User Tools

Site Tools


Sidebar

Top
Profile
Freelancing
Seminar
Courses -2016
Courses 2018-
Textbooks
Documents
Downloads (-2016)
Downloads (2016-)
Weblog
RSS aggregates
Discussions
Archives
日本語


EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

—- Contact
CMCI Alumni
ALMF
EMBL Heidelberg
EMBL Intranet


Popularity Ranking


Timeline of @cmci_

cmci_ avatar

The field for bioimage analyst expanding. British museum! https://t.co/KClNvxP948
About 2 days, 7 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @dgaboriau: Panel session: should I aim to become a bioimage analyst? With Robert Hasse @haesleinhuepf , Kota Miura @cmci_ and Arianne B…
About 3 days, 21 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @martinjones78: Shoutout by @cmci_ for @clathrin's book https://t.co/x6d2OmfdxR as a great resource, here at #CBIAS2022 in the panel ses…
About 3 days, 21 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @alex_paynedwyer: The one and only Kota Miura @cmci_ calling out all those dodgy contrast-mismatched figures #ethics in classic humorou…
About 4 days, 5 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @RekadZeinab: Kicking the last session of #CBIAS2022 with the great master @cmci_ on the challenges of doing image analysis at the inter…
About 4 days, 5 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @MaKaefer: Fear not: there is something that can be done! Abide by the guidelines or report everything that has been done - whether it i…
About 4 days, 5 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 12:46 (external edit)