Slicer 5.0: Summary, Highlights and Changelog

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

Table of Contents

• Summary
• Highlights
• Detailed Changelog

Summary

The community of 3D Slicer developers is proud to announce that version 5.0 is now available for download. This version introduces hundreds of feature enhancements and bug fixes for better performance and stability. It includes many new-and-improved core modules and more than 40 new-and-improved extensions. Many of these features have been available for months to users of the Slicer Preview version, but now there is a release that developers and users can rely on for stability and maintenance.

3D Slicer 5.0 builds on the success of the version 4 with over one million downloads of the core program and 5.3 million downloads of extensions during the last decade.

The development of 3D Slicer—including its numerous modules, extensions, datasets, pull requests, patches, issues reports, suggestions—is made possible by users, developers, contributors and commercial partners around the world. 3D Slicer is based on a stack of open-source softwares and we are working constantly on updating the underlying packages. This development is funded by various grants and agencies. For more details, please see the 3D Slicer Acknowledgments page.

One of the main distinguishing features of 3D Slicer is its easy extensibility enabled by good quality documentation, a thriving community, cross-platform support & open source code. 3D Slicer supports a number of extension types which offer a different mix of simplicity and range of control of the software.
A rigorous quality assurance system leveraging automated testing and user feedback ensures the timely detection of issues caused by ongoing work in different components of the platform. See the contributing guidelines

slicer.org is the portal to the application, training materials, and the development community.

The Slicer Tutorials page provides a series of tutorials and data sets for training in the use of Slicer.

Please note that Slicer continues to be a research package and is not intended for clinical use (clinical users must obtain the necessary ethics or regulatory approvals).

Highlights

Markups improvements

• New built-in markups types
  

• Support for computing markups measurements (length for line and curve, angle for angle markups, curvature mean and curvature max for curve markups and area for plane and curve markups)
  

• New interaction handles for translating, rotating and scaling markups from 2D and 3D views.
  

• Pluggable markups infrastructure: The infrastructure has been generalized to enable developers add new markup types in extensions. For example, the SurfaceMarkups extension adds editable NURBS surfaces for modelling thin objects.

Artificial Intelligence support

MONAILabel extension

The MONAILabel extension builds on the very popular MONAI toolkit for building AI models for automatic segmentation of medical images. The extension allows users to segment images (using classic and AI-assisted Segment Editor effects) and uses these data sets to train an AI model. MONAILabel can be set up without a dedicated server, on any computer with a strong GPU.

This is the most popular framework for users who want to train their own AI models for image segmentation.

3D Slicer and MONAI Label were highlighted by the CEO of NVIDIA during his 2022 GCT Keynote Address as the suggested tools for working with DICOM data.

NVIDIA AI-assisted annotation extension

The new Slicer extension Nvidia AI-assisted annotation (AIAA) adds a new effect in the Segment Editor module.

Example result of automatic segmentation:

A community-supported AI segmentation server is provided for Slicer users to allow easy evaluation of the extension, without the need for users to have access to a computer with a strong GPU. The server hosts a number of trained models for segmentation of liver, lungs, brain tumor, etc. This extension is recommended quick evaluation and for users who find the already available pre-trained models suitable for their work. For creating new AI models, MONAILabel extension is recommended.

More AI tools deployed via 3D Slicer

Several other AI-assisted extensions are added to the Extensions Manager, including:

HD Brain Extraction Tool	HD-BET skull stripping tool from DKFZ/Heidelberg
DensityLungSegmentation	AI-based lung segmentation
RVXLiverSegmentation	AI-based liver segmentation
SlicerAIGT	Real-time ultrasound and optical image stream segmentation and volume reconstruction
SlicerPyTorch	Helper extension for installing Pytorch, used by extensions that require PyTorch
TorchIO	Graphical user interface for the TorchIO AI helper toolkit

DICOM improvements

• Reworked DICOM browser including performance and UI improvements.
  

  

• New DICOMweb features allowing to launch Slicer from web browser and download/upload data sets to the cloud using DICOMweb.

Cloud/Web support

• WebServer module is added with the following features:
  • allow Slicer features to be accessed via web requests using a REST API
  • expose the Slicer DICOM database content via DICOMweb interface
  • serve webpages to allow hosting simple web applications directly in Slicer
• Slicer can be launched from a web browser to load a selected study, for example from Kheops
• Multiple docker images are provided to run Slicer in docker containers, with CPU rendering and with GPU accelerated rendering; standalone or as a Jupyter kernel (with JupyterHub compatible interface).
• Slicer is compatible with AWS AppStreaming for cloud-hosted virtual workstation. This was used for MONAI Label training workshops.
• SlicerVR can be used with NVIDIA CloudXR on cloud-hosted machines

Extensions Manager improvements

We have implemented some long-awaited improvements in the Extensions Manager in Slicer-5.0.3. Most importantly extensions can be updated automatically and bookmarks can be used for convenient reinstallation of a list of extensions across different Slicer versions, computers, or users.

For the list of new features as well as usability, stability and performance improvements. See New feature: Automatic update of extensions

Translation (internationalization) support

Slicer was awarded a CZI Essential Open Source Software grant for translation of the application and extensions to French and develop infrastructure for allowing translation to any other languages. This is still a work in progress (expected to be complete in September 2023), but language selection and translation of a large part of the displayed text in the Slicer core application is already translatable.

• LanguagePacks extension is provided for creating, editing, and storing translations for Slicer core and extensions.
  

  

• Weblate online collaborative translation system is used for for crowdsourcing translation work to the Slicer community.

Infrastructure improvements

• Redesigned documentation website and improve documentation workflow

  • Transitioned user and developer guides from mediawiki to readthedocs allowing to contribute, maintain and preview updates along side the Slicer source code.
  Click to compare Before and After

  Before	After

• Revamped landing page

  • Improved search engine indexing and social networks integration by adding relevant metadata tags
  • Mobile “friendly” landing page
  • Improvements to the landing page can be proposed and previewed on GitHub at Slicer/slicer.org
  • The new website was collaboratively developed by the Slicer community
    between July 2020 and March 2021. See here.
  Click to compare Before and After

  Before	After

• Redesigned Slicer logo

  • Assets are currently organized in this public Google folder.
  • The discussions leading to the new design are available on discourse here.
  • See issue #6161 for proposal to better organize Slicer logos material.
  Click to compare Before and After

  Before	After

• Improved frontend for searching and downloading extensions. See https://extensions.slicer.org

  • Source code of the site available at KitwareMedical/slicer-extensions-webapp
  Click to compare Before and After

  Before	After

• Updated download.slicer.org.

  • Source code of the site available at Slicer/slicer_download
  • Learn about the history here.
  Click to compare Before and After

  Before	After

• Updated backend infrastructure for managing and organizing Slicer application and extension packages.

  • The new infrastructure was designed built on Girder to scale and support management of packages associated with custom Slicer-based applications.
  • See https://slicer-packages.kitware.com/ and girder/slicer_package_manager

Other improvements

• Integration with the Python ecosystem. See details in the Scripting and Dependencies sections below

• Library updates. See details in the Dependencies section below

• More than 40 new extensions have been added. See complete list in the Extensions section below.

• Although we have a common understanding about how to conduct operations in the Slicer community, consensus was reached and we now formally adopted a code of conduct.

[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