Higher Education

Our work in higher education currently falls into three main areas:

 
Low Cost Stereo Visualisation for Higher Education:
Over the last few years Phil Lavery has been doing a series of events and seminars to introduce low cost, easy to use, but very powerful Real time Interactive 3D Stereoscopic Visualisation to Higher education and Research Institutions. More...
 
Developing new Open Source tools for educational use:
Adoption of stereoscopic visualisation for education is dependant on there being applications available or developed to meet the needs of both educators and students. Our discussions with members of the Scottish medical education community has identified a need for a stereoscopic visualisation tool that can handle high quality volumetric data. More...
 
Contact us
If you would like to host an event or more information on stereoscopic visualisation our contact information is here. We will then contact you to discuss your requirements in more detail.
 

Low Cost Stereo Visualisation

 Low Cost Stereo Visualisation for Higher Education:

Over the last few years Phil Lavery has been doing a series of events and seminars to introduce low cost, easy to use, but very powerful Real time Interactive 3D Stereoscopic Visualisation to Higher Education and Research Institutions.

 

What is Stereoscopic Visualisation?
It is the way your brain expects to see things, with a left eye view and a right eye view, and from the minor differences that around 60mm of eye separation creates in these two views, the brain is able to calculate depth and therefore able to construct and understand the real world we experience every day. It is the difference between looking at a flat photograph or illustration of an object and feeling that you can reach out and touch the object itself. Realtime Interactive Stereoscopic Visualisation combines modern stereoscopic display technologies with a powerful computer that can handle huge amounts of data and allow it to be manipulated interactively in realtime. Until very recently the prohibitive costs and complexity of large scale, real time, interactive stereoscopic visualisation limited its use to multi national companies like BP, Shell, BMW, Mercedes, Nokia or to some very fortunate University Computing Science or Research labs.... But times have now changed, a standard consumer computer based system can not only compete, but blow away, those big systems of only last year. Complete passive stereo projection based systems are now available for less than £10,000 and new autostereoscopic systems are coming on the market offering many more opportunities to benefit education.

For over ten years Phil Lavery has been pioneering the use of realtime stereoscopic visualisation in education, first at the Glasgow Science Centre and now with the DLF.

 

 

Contact us
If you would like to host an event or more information on stereoscopic visualisation our contact information is here. We will then contact you to discuss your requirements in more detail.

 

JMVP : Joint Medical Visualisation Project

Feet CT Scan Volume Render Visualised with Present3D

There is a common problem facing medical teaching - access to dissection is becoming more and more limited and there is currently a reducing number of anatomists, thus radiological data will, of necessity, become an important teaching tool for anatomy in the near future. The purpose of this project is to develop new tools, resources that make use of 3D stereoscopic visualisation and investigate the new methods of teaching and learning that these tools enable.

 

 

The proposed solution is a combination of elements: low cost stereoscopic visualisation systems, a powerful volume rendering tool (OsgVolume) and an easy to use authoring environment (Present3D) that enables course materials, lectures and individual learning programs to be created.

 

Rather than view MRI/CT scan data as a series of individual slices, a volumetric program processes those slices and combines to create a complete 3 dimensional volume which can then be manipulated interactively. The use of stereoscopic visualisation gives true depth perception essential for understanding complex 3d data and volumetric data benefits greatly from this.

 

To work with the volume data interactively and in realtime a range of tools are required, clipping planes, adjustment of transparency of particular colours or luminance values, selection tools and others, so the area of interest can then be extracted or viewed as a complete entity within the overall volume, dramatically improving understanding of the actual shape, form and interconnectivity of, for instance, a brain tumour. Other more specific tools will be required to meet demands of the wide range of practitioners who will benefit from this project, but the first aim is to concentrate on the requirements for medical teaching and research, with use for patient information systems probably following.

 

The visual quality of MRI/CT scans and Confocal Microscopy data may be variable and this can be dramatically improved by preprocessing techniques. For instance, the attached image (volume.jpg) has had normals calculated as part of the volume creation process, this produces apparent iso-surfaces and enables the light source to be moved interactively over the surface allowing fine detail to be revealed.

Current medical volume rendering programs are usually limited in the size of volume dataset and resolution of images that can be displayed. It is the aim of this project to enable much larger datasets and extremely high resolution images to be used and still be fully interactive on standard computer hardware. The ultimate goal is to be be able to handle the entire Visible Human 2 data where each slice can be 120,000 x 90,000 pixels. Where possible, this will be achieved by using already available and proven techniques, like the paging of high resolution imagery currently used in the OSG for terrain visualisation.

