonymize
  • SlicerPipelines
  • LanguagePacks
  • Parallel Processing
  • SlicerPRISM
  • ImageCompare
  • OpenAnatomy
  • Osirix ROI importer
  • StyleTester
  • FreeSurfer support moved to extension
  • RawImageGuess - loading data in unknown formats
  • New module for user statistics
• Markups
  • MRUSLandmarking
  • SurfaceMarkup
    • Discourse
  • Centerline extraction in SlicerVMTK
• IGT
  • Mandibular reconstruction planning and custom surgical guides
  • SlicerAblationPlanner
  • OrthodonticAnalysis
  • BreastImplantAnalyzer
  • Auto3dgm
  • SlicerCMF
  • KidneyStoneCalculator
  • SlicerHeart - Baffle Planner
  • Lung CT Analyzer
• Machine learning
  • SlicerPyTorch
  • SlicerAIGT
  • TorchIO
  • NVIDIA Ai assisted segmentation
• Registration
  • SlicerNetstim
  • SlicerANTS
• Hardware support
  • SlicerLookingGlass
  • Arduino Controller
• Web/Cloud
  • FlywheelSlicerConnect
• Dosimetry
  • OpenDose

Updated

Referenced below are new features added to existing extensions. Note all the existing extensions have been maintained and updated to account for API and build environment changes.

• IGT

  • Updates to the Chest Imaging Platform
  • SlicerIGT - adds real time 3D ultrasound reconstruction

• Web/Cloud

  • SlicerJupyter improvements

Removed

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