Optimization of Curve Tracing for Automated Analysis of Cargo Transport …tv061gc5273/Xie... ·...
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Optimization of Curve Tracing for Automated Analysis of Cargo Transport in Axons Wenjun Xie, Sai Sravan Bharadawaj Karri, Daphne Che, and Bianxiao Cui Stanford University Motivation Improved Algorithm Previous Algorithm Analysis Results •Convolve image – 1D Gaussian filter – Mean filter •Detect seeds – global threshold, local supermum (dilation) Seed points detected: 300 •Tracing – angle response, edge response (3) •Connecting – connect short segments (orientation, intensity) Trace detected: 28 • Process image with bilateral filter (a line filter) (4) • Detect and mask out straight lines (Hough transform) •Detect seeds – local Ostu’s method Seed points detected: 408 •Tracing and connecting – as previous Traces detected: 21 •Make training sets (manual trace-selecting) to optimize parameters Position correlation = sum (closest point in tracing result, each point in reference traces)/num points in reference False positive = num of points in tracing result but not in reference/num points in reference Improved tracing result: Position correlation = 1.4682 False positive = 1.3004 Original tracing result: Position correlation = 1.7046 False positive = 1.7577 Manually selected traces (1) Racine, V., M. Sachse, et al. (2007). "Visualization and quantification of vesicle trafficking on a three‐dimensional cytoskeleton network in living cells." J Microsc 225(Pt 3): 214‐28. (2)Zhang, K., Y. Osakada, et al. "Automated image analysis for tracking cargo transport in axons." Microsc Res Tech. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2 0945466 (3)Zhang, Y., X. Zhou, et al. (2007). "A novel tracing algorithm for high throughput imaging Screening of neuronbased assays." J Neurosci Methods 160(1): 149‐62. (4)C. Tomasi R. Manduchi. et al.(1998). ”Bilateral Filtering for Gray and Color Images.” Proceedings of the 1998 IEEE International Conference on Computer Vision, Bombay, India References Axonal transport is related to neuron function and neuro-degradation; usually a large number of transport data need to be analyzed to get statistically significant result. Automation? Convert to kymograph: 3D – particle tracking →2D curve tracing (1, 2) *Optimizing parameters using these results is in process.
Transcript of Optimization of Curve Tracing for Automated Analysis of Cargo Transport …tv061gc5273/Xie... ·...
Optimization of Curve Tracing for Automated Analysis of Cargo Transport in AxonsWenjun Xie, Sai Sravan Bharadawaj Karri, Daphne Che, and Bianxiao Cui
Stanford University
Motivation Improved Algorithm
Previous Algorithm
Analysis Results•Convolve image – 1D Gaussian filter – Mean filter
•Detect seeds – global threshold, local supermum (dilation)Seed points detected: 300
•Tracing – angle response, edge response (3)
•Connecting – connect short segments (orientation, intensity)Trace detected: 28
• Process image with bilateral filter (a line filter) (4)
• Detect and mask out straight lines(Hough transform)
•Detect seeds – local Ostu’s methodSeed points detected: 408
•Tracing and connecting – as previousTraces detected: 21
•Make training sets (manual trace-selecting) to optimize parametersPosition correlation = sum (closest point in tracing result, each point in
reference traces)/num points in referenceFalse positive = num of points in tracing result but not in reference/num
points in reference
Improved tracing result:Position correlation = 1.4682False positive = 1.3004
Original tracing result:Position correlation = 1.7046False positive = 1.7577
Manually selected traces
(1) Racine, V., M. Sachse, et al. (2007). "Visualization and quantification of vesicle trafficking on a three‐dimensional cytoskeleton network in living cells." J Microsc 225(Pt 3): 214‐28.(2)Zhang, K., Y. Osakada, et al. "Automated image analysis for tracking cargo transport in axons." Microsc Res Tech. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2 0945466(3)Zhang, Y., X. Zhou, et al. (2007). "A novel tracing algorithm for high throughput imaging Screening of neuronbased assays." J Neurosci Methods 160(1): 149‐62.(4)C. Tomasi R. Manduchi. et al.(1998). ”Bilateral Filtering for Gray and Color Images.” Proceedings of the 1998 IEEE International Conference on Computer Vision, Bombay, India
References
Axonal transport is related to neuron function and neuro-degradation; usually a large number of transport data need to be analyzed to get statistically significant result.
Automation? Convert to kymograph:3D – particle tracking →2D curve tracing (1, 2)
*Optimizing parameters using these results is in process.