 

A proof of concept has been completed which enables example MRI or CT scan data to be processed to recreate a 3D volume data that can then be loaded in Present3D an easy to use, open source, realtime interactive stereoscopic visualisation authoring tool. The results of this have informed the technical requirements for the OsgVolume project. As the project has developed it has become clear that there are potentially three complementary joint projects:

 

2.1 OsgVolume:

The open source project to develop an advanced medical volume rendering core and specific medical tools that are built on it. By its nature this project will be incremental and modular.

 

2.1.1 Phase One :

An initial enabling project this will include the development of the OsgVolume core volumetric module, OSG loaders to directly handle the Dicom format from the various medical scanners and incorporation of simple (easy to use) volumetric tools. As a minimum this project would aim to provide the basic functionality required to enable OsgVolume to be used for teaching purposes. Implement the required application(s), developing incrementally to provide opportunities to test out work in progress and refine the requirements and deliverables of the application(s) within the time/financial constraints of the project.

 

2.1.2 Phase Two and beyond:

Ongoing development of OsgVolume to increase size of dataset and improve imaging techniques and tools available. It is already obvious that a number of medical research projects will benefit from the availability of OsgVolume and it is anticipated that many custom applications will be built on the foundations of the OsgVolume project. For instance, the Royal College of Surgeons has indicated that it considers a pre-operative planning tool to be highly desirable. At this point it is hoped that the project will start to take a life of its own with a growing community of developers contributing back to the core project to ensure its ongoing development as has happened with the OSG itself.

 

 

2.2 Medical Data Repository:

It is essential to have access to a shared resource of high quality anonomised volumetric, polygonal, point cloud, video and image data that can be used in the creation of teaching materials. Although a major feature of the overall project is the OsgVolume project and the collection of MRI, CT and Confocal Microscopy is key to the success of this, the huge benefits of stereo photography and stereo video should not be overlooked. Laser scans, 3D models, segmented from volume data, built by hand or exported from other medical software should also be included. It is critical that accurate and relevant metadata is associated with each dataset. This project could be undertaken by a single institution but would benefit enormously from becoming a national or international resource. It is anticipated that this would be an internet based project and would be jointly funded by the participants.

 

2.3 Courseware Materials:

The use of Present3D as an authoring environment does mean that lecturers can create their own course materials, however, it would make sense for the schools to collaborate on the development of core materials that set the standards and develop the new techniques that will ensure that maximum benefit is derived from this step change in medical education and that proper assessment and quality control procedures are put in place and feed back into the ongoing development of OsgVolume. A Centre of Excellence is an obvious goal for this project that then brands the courseware materials and distributes for worldwide use on a non-profit basis.

 

Colon CT Scan : Volume Render Visualised with Present3D from Digital Learning Foundation on Vimeo.

 

Additional Images & Movies :

Early movies and downloads

Images of facility & press launch

Youtube 3D Movie

 

Present3D

Information on using Present3D and OsgVolume can be found here :

Using Present3D

 

JMVP : OsgVolume

 

The OsgVolume Project:

 

1.0 The OpenSceneGraph:

The OpenSceneGraph is a cross platform, scalable, real time, open source scene graph that has over 1500 active developers world wide and users such as NASA, European Space Agency, Boeing, Magic Earth, American Army, and many others. Enabling the rapid development of custom visualisation programs, the OSG is also the power behind OsgVolume and Present3D.

 

2.0 OsgVolume:

Currently there is an opportunity to become involved in the new OSGVolume project that will add high resolution volume rendering to the OSG. This project would result in a suite of core volume rendering tools being developed to meet the joint aims of the Scottish Medical Schools and other researchers, additional custom tools can then be created to meet each Schools/researchers/practitioners individual requirements. Present3D, also open source, currently supports the OsgVolumeproject and will continue to be developed to take advantage of new features as they become available.

 

OsgVolume is an open source project, this means that the source code is freely available and shared with developers world wide and has many advantages:

 

2.1 An open source license grants end users rights to use, and distribute the software free of charge - this makes it cost effective and logistically simple to make the software widely available.

 

2.2 An open source license grant developers the right to freely develop applications on top of the open source product - this allows many new products to be developed that leverage the common open source base

.

2.3 An open source license grant developers the right to modify the source code of the product, and to publish these modifications for folding back in to the core open source products.

 

2.4 The rights granted to developers and end users breaks the dependancy on a single provider, reducing risk on the end user from vendor lock in, and the consequences that this has, such as when a vendor stops supporting a particular product.

 

2.5 Open source projects create large communities of like minded developers and users that can help provide support and to contribute to the open source products development. For instance the OSG development community is over 1000 strong, and composed of many industry leading experts in the field of real-time computer graphics.

