Presentation on theme: "What do Oxford want? Visualising rabbit hearts. Integrative Biology e-Science project investigating the causes of heart attacks how cancers develop Together."— Presentation transcript:
What do Oxford want? Visualising rabbit hearts
Integrative Biology e-Science project investigating the causes of heart attacks how cancers develop Together these account for 60% of all UK deaths The IB project brings together numerical modellers, experimentalists, computer scientists, and even mathematicians
The Oxford Conference Everybody meets up each September In 2005 Ken and James (Handley) presented the multivariate visualisation work In 2006 the other half of the computer scientists contingent (Lakshmi Sastry from CCLRC) presented the Grid computing environment theyve built (using gViz amongst others) At the questions stage Peter Kohl from Oxford asked Arent you supposed to be providing cool visualisations for us?
Who is Peter Kohl? Marital status: Married, three children Nationality: German, resident in UK since August 1992 Languages: Fluent in German, English and Russian Hobbies: Preparing (and having!) a good dinner and landscape photography
Who is Peter Kohl? Reader in Cardiac Physiology, Department of Physiology, Anatomy and Genetics, Oxford University Head of the Mechano-Electric Feedback lab The purpose of our group is to incorporate kinetic properties of molecular and cellular mechanism of cardiac activity into cellular and multicellular mathematical models of the heart.
What data does he have? Five valiant bunnies put their hearts into this research They were scanned using an 11.7Tesla magnet to give about 1500 slides, each 25 m with resolution 1024x1024 points. The hearts were then sliced to a thickness of 10 m, stained, and photographed using a scanning microscope (1800 slices, resolution of up to about 6000x4000)
What weve done already 1. MRI data VTK Loads and isosurfaces Save pre-computed isosurfaces for later rendering Powerwall vjVTK Performance not good enough – especially on the headnode Homegrown OpenGL version in VRJuggler Smoothing and decimation of the original VTK surfaces
What weve done already 2. Histology data Slide viewer Desktop OpenGL and VRJuggler versions Slides much smaller than the pathology ones so not using the multi-tiled textures Multiple slices viewing Individual slides need much preprocessing Adding transprency Removing reference marker Still need to clean up the background Can manipulate between 16 and 32 slices in 3-d Memory is the killer
What Im working on a the minute Automatic Level of Detail operations Using GLOD library Precomputing hierarchy of levels Very computationally expensive on large datasets 6Mb = 1 min 24Mb = 30 mins 40Mb = 3hrs …hence need to break the geometries down into smaller sections This will also help at display time
What do Oxford want? To combine the histology with the MRI Complete data registration between slices To the MRI set Need to decide on what viz Adding one slice every ? Colour isosurface by histology value? Showing histology in a separate window matching cut plane
Cool things that are probably too hard Volume rendering Memory requirements are too large May work for one off pictures to be preprocessed Knowledge of suitable transfer functions needed 3-d texture environments Again, enormous memory requirements No segmentation done (that we know of)
Cool things that should be do-able Heart Atlas Multiple hearts loaded across the display Comparisons between structure recognisable More ideas needed… We want these techniques to scale to hearts that are up to 20 times larger!