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downloads:3dtrackviewer [2012/06/29 21:35] – example data added kotadownloads:3dtrackviewer [2016/05/24 12:46] (current) – external edit 127.0.0.1
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   * 2012-04-23 First Version   * 2012-04-23 First Version
- +  * 2012-07-11 2nd version 
-  * recent log+    * new: single track extractor to evaluate tracks by comparing to the volume rendering of the original stack.  
 +    * new: Capability to use track color-coding from the output of MTrackJ. FOr using the output of MTrackJ, another jython script that converts the data structure is required (description will be added later). 
 +  * recent log in detail
 {{rss>https://github.com/cmci/3Dviewer_TrackVisualization/commits/simple.atom 10 date 12h}} {{rss>https://github.com/cmci/3Dviewer_TrackVisualization/commits/simple.atom 10 date 12h}}
  
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 Download the plugin using this link:  Download the plugin using this link: 
-  * [[https://github.com/cmci/3Dviewer_TrackVisualization/blob/simple/Plot_4D.jar?raw=true|Plot_4D.jar]]+  * [[https://github.com/cmci/3Dviewer_TrackVisualization/blob/simple/target/3Dtrack_viewer-1.0.0.jar?raw=true|3Dtrack_viewer-1.0.0.jar]]
  
 The plugin will appear under the following menu tree: [Plugins -> EMBLTools -> 4D track Plotter].  The plugin will appear under the following menu tree: [Plugins -> EMBLTools -> 4D track Plotter]. 
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 ===== Description ===== ===== Description =====
  
-This 3D visualization tool is an extended functionality for [[http://3dviewer.neurofly.de/|3D viewer plugin written by Bene Schmid]] for plotting 3D track data for evaluation of the tracking quality. Source data should be a CSV file with the following column order:+This 3D visualization tool is an extended functionality for [[http://3dviewer.neurofly.de/|3D viewer plugin written by Bene Schmid]] for plotting 3D track data for evaluation of the tracking quality. Source data should be a CSV file with the following column order (see the example below):
  
 index - trackID - frame - x - y - z - scaled x - scaled y - scaled z  - particleID index - trackID - frame - x - y - z - scaled x - scaled y - scaled z  - particleID
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 [{{ :documents:downloadimg:3dtrackviewer_gui.png?400 |3D track viewer, GUI}}] [{{ :documents:downloadimg:3dtrackviewer_gui.png?400 |3D track viewer, GUI}}]
  
-===== an example of coordinate data =====+==== workflow ==== 
 + 
 +  - Click "Choose Track File" and select your csv file with track data.  
 +  - Decide if you would like to visualize tracks as a static 3D path, or dynamic 4D path ("Dynamic").  
 +    - 4D path consumes memory. If your machine does not have enough memory or CPU power, you might need to wait for a very long time if your data is large.  
 +   - Decide if you want to also see path nodes.  
 +   - Activate the checkbox according to your decision. 
 +     - 4D path / nodes cannot be visualized together with 3D path and vice versa.  
 +   - click "plot"
 + 
 +=== MTrackJ file  === 
 +For loading MTrackJ output file, the file should first be converted using [[https://github.com/cmci/ijmacros/blob/master/dataconvert/MTrackJ23Dviewer.py|this file]]. The resulting converted text file has an extra column that defines the color for each tracks.  
 + 
 +==== Example of coordinate data ==== 
 + 
 +Below is an example of data file that could be loaded from 3D tracker viewer. SXpos,SYpos &SZpos are the columns of 3D coordinates that will be used for the plotting. S stands for scaled.  
  
 <code> <code>
downloads/3dtrackviewer.1341005730.txt.gz · Last modified: 2016/05/24 12:46 (external edit)

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