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EMBL BioImage Data Analysis



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EMBL Heidelberg
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Miyo Terao Morita showing analysis of gravitropism using centrifuge microscope they newly developed. I only know…
About 25 mins, 34 secs ago by: Kota Miura (@cmci_)

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@KeikoUTorii ... which then became the cover page of Development cell. convincing.
About 1 hour, 22 mins ago by: Kota Miura (@cmci_)

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@KeikoUTorii model-based hypothesis lead to experiment results with single guard cell development or multiple >2 gu…
About 1 hour, 30 mins ago by: Kota Miura (@cmci_)

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now, @KeikoUTorii on stomata development - how very specific cell fate decisions are made, with proper spacing bet…
About 1 hour, 47 mins ago by: Kota Miura (@cmci_)

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@YvonJaillais talk on nanoclustering of ROP6, great analyses using various approaches to assess protein mobility…
About 2 hours, 3 mins ago by: Kota Miura (@cmci_)

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RT @haesleinhuepf: I need to add this one, because I believe in the power of beautiful data. Same optics, just earlier stage in development…
About 13 hours, 35 mins ago by: Kota Miura (@cmci_)
Measure Movement directly from kymograph


Quantitative analysis of ambiguous patterns in kymograph


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


  • 10-03-03 ? first version released


Released under the GNU General Public License.


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


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


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.

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