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EMBL BioImage Data Analysis



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RT @napari_imaging: Thanks to all our contributors! If you're interested in learning more about how to use napari then join our upcoming w…
About 3 days, 17 hours ago by: Kota Miura (@cmci_)

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RT @oozguc: Due to the circumstances, we are postponing the meeting to June 12; hopefully, a time we can all go back to scientific and inte…
About 4 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @jytinevez: We finished listing and formatting the Q&A we had during the #TrackMate session of the @NEUBIAS_COST #NEUBIAS_Academy even…
About 4 days, 21 hours ago by: Kota Miura (@cmci_)

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RT @EntraCod: @olivier_debora @jytinevez @NEUBIAS_COST Or in other words, we are doing this for a very specific case rather than generic on…
About 4 days, 21 hours ago by: Kota Miura (@cmci_)

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RT @BoSoxBioBeth: Available now on Youtube at the link below. Thanks @NEUBIAS_COST for having me, it was a ton of fun to talk about @CellP
About 4 days, 21 hours ago by: Kota Miura (@cmci_)

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RT @cytomine_uliege: @HenriquesLab @BioTurboNick @AndrewGYork @coppola_s_PhD Also what we thought years ago. The results is
About 4 days, 21 hours 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)