2012 Progress Report Science Wiki Version Engineering - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T17:10:09Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Aylward: /* 5.3.3. Roadmap */

2012-04-21T18:05:43Z

5.3.3. Roadmap

Aylward: /* 5.3.2. Expansion */

2012-04-21T17:56:01Z

5.3.2. Expansion

Aylward: /* 5.3.1. Maturation */

2012-04-21T17:40:11Z

5.3.1. Maturation

Aylward: /* Major Developments */

2012-04-21T17:39:39Z

Major Developments

Aylward at 17:39, 21 April 2012

2012-04-21T17:39:13Z

Aylward at 17:34, 21 April 2012

2012-04-21T17:34:38Z

Aylward: /* 5.3. NA-MIC Kit */

2012-04-21T11:06:48Z

5.3. NA-MIC Kit

Aylward: /* 5.3. NA-MIC Kit */

2012-04-20T22:37:58Z

5.3. NA-MIC Kit

Aylward: /* 5.2.3. Data Management Platform */

2012-04-20T21:42:30Z

5.2.3. Data Management Platform

@@ Line 132: / Line 132: @@
 * Slicer 4.0: Major Changes (November, 2011)
 ** Slicer 4.0 includes a major overhaul of the user interface, improved and simplified workflows for major tasks, simplified procedures for developers, and improved Python support.
-** http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Announcements
+** https://www.slicer.org/wiki/Documentation/4.0/Announcements
 * Slicer 4.0.1: Major Changes (January, 2011)
 ** Notable changes in Slicer 4.0.1 include new support for Ubuntu 11.04 and Fedora FC 13, and for DWI tractrography modules on Mac OS X.  VTK GPU raycast method support of ATI GPU cards for Mac OS X is also included in this release, as well as major improvements to restoring scenes, which now provides significantly faster speeds.  Additionally, in Slicer 4.0.1, users can now drag-and-drop files, including volumes, meshes, annotations, etc., into Slicer from Window Explorer, Mac Finder, and Linux Nautilus.
-** http://www.slicer.org/slicerWiki/index.php/Slicer4:QtPort/Releases#Slicer_4.0.1
+** https://www.slicer.org/wiki/Slicer4:QtPort/Releases#Slicer_4.0.1
 * Slicer 4.1: Major Changes (April, 2012)

@@ Line 143: / Line 143: @@
 ** http://www.kitware.com/news/home/browse/401
-[[image:Slicer_4_1_MultiVolumeCharts.png|500px|center]]
+<center>[[image:Slicer_4_1_MultiVolumeCharts.png|500px|center]]
-<em>Figure 3. Slicer 4.1 introduced support for 4D images and charting.</em>
+<em>Figure 3. Slicer 4.1 introduced support for 4D images and charting.</em></center>
 * Slicer 4.2: Plans (August, 2012)
-** QtTesting
+** The next major release of Slicer 4.2 is still in the planning phase, but certain features are likely to be present.   In particular, we anticipate the following will be released in Beta/1.0 format in Slicer 4.2:
-** DICOM Lollipops
+*** QtTesting
-** Slicer Catalog
+*** DICOM Lollipops

@@ Line 116: / Line 116: @@
 The maturation of the foundation of the NA-MIC Kit (discussed in Section 5.3.1) has allowed NA-MIC to pursue new opportunities with less effort and greater confidence.   Highlights regarding the expansion of the NA-MIC Kit into new areas include:
-* Slicer Catalog:
+* Slicer Catalog: The NA-MIC community was introduced to the Slicer Catalog in Slicer 4.1.  This system allows users to install, unstall, search, browse, and rank Slicer extensions.  This user experience is available from within Slicer and over the web - much like the Android and Apple App Stores.   Developers can contribute, update, document, and post screenshots on their modules and receive community feedback.   We see this work as a launchpad for new levels and avenues for community involvement in Slicer.
-* CDash Package Manager:
+* CDash Package Manager: We have automated the nightly release of pre-compiled packages for Slicer on multiple platforms.  This new process is built on CDash and allows executables and packages created during nightly regression testing to be submitted to a Midas system for download: http://slicer.kitware.com
 * CTK is the toolkit NA-MIC created in collaboration with other open-source toolkits (e.g., MITK from the German Cancer Research Center in Heidelberg, XIP from Siemens, GIMIAS from UPF in Spain, and OpenMAF from U of Bologna) to host custom Qt and DCMTK modules for crafting medical applications.   CTK now provides several innovative GUI and DICOM elements that specifically save GUI space, user-time, and developer effort in medical applications.   Examples of the widgets provided by CTK are discussed in the blog: http://www.kitware.com/blog/home/post/169
-* GUI Testing
+* GUI Testing is being offered in a maintenance release to follow Slicer 4.1 in May/June 2012.   This work will allow user interactions with Slicer to be recorded on one machine and played back on another - and the results of those interactions can be compared.   This GUI testing will be integrated into Slicer's nightly regression testing process.  We propose to base the tests on the features demonstrated in the Slicer tutorials.
-* DICOM Lollipops
+* DICOM Lollipops are a novel method for embedding entire Slicer (MRML) scenes into a DICOM object.   Via this embedding, Slicer data can be read to/from PACS - enabling better integration of Slicer with clinical workflows.
 == 5.3.3. Roadmap ==

