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EMBL BioImage Data Analysis

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RT @empleo_mid: Puesto: 1 PhD student position available for "Image analysis of cardiac development in the mouse" - CNIC https://t.co/0AfJ8
About 14 hours, 19 mins ago by: Kota Miura (@cmci_)

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RT @CanonMedicalEDI: Five #vacancies currently open: Image Analysis Scientist, Software Engineer (various) & IT Administrator. Rewarding #H…
About 1 day, 15 hours ago by: Kota Miura (@cmci_)

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@haesleinhuepf @ReynaudEmmanuel @BioImagingUK @BBSRC @NEUBIAS_COST ... and fun!
About 1 day, 15 hours ago by: Kota Miura (@cmci_)

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RT @thewtex: @cmci_ @ProjectJupyter @UCBIDS @stefanvdwalt @cziscience @thefreemanlab @ctrueden @FijiSc @cmci_ sorry about the quality. Here…
About 1 day, 16 hours ago by: Kota Miura (@cmci_)

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@thewtex @ProjectJupyter @UCBIDS @stefanvdwalt @cziscience @thefreemanlab @ctrueden @FijiSc thanks!
About 1 day, 16 hours ago by: Kota Miura (@cmci_)

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@thewtex @ProjectJupyter @UCBIDS @stefanvdwalt @cziscience @thefreemanlab @ctrueden @FijiSc great! do you have an y… https://t.co/Xnyd9VhAip
About 1 day, 16 hours ago by: Kota Miura (@cmci_)
downloads:kymoquant
Measure Movement directly from kymograph

Kymoquant

Quantitative analysis of ambiguous patterns in kymograph

Author

Kota Miura
Centre for Molecular and Cellular Imaging (CMCI)
EMBL Heidelberg
miura at embl dot de
Tel: +49 6221 387 404

History

  • 10-03-03 ? first version released

Source

Released under the GNU General Public License.

Requires

ImageJ ver 1.43o or higher (ImageJ, upgrade page).

Installation

Download K_kymoquant.ijm to a place where you can access easily. Install the macro by [Plugins→Macros→Install…].

Description

Measures orientation of kymograph by estimating the direction of image texture. Outputs movement velocity in pixels / frame.

(more explanation on measurement principle is planned here)

Tip: When kymograph traces are steep, analysis results become unstable since calculation of direction involves tanθ. Be sure to capture original sequence with high time resolution if possible.

Work Flow

Kymograph should be prepared by your self either by manually using stack reslicing function in ImageJ, or ImageJ Kymograph plugin.

If you want to measure full frame of the kymograph, simply apply [Plugins → Macros → Measure Velocity from Kymograph: Full Frame].

If you want to measure only part of the kymograph, then select a area by rectangular ROI tool and then [Plugins → Macros → Measure Velocity from Kymograph: ROI].

[Plugins → Macros → Scan Kymograph and Measure - Automatic Multiple Measurements] will automatically divide the kymograph into segments and sequentially measure the kymograph along the time line.

overview_kymoquant.jpg
downloads/kymoquant.txt · Last modified: 2016/05/24 05:46 (external edit)