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downloads:kymoquant [2012/07/11 08:10]
127.0.0.1 external edit
downloads:kymoquant [2016/05/24 05:46] (current)
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 +~~NOTOC~~
 +[{{ http://​cmci.embl.de/​dls/​Kymoquant/​overview_kymoquant.jpg?​200|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 ([[http://​rsb.info.nih.gov/​ij/​upgrade/​|ImageJ,​ upgrade page]]). ​
 +===== Installation =====
 +
 +Download [[https://​raw.github.com/​cmci/​ijmacros/​master/​K_kymoquant.ijm|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.
 +
 +[{{ http://​cmci.embl.de/​dls/​Kymoquant/​overview_kymoquant.jpg }}]     
downloads/kymoquant.txt · Last modified: 2016/05/24 05:46 (external edit)