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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
@@ Line 21: / Line 21: @@
 Using sevral available tools for Quantification, find a best strategy for quantifying the microtubule polarity from EB1 labeled cells.
 ==== Tools: ====
-ImageJ/Fiji Plugins
+ImageJ/Fiji Plugins (http://pacific.mpi-cbg.de/wiki/index.php/Fiji)
   - Manual Tracking (Manual_Tracking.class)
+    * bundled in Fiji
     * http://rsbweb.nih.gov/ij/plugins/track/track.html
   - Particle Tracking (ParticleTracker.jar)
     * https://weeman.inf.ethz.ch/ParticleTracker/
-  - Optical Flow Analysis (KBI_flow.jar)
+  - Flow Analysis (kbi_ij_plugins_882b-101003.jar)
     * http://hasezawa.ib.k.u-tokyo.ac.jp/zp/Kbi/KbiFlow
     * SCALA runtime library (http://www.scala-lang.org/downloads/index.html)
@@ 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