Difference between revisions of "Dynamic Kymograph"

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Revision as of 20:58, 13 January 2020

Dynamic_Kymograph (Fiji)
Author Rudy Zhou
Maintainer Rudy Zhou
Source on GitHub


Basics

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

Usage

  • In fiji, open the image stack that you would like to analyze
  • Run the dynamic kymograph plugin (in “Process” -> “Dynamic Kymograph”).
  • The UI has the following features:
  • 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
  • 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)
  • 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.
  • If you want to close the plugin, press the “x” button on the “Dynamic Kymograph” window

Authors