@@ Line 99: / Line 99: @@
 == 5.3.1. Maturation ==
 <em>Stephen R. Aylward</em>
 As mentioned in Section 5.2., Slicer has undergone massive expansion while also achieving improved stability.  The same is true for the NA-MIC Kit as a whole.   This evolution represents a maturation of our tools as well as the community.   Open-source software, good software practices, and our tools are becoming the leading standards in our fields.   Large communities of users and developers are forming around many of the components that we have chosen to use and that we have created for the NA-MIC Kit.  The many improvements and new features of Slicer are discussed in Section 5.2.  Below we highlights the evolution of the other tools in the NA-MIC:

@@ Line 50: / Line 50: @@
 * ''Networking logic:'' An alpha implementation of the infrastructure for actually exchanging data between XNAT and Slicer has been developed and revealed that significant additional work is required to handle parsing of MRML files within Slicer in the context of remotely hosted data.  This work is now underway and will require several months to complete.
 * ''Use cases:'' Several use cases have been identified, including projects within the Quantitative Imaging Network (QIN), to drive the development of the Slicer/XNAT integration.
-* '''DICOM-RT and QIN support:''' Via DCMTK and custom classes, Slicer is being extended to support RT Plans, Images, Annotations, etc.  Much of the support is being driving by the head-and-neck cancer core.  Additional developments are being driven by an ongoing effort to integrate Slicer as an annotation module in the Quantitative Imaging Network (QIN).
+* ''DICOM-RT and QIN support:'' Via DCMTK and custom classes, Slicer is being extended to support RT Plans, Images, Annotations, etc.  Much of the support is being driving by the head-and-neck cancer core.  Additional developments are being driven by an ongoing effort to integrate Slicer as an annotation module in the Quantitative Imaging Network (QIN).
-* '''DICOM database and networking:''' Slicer DICOM support is approaching clinical quality in terms of speed of searching and IO by maintaining a database that indexes previously loaded DICOM objects.  Via this database, it is no longer necessary to parse each object in order to search and/or load an entire series, study, or patient into Slicer.
+* ''DICOM database and networking:'' Slicer DICOM support is approaching clinical quality in terms of speed of searching and IO by maintaining a database that indexes previously loaded DICOM objects.  Via this database, it is no longer necessary to parse each object in order to search and/or load an entire series, study, or patient into Slicer.
 === Plans ===

@@ Line 16: / Line 16: @@
 As shown in Figure 1, 3D Slicer version 4.0 (commonly called Slicer4) is having an immediate world-wide impact.  Version 4.0, released at the Radiology Society of North America (RSNA) meeting in late November 2011, is the result of a major effort by the NA-MIC engineering cores, in collaboration with the wider Slicer community, to re-implement and streamline the software in response to feedback from NA-MIC DBPs and algorithm developers.  A new 3D Slicer version 4.1 release, being finalized at the time of this writing, adds back many of the advanced features of Slicer3, notably the Extension system by which new functionality can be downloaded and installed independent of the main executable.  As described more fully below, these sweeping changes required touching not only most of the code in Slicer, but also feeding important feature and bug fix changes back into the rest of the NA-MIC Kit and upstream libraries.  As a result of these efforts, 3D Slicer in now an improved reference implementation of a modern medical image computing package and a strong foundation for research.
-[[image:2012_Engineering_EndUserPlatform_Fig1.png]]
+[[image:2012_Engineering_EndUserPlatform_Fig1.png|500px|center]]
 <em>Figure 1: 3D Slicer version 4.0 end-user downloads during the first 3 months of 2012, a rate of 45,360 per year (over 100 downloads per day).  Interactive geolocated download statistics are available at http://download.slicer.org/stats.</em>
@@ Line 143: / Line 142: @@
 ** http://www.kitware.com/news/home/browse/401
-[[image:Slicer_4_1_MultiVolumeCharts.png]]
+[[image:Slicer_4_1_MultiVolumeCharts.png|500px|center]]
 * Slicer 4.2: Plans (August, 2012)

