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--- documents:101021cbbpractical [2010/10/25 13:51] – kota
+++ documents:101021cbbpractical [2016/05/24 12:46] (current) – external edit 127.0.0.1
@@ Line 38: / Line 38: @@
 ==== 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
+pixel = 0.266 micrometrer
+Time/Frame
+We analyze movement of EB1 signal using three strategies with following steps:
   * Track them either manually or automatically.
@@ Line 45: / Line 52: @@
 Our aim is to plot a histogram of movement orientation, and test whether there is bias in the movement. Compare three tools, and find the best way to analyze the microtubule orientation.
+=== Circular Statistics ===
+Conversion of Cartesian Coordinates to Polar Coordinates
+  * R Package: fisheyeR
+  * http://finzi.psych.upenn.edu/R/library/fisheyeR/html/toCartesian.html
+  * function toPolar(x, y)
+  * see maybe also
+    * http://en.wikipedia.org/wiki/Polar_coordinate_system
+von Mises likelihood estimates
+  * see http://en.wikipedia.org/wiki/Von_Mises_distribution
+  * R Package: CircStats
+  * http://finzi.psych.upenn.edu/R/library/CircStats/html/vm.ml.html
+  * vm.ml(...)
+  * mu (mean), kappa (concentration parameter) is returned.
+  * R Package: circular (more parameters)
+  * http://finzi.psych.upenn.edu/R/library/circular/html/mle.vonmises.html
+  * function mle.vonmises(...)
+  * Maximum likelihood estimate of concentration parameter (kappa) is a good indicator of bias in directionality.
+Data Plotting
+  * R Package: CircStats
+  * http://finzi.psych.upenn.edu/R/library/CircStats/html/00Index.html