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RT @jytinevez: LimeSeg on bioRXiv: LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation https://t.co/jECl7deOVG
About 9 hours, 22 mins ago by: Kota Miura (@cmci_)

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Impressive and swift moderation @helenajambor !
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @LuisDVerde: Now available as a #ggplot2 geom thanks to @naupakaz https://t.co/zOaMWvzd8k https://t.co/AXYBCeGyw6
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @helenajambor: awesome, within 2 days .@naupakaz made a code publicly available for anyone wanting to make the half-and-half-plot FYI @…
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @dgaboriau: Thread on data visualisation: ggplots, boxplots and violin plots https://t.co/QZE7xQtaa3
About 2 days, 20 hours ago by: Kota Miura (@cmci_)

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RT @christlet: SUSHI from Valentin Nāgerl lab allows super-resolution microscopy of neuronal morphology by STED imaging of extracellular sp…
About 2 days, 23 hours ago by: Kota Miura (@cmci_)
documents:101021cbbpractical

CBB Predoc course, October 2010

Kota Miura, Centre for Molecular and Cellular Imaging, EMBL

Journal Club

… Maybe also

Practical

Theme title: Optimization of Analysis Strategy for Studying Microtubule Plolarity 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.

Using sevral available tools for Quantification, find a best strategy for quantifying the microtubule polarity from EB1 labeled cells.

Tools:

Methods:

Drosophila EMbryo sequence was provided by Sasha Necakov @ Stefano De Renzis lab.

XY scale 1 pixel = 0.266 micrometrer

Time/Frame

We analyze movement of EB1 signal using three strategies with following steps:

  • Track them either manually or automatically.
  • Using coordinates, calculate the directon of EB1 movement (hence MT orientaiton)
  • Plot the results in 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

von Mises likelihood estimates

Data Plotting

documents/101021cbbpractical.txt · Last modified: 2016/05/24 05:46 (external edit)