 

2.6 The result of this project will not just be those directly funded, but many other medical and research projects world wide will benefit from this work and contribute back to the original project ensuring ongoing development and a growing community.

 

 

3.0 Present3D:

Present3D allows anyone to create amazing realtime, fully interactive stereo presentations that include point cloud and polygonal models, images and stereo pairs, movies and stereo movies, audio, text and bulleted text and combine with animation paths, alpha blending and much much more..... there is no other tool that allows all these different data types to be combined into a seamless presentation with such simplicity and of course it all works in stereo as well. Present3D can also be used to create stand alone programs or interactive kiosks. The addition of volume rendering for MRI/CT scans and Confocal Microscopy to Present3D allows this powerful tool to be used in the creation of medical education materials, lectures and courseware. These can then be presented in stereo using projection based displays in lecture theatres and seminar rooms, can be made available in libraries for individual study by use of autostereoscopic monitors, and can also be shared with students for use on their own hardware where it will run in mono if a stereo system is not available. Present3D is open source.

 

 

4.0 OsgVolume Project Outline:

Follows is an outline for a proposed volume rendering NodeKit? from the OpenSceneGraph. The project has partial funding approval. If you'd like to help fund or contribute to this development please contact us.

 

Phase one:

1) Interoperability:

1.a) DICOM reading

1.b) Integration with Present3D and other OpenSceneGraph based viewers.

1.c) ASCII and binary support for reading and writing osgVolume scene graphs.

2) Rendering:

2.a) Multi texture bricks - arranged as a multi-resolution hierarchy

2.b) Transfer functions:

i) pre-computed on CPU,

ii) encoded into 1D textures

iii) computed on GPU as part of a shader

2.c) Handling of mixed data types - polygons, lines, text and volumes in one space

2.d) Support for range of hardware/driver capabilities

i) Standard Texture3D, with a range of max texture sizes

ii) ARB vertex and fragment program

iii) OpenGL 2.0 Shader Language

iv) NVidia's compressed 3D textures

2.e) Clipping planes + boxes

2.f) Polygonal segmentation

2.g) Automatic quality control - render at high speed/lower quality when moving vs

high quality techniques when rendering slowly.

2.h) Dynamic Video Resizing.

3) Data processing:

3.a) Iso-surface generation

3.b) Length, Area and Volume computation

3.c) Image Processing:

i) Biasing / Transfer functions

ii) Flood fill segmentation

iii) Manifold segmentation

4) User interface:

4.a) Support for mouse, keyboard and gamepad in an interchangeable way

4.b) Control of eye point

4.c) Control of clipping planes/boxes

4.d) Control of transfer function curves and colours

4.e) Annotation

4.f) Flood fill segmentation control

4.g) Isosurface generation/segmentation control

4.h) Measurement of lengths, areas and volumes

4.i) File selection, quality specification

 

Second phase :

1) Interoperability

1.d) DICOM writing

1.e) Full DICOM system integration

1.f) 3rd Party tool integration i.e. browsers, other medical tools

2) Rendering

2.i) Volume Paging

2.j) Multiple GPU rendering + compositing

2.k) Cluster rendering

2.l) 3D video texturing via either of:

i) custom stream 3D texture format

ii) 2D video stream built to stream one or more slices at one time to build up animated 3D texture.

3) Data processing

3.d) Image processing cont.

i) Sharpening

ii) Edge detection

iii) Smoothing

iv) Correlations

4) User Interface

j) Control of the above phase two items

 

 

Support OsgVolume

You can support the development of OsgVolume by making a donation or, if you are a developer, by getting your hands dirty and becoming directly involved..

 

You will find information on making a donation here:

 

http://dlfresources.pbwiki.com/donations%20Open%20Source

 

To register an interest in becoming involved please contact us:

 

osgvolume "at" digitallearningfoundation.org

 

replacing the "at" with @ as usual :-)

 

JMVP : Images & Stereo Movies

 

Volume Stereo Movies :  

Below is short clip (realtime screen capture) of a volume created from a CT scan (DICOM) with Present3D. A full length, full screen, stereo version of the movie can be downloaded here: he001.mov

You can change the viewing options by mousing over the video and then selecting 3D and change as required either for stereo or mono viewing.

 

Some still images from the stereo movie:

 

 


Torso Stereo Movie

Another short clip (realtime screen capture) from a stereo movie created with Present3D from a dicom series of CT slices.

A full length, full screen, stereo version of the movie can be downloaded here:  jmvp3h.mov

 

 


Other Volume Stereo Movies :

cenovix.zip

manix.zip

  


 

Laser Scan Cormorant  Skull Stereo Movie :

cormorant.zip

 

3D Model Protein Stereo Movie :

protein1b.mov