@@ Line 93: / Line 93: @@
 = 5.3. NA-MIC Kit =
-The NA-MIC Kit is designed to accelerate the pace of research and transition to clinical evaluation providing (a) a flexible yet stable execution and visualization engine with strong support for clinical data (Slicer), (b) methods for extending that platform and sharing those extensions with others, and (c) tools for community software development.  The major components of the NA-MIC Kit are illustrated in Fig. 2.
+The NA-MIC Kit is designed to accelerate the pace of research and facilitate clinical evaluation.  It provides (a) a flexible yet stable execution and visualization engine with strong support for clinical data (Slicer), (b) methods for extending that platform and sharing those extensions with others, and (c) tools for community software development.  The major components of the NA-MIC Kit are illustrated in Fig. 2.
 [[image:2012_Engineering_NAMICKit.png|500px|center]]
-Figure 2. The NA-MIC Kit is a collection of applications, libraries, and processes for bridging algorithm developers, engineers, and clinical researchers.  Slicer is the primary vehicle for deploying algorithms.  The other components of the NA-MIC Kit addresses the critical yet often overlooked elements of data sharing, integration into clinical workflows, code quality assurance, cross-platform development, and much more.
+<em>Figure 2. The NA-MIC Kit is a collection of applications, libraries, and processes for bridging algorithm developers, engineers, and clinical researchers.  Slicer is the primary vehicle for deploying algorithms.  The other components of the NA-MIC Kit addresses the critical yet often overlooked elements of data sharing, integration into clinical workflows, code quality assurance, cross-platform development, and much more.</em>
-== 5.3.1. Expansion ==
+== 5.3.1. Maturation ==
 <em>Stephen R. Aylward</em>
 === Progress ===

@@ Line 45: / Line 45: @@
 <em>Dan Marcus</em>
-Efforts in the Data Management Platform have focused on developing an ergonomic user interface and internal networking logical to efficiently exchange data between Slicer and XNAT.
+Efforts in the Data Management Platform have focused on (1) developing an ergonomic user interface and internal networking logical to efficiently exchange data between Slicer and XNAT and (2) expanding Slicer's support for importing from and exporting to local DICOM Objects and networked DICOM PACS.
 === Major Developments ===
 * ''User Interface:'' The XNAT development team is working with a web usability firm (Integrity St. Louis) to design and implement a web interface that can be deployed in Slicer 4's Qt framework for exploring data hosted in a remote XNAT data repository.  Prototypes have been implemented and are currently being reviewed by stakeholders with the goal of a functioning interface by June, 2012.
 * ''Networking logic:'' An alpha implementation of the infrastructure for actually exchanging data between XNAT and Slicer has been developed and revealed that significant additional work is required to handle parsing of MRML files within Slicer in the context of remotely hosted data.  This work is now underway and will require several months to complete.
 * ''Use cases:'' Several use cases have been identified, including projects within the Quantitative Imaging Network (QIN), to drive the development of the Slicer/XNAT integration.
 === Plans ===
-The bulk of the effort in the coming year will continue to focus on the user interface and networking logic for remote data management.  As the initial development completes, we will turn to developing more efficient mechanisms for caching data locally and synchronizing local caches with remote repositories.
+The bulk of the effort in the coming year will continue to focus on (1) the user interface and networking logic for remote data management in XNAT and (2) import and export of Slicer results (i.e., entire MRML scenes) as DICOM objects.  Regarding XNAT, as the initial development completes, we will turn to developing more efficient mechanisms for caching data locally and synchronizing local caches with remote repositories.  Regarding importing and exporting Slicer data as DICOM objects, we are pursuing the concept of a '''DICOM Lollipop.''' In a DICOM Lollipop, a complete Slicer (MRML) Scene, with annotations, segmentations, viewing conditions, etc, can be saved as a binary payload in a standard DICOM object.   In this manner, Slicer's data can be pushed/pulled from PACS for integration with and sharing across hospital workflows.
 == 5.2.4. Community Software Process ==