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EMBL BioImage Data Analysis

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RT @BoSoxBioBeth: 2 days left to submit an abstract proposal! We want all your best ideas on image analysis!
About 8 hours, 16 mins ago by: Kota Miura (@cmci_)

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RT @ManuelTHERY: Here we are. The combination of biochemically controled differentiation of iPS cells with microprinting to direct cell sel…
About 8 hours, 17 mins ago by: Kota Miura (@cmci_)

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RT @haesleinhuepf: "Do you also spend a substantial amount of your time waiting for automated image analysis to finish? [...] And, then, th…
About 19 hours, 43 mins ago by: Kota Miura (@cmci_)

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RT @ALM_i3S: Do you want to extract quantitative data from images and automate this process by learning ImageJ Macro Language? Apply to t…
About 1 day, 14 hours ago by: Kota Miura (@cmci_)

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RT @martinjones78: Very interesting #BioImageAnalysis PhD position! https://t.co/85QLBKiANx
About 1 day, 14 hours ago by: Kota Miura (@cmci_)

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RT @jobRxiv: #ScienceJobs: Image Analyst / Python programmer Francis Crick Institute (@TheCrick), London, UK https://t.co/T7cDhv9PX0 #P…
About 1 day, 14 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)