Difference between revisions of "Dynamic Kymograph"

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| name = Dynamic_Kymograph
 
| name = Dynamic_Kymograph
 
| software = Fiji
 
| software = Fiji
| author = rudyzhou
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| author = {{Person|Rudy Zhou}}
| maintainer = rudyzhou
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| maintainer = {{Person|Rudy Zhou}}
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| released = 26 July 2018
 
| source = {{GitHub|org=rudyzhou|repo=Dynamic_Kymograph}}
 
| source = {{GitHub|org=rudyzhou|repo=Dynamic_Kymograph}}
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| category = [[:Category:Plugins|Plugins]]
 
}}
 
}}
 
== Basics ==
 
  
 
Dynamic_Kymograph is a plugin for ImageJ that generates kymographs from stack videos using key-framing and linear interpolation.
 
Dynamic_Kymograph is a plugin for ImageJ that generates kymographs from stack videos using key-framing and linear interpolation.
  
== Usage ==
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== Features ==
  
* In fiji, open the image stack that you would like to analyze
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The main features are:
 +
* Allows user to specify polyline ROIs on multiple frames of a stack video
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* Automatically interpolates between ROIs drawn on different frames
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* Generates a kymograph using the interpolated ROI throughout the stack video
  
* Run the dynamic kymograph plugin (in “Process” -> “Dynamic Kymograph”).
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== Download and Usage ==
  
* The UI has the following features:
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See [https://github.com/rudyzhou/Dynamic_Kymograph https://github.com/rudyzhou/Dynamic_Kymograph] for download and detailed usage instructions.
* Select anchor point – Prompts the user to click on a vertex to set it as the anchor point (the anchor point status is reflected in the status message below the buttons)
 
* Make kymograph – Prompts the user for line width and then generates a kymograph using all interpolated key frames and the selected anchor point
 
* Save Current ROI -  Records and numbers the current ROI on the “Saved ROIs” window. Draws the ROI using a random color
 
* Reset key frames – Clears all key frames and anchor point
 
* Log window – Records events such as when a keyframe is generated, when an anchor point is set, when the plugin is closed, etc. Mainly used for debugging
 
* Saved ROIs window – Displays the first frame of the stack. Any ROIs saved using the “Save Current ROI” button will appear here
 
  
* Once you have surveyed the stack and found a microtubule to analyze, use the polyline tool to trace the microtubule
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== Authors ==
  
* Make sure that one of the points you drew is located on the seed of the microtubule (the bright spot that remains static throughout the stack.) You may want to scroll through the video to confirm that you have found such a point. Then you can either use the “Select anchor point” button or simply press “ctrl” while your mouse is hovering over the vertex to set this vertex as the anchor point. (You should see a message in the “Log” confirming this)
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* Rudy Zhou - [rudyzhou](https://github.com/rudyzhou)
 
 
* Once you have your initial polyline and anchor point, you can simply scroll through the video and modify your polyline on any frame to best capture the dynamics of the microtubule (by dragging the polyline vertices or translating the whole polyline using the arrow keys.)
 
 
 
* Once you watch the video and are happy with your polyline, you can press the “Make kymograph” button to generate your kymograph.
 
 
 
* If you are not satisfied with your kymograph, you can simply continue editing the polyline as in step 4 and generate a new kymograph.
 
  
* If you want to analyze a new microtubule on the same stack, press “Save current ROI” to keep track of your analyzed microtubule, and then press “Reset key frames” to begin working on the next microtubule.
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== License ==
  
* If you want to close the plugin, press the “x” button on the “Dynamic Kymograph” window
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This project is licensed under the [https://imagej.net/GPL GNU General Public License].
  
== Authors ==
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== Acknowledgements ==
  
* Rudy Zhou - [rudyzhou](https://github.com/rudyzhou)
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Some code used from [https://imagej.net/Multi_Kymograph Multiple Kymograph Plugin] by Jens Reitdorf, Arne Seitz, and Johannes Schindelin.

Latest revision as of 12:44, 18 January 2020

Dynamic_Kymograph (Fiji)
Author Rudy Zhou
Maintainer Rudy Zhou
Source on GitHub
Initial release 26 July 2018
Category Plugins


Dynamic_Kymograph is a plugin for ImageJ that generates kymographs from stack videos using key-framing and linear interpolation.

Features

The main features are:

  • Allows user to specify polyline ROIs on multiple frames of a stack video
  • Automatically interpolates between ROIs drawn on different frames
  • Generates a kymograph using the interpolated ROI throughout the stack video

Download and Usage

See https://github.com/rudyzhou/Dynamic_Kymograph for download and detailed usage instructions.

Authors

License

This project is licensed under the GNU General Public License.

Acknowledgements

Some code used from Multiple Kymograph Plugin by Jens Reitdorf, Arne Seitz, and Johannes Schindelin.