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EMBL BioImage Data Analysis

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RT @xuepan3: @palankarr @manorlaboratory Hi Raghva, We compared the results generated by IMARIS and Trackmate in ImageJ. There are some min…
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @albertcardona: Plotting from your @FijiSc #python scripts, using ImageJ's internal plotting library, and with @jfreechart for prettier…
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @CefapConfocal: If you struggle with image analysis, check our webpage with few ImageJ and Zen tutorials: https://t.co/9ExHi8MkL1 ps .:…
About 3 days, 11 hours ago by: Kota Miura (@cmci_)

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RT @iefforts: The cells were visualized on a Nikon AR1 or Leica SP8 confocal microscope. At least 30 cells were analysed for each condition…
About 3 days, 11 hours ago by: Kota Miura (@cmci_)

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RT @MarJungle: BigStitcher on ImageJ for 3D model reconstructions. A beta-version is available via the Fiji Updater. I am going to try this…
About 3 days, 11 hours ago by: Kota Miura (@cmci_)

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RT @ARVOtvst: New in the August issue: 25-MHz ultrasound biomicroscopy combined with #ImageJ software can be used to evaluate the opacity d…
About 3 days, 11 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)