The Digital Anatomist Information System and Its Use in the Generation and Delivery of Web-Based Anatomy Atlases

Advances in network and imaging technology, coupled with the availability of 3-D datasets such as the Visible Human, provide a unique opportunity for developing information systems in anatomy that can deliver relevant knowledge directly to the clinician, researcher or educator. A software framework is described for developing such a system within a distributed architecture that includes spatial and symbolic anatomy information resources, Web and custom servers, and authoring and end-user client programs. The authoring tools have been used to create 3-D atlases of the brain, knee and thorax that are used both locally and throughout the world. For the one and a half year period from June 1995–January 1997, the on-line atlases were accessed by over 33,000 sites from 94 countries, with an average of over 4000 ‘‘hits’’ per day, and 25,000 hits per day during peak exam periods. The atlases have been linked to by over 500 sites, and have received at least six unsolicited awards by outside rating institutions. The flexibility of the software framework has allowed the information system to evolve with advances in technology and representation methods. Possible new features include knowledge-based image retrieval and tutoring, dynamic generation of 3-D scenes, and eventually, real-time virtual reality navigation through the body. Such features, when coupled with other on-line biomedical information resources, should lead to interesting new ways for managing and accessing structural information in medicine

Imaging Informatics and the Human Brain Project: the Role of Structure, Review

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Slisp: A Flexible Software Toolkit for Hybrid, Embedded and Distributed Applications

We describe Slisp (pronounced ‘Ess-Lisp’), a hybrid Lisp–C programming toolkit for the development of scriptable and distributed applications. Computationally expensive operations implemented as separate C-coded modules are selectively compiled into a small Xlisp interpreter, then called as Lisp functions in a Lisp-coded program. The resulting hybrid program may run in several modes: as a stand-alone executable, embedded in a different C program, as a networked server accessed from another Slisp client, or as a networked server accessed from a C-coded client. Five years of experience with Slisp, as well experience with other scripting languages such as Tcl and Perl, are summarized. These experiences suggest that Slisp will be most useful for mid-sized applications in which the kinds of scripting and embeddability features provided by Tcl and Perl can be extended in an efficient manner to larger applications, while maintaining a well-defined standard (Common Lisp) for these extensions. In addition, the generality of Lisp makes Lisp a good candidate for an application-level communication language in distributed environments

Real-time volume rendering and tractography visualization on the web

In the field of computer graphics, Volume Rendering techniques allow the visualization of 3D datasets, and specifically, Volume Ray-Casting renders images from volumetric datasets, typically used in some scientific areas, such as medical imaging -- This article aims to describe the development of a combined visualization of tractography and volume rendering of brain T1 MRI images in an integrated way -- An innovative web viewer for interactive visualization of neuro-imaging data has been developed based on WebGL -- This recently developed standard enables the clients to use the web viewer on a wide range of devices, with the only requirement of a compliant web-browser -- As the majority of the rendering tasks take place in the client machine, the effect of bottlenecks and server overloading are minimized -- The web application presented is able to compete with desktop tools, even supporting high graphical demands and facing challenges regarding performance and scalability -- The developed software modules are available as open source code and include MRI volume data and tractography generated by the Diffusion Toolkit, and connectivity data from the Connectome Mapping Toolkit -- Our contribution for the Volume Web Viewer implements early ray termination step according to the tractography depthmap, combining volume images and estimated white matter fibers -- Furthermore, the depthmap system extension can be used for visualization of other types of data, where geometric and volume elements are displayed simultaneousl

