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downloads:3dtrackviewer [2012/06/29 21:15] 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}}
  
Line 29: Line 31:
  
 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]. 
Line 35: Line 37:
 ===== 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
  
 [{{ :documents:downloadimg:3dtrackviewer_gui.png?400 |3D track viewer, GUI}}] [{{ :documents:downloadimg:3dtrackviewer_gui.png?400 |3D track viewer, GUI}}]
 +
 +==== 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>
 + ,TrackID,frame,Xpos,Ypos,Zpos,SXpos,SYpos,SZpos,ParticleID
 +1,1.000,0.000,269.900,177.850,3.400,111.730,73.620,2.570,1.000
 +2,1.000,1.000,271.630,185.670,4.030,112.450,76.860,3.050,194.000
 +3,1.000,2.000,269.300,187.770,4.410,111.480,77.730,3.330,376.000
 +4,1.000,3.000,273.620,191.100,4.200,113.270,79.110,3.170,551.000
 +5,1.000,4.000,273.590,190.140,4.470,113.260,78.710,3.370,685.000
 +6,1.000,5.000,278.310,192.080,4.080,115.210,79.510,3.080,866.000
 +7,1.000,6.000,276.690,196.510,3.310,114.540,81.350,2.500,1131.000
 +8,1.000,7.000,278.320,200.520,2.410,115.220,83.010,1.820,1232.000
 +9,1.000,8.000,278.580,199.460,2.820,115.330,82.570,2.130,1422.000
 +10,1.000,9.000,278.270,205.200,2.080,115.200,84.950,1.570,1668.000
 +11,1.000,10.000,283.620,208.230,2.840,117.410,86.200,2.140,1871.000
 +12,1.000,11.000,287.270,212.960,2.310,118.920,88.160,1.750,2069.000
 +13,1.000,12.000,290.670,212.200,2.740,120.330,87.850,2.070,2282.000
 +14,5.000,0.000,165.490,276.340,22.330,68.510,114.400,16.860,14.000
 +15,5.000,1.000,168.620,282.480,22.230,69.800,116.940,16.790,245.000
 +16,5.000,2.000,171.820,286.050,21.890,71.130,118.420,16.530,475.000
 +17,5.000,3.000,170.620,290.540,23.450,70.630,120.270,17.710,581.000
 +18,5.000,4.000,174.590,292.500,22.440,72.270,121.090,16.950,738.000
 +19,5.000,5.000,175.120,296.130,22.090,72.500,122.590,16.680,911.000
 +20,5.000,6.000,174.030,299.370,21.140,72.040,123.930,15.970,1048.000
 +21,5.000,7.000,177.450,299.420,19.500,73.460,123.950,14.730,1245.000
 +22,5.000,8.000,180.100,300.520,19.230,74.560,124.410,14.520,1520.000
 +23,5.000,9.000,179.770,303.730,19.500,74.420,125.740,14.730,1695.000
 +24,5.000,10.000,187.750,311.050,19.080,77.720,128.760,14.410,1821.000
 +25,5.000,11.000,189.310,313.800,19.640,78.370,129.910,14.840,2098.000
 +26,5.000,12.000,193.480,314.820,18.160,80.090,130.330,13.710,2307.000
 +27,5.000,13.000,194.950,314.130,16.230,80.700,130.040,12.260,2519.000
 +28,5.000,14.000,192.840,316.030,17.400,79.830,130.820,13.140,2751.000
 +29,5.000,15.000,196.570,318.060,17.750,81.370,131.670,13.410,2989.000
 +30,7.000,0.000,267.320,195.790,4.300,110.660,81.050,3.250,16.000
 +31,7.000,1.000,257.490,195.580,3.400,106.590,80.970,2.570,165.000
 +32,7.000,2.000,256.440,201.920,3.580,106.160,83.590,2.700,378.000
 +33,7.000,3.000,259.960,205.240,3.530,107.620,84.960,2.670,550.000
 +34,7.000,4.000,259.070,203.650,3.800,107.250,84.310,2.870,721.000
 +35,7.000,5.000,263.780,203.080,3.300,109.200,84.070,2.490,871.000
 +36,7.000,6.000,265.290,211.240,2.450,109.820,87.450,1.850,1132.000
 +37,7.000,7.000,267.750,218.160,1.580,110.840,90.310,1.190,1301.000
 +38,7.000,8.000,264.150,214.500,1.700,109.350,88.800,1.280,1505.000
 +39,7.000,9.000,272.130,220.230,1.670,112.650,91.170,1.260,1669.000
 +40,7.000,10.000,282.190,223.640,1.960,116.820,92.580,1.480,1820.000
 +41,7.000,11.000,286.100,229.080,4.020,118.440,94.830,3.040,2084.000
 +42,7.000,12.000,290.690,230.530,3.930,120.340,95.430,2.970,2300.000
 +43,7.000,13.000,288.420,231.330,3.280,119.400,95.770,2.480,2509.000
 +44,7.000,14.000,287.250,232.340,3.480,118.910,96.180,2.630,2681.000
 +45,7.000,15.000,280.830,234.190,4.620,116.250,96.950,3.490,2965.000
 +46,7.000,16.000,274.010,230.320,5.140,113.430,95.350,3.880,3189.000
 +47,7.000,17.000,276.130,230.450,5.250,114.310,95.400,3.960,3444.000
 +48,7.000,18.000,274.230,240.340,6.040,113.520,99.490,4.560,3701.000
 +49,7.000,19.000,281.550,233.380,5.210,116.550,96.610,3.930,3948.000
 +50,7.000,20.000,281.240,244.430,5.380,116.430,101.180,4.070,4203.000
 +51,7.000,21.000,281.250,245.930,5.620,116.430,101.810,4.250,4460.000
 +</code>
    
downloads/3dtrackviewer.1341004556.txt.gz · Last modified: 2016/05/24 12:46 (external edit)

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