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--- documents:101021cbbpractical [2010/10/21 14:20] – created kota
+++ documents:101021cbbpractical [2025/05/16 13:58] (current) – kota
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 ===== Practical =====
-**Theme title: Optimization of Analysis Strategy for Studying Microtubule Plolarity in Drosophila embryo**
+**Theme title: Optimization of Analysis Strategy for Studying Microtubule Polarity in Drosophila embryo**
-Regulation of cytoskeletal orientation is a basic mechanism for controlling cell polarity, and hence the dynamics of coordinated cell movment. We try to establish analysis protocol for studying microtubule orientation within Drosophila embryo as a first step to examine the role of MT orientation in tissue dynamics. For this, we use Microtubule binding protein EB1. This protein moves towards the plus end of microtubule, so we could know MT polarity by tracking EB1 movement.
+Regulation of cytoskeletal orientation is a basic mechanism for controlling cell polarity, and hence the dynamics of coordinated cell movement. We try to establish an analysis protocol for studying microtubule orientation within the Drosophila embryo as a first step to examine the role of MT orientation in tissue dynamics. For this, we use Microtubule microtubule-binding protein EB1. This protein moves towards the plus end of the microtubule, so we could know MT polarity by tracking EB1 movement.
-Using sevral available tools for Quantification, find a best strategy for quantifying the microtubule polarity from EB1 labeled cells.
+Using several available tools for Quantification, find the 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)
-    * KBI olugins (http://hasezawa.ib.k.u-tokyo.ac.jp/zp/Kbi/kbi_ij_plugins_882b-101003.jar)
+    * KBI plugins (http://hasezawa.ib.k.u-tokyo.ac.jp/zp/Kbi/kbi_ij_plugins_882b-101003.jar)
     * a bit more in http://hasezawa.ib.k.u-tokyo.ac.jp/zp/Kbi/ImageJKbiPlugins
 ==== 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 the movement of EB1 signal using three strategies with the following steps:
   * Track them either manually or automatically.
-  * Using coordinates, calculate the directon of EB1 movement (hence MT orientaiton)
+  * Using coordinates, calculate the direction of EB1 movement (hence MT orientation)
-  * Plot the results in histogram. Do some statistics.
+  * Plot the results in the histogram. Do some statistics.
+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 the 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
-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.