Web-based Stereoscopic Collaboration for Medical Visualization

Medizinische Volumenvisualisierung ist ein wertvolles Werkzeug zur Betrachtung von Volumen- daten in der medizinischen Praxis und Lehre. Eine interaktive, stereoskopische und kollaborative Darstellung in Echtzeit ist notwendig, um die Daten vollständig und im Detail verstehen zu können. Solche Visualisierung von hochauflösenden Daten ist jedoch wegen hoher Hardware- Anforderungen fast nur an speziellen Visualisierungssystemen möglich. Remote-Visualisierung wird verwendet, um solche Visualisierung peripher nutzen zu können. Dies benötigt jedoch fast immer komplexe Software-Deployments, wodurch eine universelle ad-hoc Nutzbarkeit erschwert wird. Aus diesem Sachverhalt ergibt sich folgende Hypothese: Ein hoch performantes Remote- Visualisierungssystem, welches für Stereoskopie und einfache Benutzbarkeit spezialisiert ist, kann für interaktive, stereoskopische und kollaborative medizinische Volumenvisualisierung genutzt werden. Die neueste Literatur über Remote-Visualisierung beschreibt Anwendungen, welche nur reine Webbrowser benötigen. Allerdings wird bei diesen kein besonderer Schwerpunkt auf die perfor- mante Nutzbarkeit von jedem Teilnehmer gesetzt, noch die notwendige Funktion bereitgestellt, um mehrere stereoskopische Präsentationssysteme zu bedienen. Durch die Bekanntheit von Web- browsern, deren einfach Nutzbarkeit und weite Verbreitung hat sich folgende spezifische Frage ergeben: Können wir ein System entwickeln, welches alle Aspekte unterstützt, aber nur einen reinen Webbrowser ohne zusätzliche Software als Client benötigt? Ein Proof of Concept wurde durchgeführt um die Hypothese zu verifizieren. Dazu gehörte eine Prototyp-Entwicklung, deren praktische Anwendung, deren Performanzmessung und -vergleich. Der resultierende Prototyp (CoWebViz) ist eines der ersten Webbrowser basierten Systeme, welches flüssige und interaktive Remote-Visualisierung in Realzeit und ohne zusätzliche Soft- ware ermöglicht. Tests und Vergleiche zeigen, dass der Ansatz eine bessere Performanz hat als andere ähnliche getestete Systeme. Die simultane Nutzung verschiedener stereoskopischer Präsen- tationssysteme mit so einem einfachen Remote-Visualisierungssystem ist zur Zeit einzigartig. Die Nutzung für die normalerweise sehr ressourcen-intensive stereoskopische und kollaborative Anatomieausbildung, gemeinsam mit interkontinentalen Teilnehmern, zeigt die Machbarkeit und den vereinfachenden Charakter des Ansatzes. Die Machbarkeit des Ansatzes wurde auch durch die erfolgreiche Nutzung für andere Anwendungsfälle gezeigt, wie z.B. im Grid-computing und in der Chirurgie

Web tools for large-scale 3D biological images and atlases

<p>Abstract</p> <p>Background</p> <p>Large-scale volumetric biomedical image data of three or more dimensions are a significant challenge for distributed browsing and visualisation. Many images now exceed 10GB which for most users is too large to handle in terms of computer RAM and network bandwidth. This is aggravated when users need to access tens or hundreds of such images from an archive. Here we solve the problem for 2D section views through archive data delivering compressed tiled images enabling users to browse through very-large volume data in the context of a standard web-browser. The system provides an interactive visualisation for grey-level and colour 3D images including multiple image layers and spatial-data overlay.</p> <p>Results</p> <p>The standard Internet Imaging Protocol (IIP) has been extended to enable arbitrary 2D sectioning of 3D data as well a multi-layered images and indexed overlays. The extended protocol is termed IIP3D and we have implemented a matching server to deliver the protocol and a series of Ajax/Javascript client codes that will run in an Internet browser. We have tested the server software on a low-cost linux-based server for image volumes up to 135GB and 64 simultaneous users. The section views are delivered with response times independent of scale and orientation. The exemplar client provided multi-layer image views with user-controlled colour-filtering and overlays.</p> <p>Conclusions</p> <p>Interactive browsing of arbitrary sections through large biomedical-image volumes is made possible by use of an extended internet protocol and efficient server-based image tiling. The tools open the possibility of enabling fast access to large image archives without the requirement of whole image download and client computers with very large memory configurations. The system was demonstrated using a range of medical and biomedical image data extending up to 135GB for a single image volume.</p

