blind source-separation for heart wall and erythrocyte motion estimation in the beating embryonic...
TRANSCRIPT
Blind Source-Separation for Heart Wall and Erythrocyte Motion Estimation in the Beating Embryonic Heart
Sandeep BhatSystems Bioimaging Lab, UCSBPresentation for ENGR 103, Nov 20, 2008
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Agenda
• Motivation• Problem Setup• Algorithm stages• Results• Conclusion
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Motivation
• Study of model organisms
– Embryonic development, toxicology, specific gene function.
– Zebrafish embryo is transparent
• Live imaging of embryos.
– Fluorescence microscopy (FM)
– Bright field microscopy (BFM)
• The algorithm aids BFM imaging of developing zebrafish heart.
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Problem Setup
• Input: BFM image sequence
– Spanning several cardiac cycles.
• Desired output: Two image sequences
– Spanning one period (cardiac cycle)
– One showing only the heart morphology
– The other with only the transient structures (Red Blood Cells)
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Algorithm Stages
• Three stages:
– Pre-processing
– Separation algorithm
– Post-processing
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Separation Algorithm
• Temporal alignment
• Heart-wall:
– “Periodic”
– Mean/Median filtering
• Red Blood Cells:
– Not periodic
– Subtraction/Variance
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• Flow analysis using FlowJ
Post-processing
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Results• frequency components. • Testing with synthetically generated data.• Testing with synthetically generated data.
• (a) Mean+Subtraction (b) Mean+Variance
• (c) Median+Subtraction (d) Median+Variance
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Results (contd.)• BFM images of zebrafish heart
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Conclusion