analysis of bone structure in brittle bone disease john jameson als user meeting – tomography...
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Analysis of bone structure in brittle
bone disease
John JamesonALS User Meeting – Tomography Workshop
10/09/2012
Osteogenesis imperfecta (OI)
• Genetic fragility disordero 25-50,000 in US
• Mutations cause impaired collagen synthesis and assemblyo Limb deformity, reduced stature, respiratory problems,
connective tissue laxity…
• 8 known types*o Mild, Type I: 50% of all caseso Moderate-Severe, Types II-VIIIo High degree of variability
Byers 1994, Chiasson 2004
Bone hierarchical structure
CollagenMineralized triple helices
(<1 µm)
FibrilsStaggered bundles
of molecules(~1 µm)
Fiber arrays“Plies” at different
orientations(~5-20 µm)
OsteonsLamellae + vasculature
(100-300 µm)
Solid materialCortical bone(>3000 µm)
Trabeculae“Plates and rods”
(100-200 µm)
Solid materialTrabecular bone
(>3000 µm)
Whole boneFemur
BONE FRAGILITY -How does bone structure affect mechanical
performance?-How do changes to OI bone cause fragility?
Micro
Nano
MOUSE HUMAN200 µm
50 µm
25 µm
5 µm
<1 µm
10 µm
Trabecular (spongy): -decreased quantity -more isotropic-poor organization
Cortical (compact): -higher porosity-thinner canals
Cortical (compact): -higher porosity-larger pores w/higher
connectivity
Additional considerations
• Tomographyo Preventing tissue damage
• SAXS/WAXDo Collagen spacing, mineral thickness
• In situ mechanical testing?o Similar to hot cell, but much simpler experimento Notch and apply different loads
• Can do this in ESEM now, but only get 2D info => 3D with tomo after
Data collection pipeline• Preparing for beamtime• Beamtime
o Average and peak data rates• 10-15 scans/beamtime => 11 GB/scan => 100-200 GB/session• Only person doing data collection, analysis
o Real-time feedback would be helpful in assuring quality of images• Working on noise study to provide feedback to users on proper settings to use
• After beamtimeo Reconstruction (1 hr/dataset)o Filtering and segmentation (1-2 hrs first dataset)
• Bilateral filtering => Usually have to downsample images, convert to 8-bit so it doesn’t take forever
• Binary morphological operations: Opening/closingo Data processing (0.5 day/dataset)
• Sphere-fitting algorithms, skeletonization, surface meshingo Visualizations
• Fiji and/or Avizo => Requires downsampling so it doesn’t crash all the time
Quantifying “resolution”• Resolution is difficult to measure
o Noiseo Instrument alignmento Imaging parameters/setup:
• Lens, #angles, counts (exp. time/scintillator), dithering…
• Fourier ring correlation (FRC)o Cardone et al (2005), J Struct Biol 151:p.117-129o Shows contribution of a single image
• Can give you an idea about the quality of your data sets and how they change over time
• Example: #Angles513 => 6.7 µm1025 => 3.5 µm2049 => 2.1 µm
Tradeoff b/w resolution and data set size
The RERC Grant Objective0-2 years: -µCT -Mechanical testing-Gait analysis
2-5 years: -SIMM-FE mesh refinement
5+ years: -Patient-specific fracture risk-Guided surgery-Assessment of existing/new
therapies
Mechanical & Imaging Data: Closing the Gap
Total crack length
(c)
Residual indent
α tip geometric factorE modulusH hardnessP applied tip loadc total crack length
Koester et al 2008
Crack
Haversion
Canals
Notched mechanical testingMicrohardness indentation
Tomography-3D crack visualization
-Crack volume
NERSC areas of interest
• Reconstruction:o Feedback on image quality/FRC
• Filtering:o Reduce amount of downsampling
• Software:o Fiji –macro capabilityo Avizo – advanced visualization of
crack propagationo Matlab – FRC for noise/resolution
calculationso Igor Pro – SAXS/WAXD