SIRF: Synergistic Image Reconstruction Framework

The combination of positron emission tomography (PET) with magnetic resonance (MR) imaging opens the way to more accurate diagnosis and improved patient management. At present, the data acquired by PET-MR scanners are essentially processed separately, but the opportunity to improve accuracy of the tomographic reconstruction via synergy of the two imaging techniques is an active area of research. In this paper, we present Release 2.1.0 of the CCP-PETMR Synergistic Image Reconstruction Framework (SIRF) software suite, providing an open-source software platform for efficient implementation and validation of novel reconstruction algorithms. SIRF provides user-friendly Python and MATLAB interfaces built on top of C++ libraries. SIRF uses advanced PET and MR reconstruction software packages and tools. Currently, for PET this is Software for Tomographic Image Reconstruction (STIR); for MR, Gadgetron and ISMRMRD; and for image registration tools, NiftyReg. The software aims to be capable of reconstructing images from acquired scanner data, whilst being simple enough to be used for educational purposes

SIRF: Synergistic Image Reconstruction Framework

The combination of positron emission tomography (PET) with magnetic resonance (MR) imaging opens the way to more accurate diagnosis and improved patient management. At present, the data acquired by PET-MR scanners are essentially processed separately, but the opportunity to improve accuracy of the tomographic reconstruction via synergy of the two imaging techniques is an active area of research. In this paper, we present Release 2.1.0 of the CCP-PETMR Synergistic Image Reconstruction Framework (SIRF) software suite, providing an open-source software platform for efficient implementation and validation of novel reconstruction algorithms. SIRF provides user-friendly Python and MATLAB interfaces built on top of C++ libraries. SIRF uses advanced PET and MR reconstruction software packages and tools. Currently, for PET this is Software for Tomographic Image Reconstruction (STIR); for MR, Gadgetron and ISMRMRD; and for image registration tools, NiftyReg. The software aims to be capable of reconstructing images from acquired scanner data, whilst being simple enough to be used for educational purposes. The most recent version of the software can be downloaded from http://www.ccppetmr.ac.uk/downloads and https://github.com/CCPPETMR/. Program summary: Program Title: Synergistic Image Reconstruction Framework (SIRF) Program Files DOI: http://dx.doi.org/10.17632/s45f5jh55j.1 Licensing provisions: GPLv3 and Apache-2.0 Programming languages: C++, C, Python, MATLAB Nature of problem: In current practice, data acquired by PET-MR scanners are processed separately. Methods for improving the accuracy of the tomographic reconstruction using the synergy of the two imaging techniques are actively being investigated by the PET-MR research and development community, however, practical application is heavily reliant on software. Open-source software available to the PET-MR community – such as the PET package (STIR) (Thielemans et al., 2012) and the MR package Gadgetron (Hansen and Sørensen, 2013) – provide a basis for new synergistic PET-MR software. However, these two software packages are independent and have very different software architectures. They are mostly written in C++ but many researchers in the PET-MR community are more familiar with script-style languages, such as Python and MATLAB, which enable rapid prototyping of novel reconstruction algorithms. In the current situation it is difficult for researchers to exploit any synergy between PET and MR data. Furthermore, techniques from one field cannot easily be applied in the other. Solution method: In SIRF, the bulk of computation is performed by available advanced open-source reconstruction and registration software (currently STIR, Gadgetron and NiftyReg) that can use multithreading and GPUs. The SIRF C++ code provides a thin layer on top of these existing libraries. The SIRF layer has unified data-containers and access mechanisms. This C++ layer provides the basis for a simple and intuitive Python and MATLAB interface, enabling users to quickly develop and test their reconstruction algorithms using these scripting languages only. At the same time, advanced users proficient in C++ can directly utilise wider SIRF functionality via the SIRF C++ libraries that we provide

MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data

Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products. These applications range from highly specific programs for a single modality, to general purpose toolkits that include many image processing functions in addition to visualization. However, few if any of these combine both stand-alone and remote multi-modality visualization in an open source, portable and extensible tool that is easy to install and use, yet can be included as a component of a larger information system. We have developed a new open source multimodality 3-D visualization application, called MindSeer, that has these features: integrated and interactive 3-D volume and surface visualization, Java and Java3D for true cross-platform portability, one-click installation and startup, integrated data management to help organize large studies, extensibility through plugins, transparent remote visualization, and the ability to be integrated into larger information management systems. We describe the design and implementation of the system, as well as several case studies that demonstrate its utility. These case studies are available as tutorials or demos on the associated website: http://sig.biostr.washington.edu/projects/MindSeer MindSeer provides a powerful visualization tool for multimodality neuroimaging data. Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine