documents:101021cbbpractical
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documents:101021cbbpractical [2010/10/21 14:20] – created kota | documents:101021cbbpractical [2016/05/24 12:46] (current) – external edit 127.0.0.1 | ||
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Using sevral available tools for Quantification, | Using sevral available tools for Quantification, | ||
- | |||
==== Tools: ==== | ==== Tools: ==== | ||
- | ImageJ/Fiji Plugins | + | ImageJ/Fiji Plugins |
- Manual Tracking (Manual_Tracking.class) | - Manual Tracking (Manual_Tracking.class) | ||
+ | * bundled in Fiji | ||
* http:// | * http:// | ||
- Particle Tracking (ParticleTracker.jar) | - Particle Tracking (ParticleTracker.jar) | ||
* https:// | * https:// | ||
- | - Optical | + | - Flow Analysis (kbi_ij_plugins_882b-101003.jar) |
* http:// | * http:// | ||
* SCALA runtime library (http:// | * SCALA runtime library (http:// | ||
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==== Methods: ==== | ==== Methods: ==== | ||
- | Drosophila EMbryo sequence was provided by Sasha Necakov @ Stefano De Renzis lab. We analyze movement of EB1 signal using three strategies with following steps: | + | Drosophila EMbryo sequence was provided by Sasha Necakov @ Stefano De Renzis lab. |
+ | |||
+ | XY scale | ||
+ | 1 pixel = 0.266 micrometrer | ||
+ | |||
+ | Time/ | ||
+ | |||
+ | We analyze movement of EB1 signal using three strategies with following steps: | ||
* Track them either manually or automatically. | * Track them either manually or automatically. | ||
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Our aim is to plot a histogram of movement orientation, | Our aim is to plot a histogram of movement orientation, | ||
+ | |||
+ | === Circular Statistics === | ||
+ | |||
+ | Conversion of Cartesian Coordinates to Polar Coordinates | ||
+ | * R Package: fisheyeR | ||
+ | * http:// | ||
+ | * function toPolar(x, y) | ||
+ | * see maybe also | ||
+ | * http:// | ||
+ | |||
+ | von Mises likelihood estimates | ||
+ | * see http:// | ||
+ | * R Package: CircStats | ||
+ | * http:// | ||
+ | * vm.ml(...) | ||
+ | * mu (mean), kappa (concentration parameter) is returned. | ||
+ | | ||
+ | * R Package: circular (more parameters) | ||
+ | * http:// | ||
+ | * function mle.vonmises(...) | ||
+ | * Maximum likelihood estimate of concentration parameter (kappa) is a good indicator of bias in directionality. | ||
+ | |||
+ | Data Plotting | ||
+ | * R Package: CircStats | ||
+ | * http:// | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ |
documents/101021cbbpractical.1287670852.txt.gz · Last modified: 2016/05/24 12:46 (external edit)