~~NOTOC~~
[{{ :documents:downloadimg:trackstatic2.gif?400|3D track, static view}}]
====== 3D Track Viewer ======

===== Author =====

Kota Miura\\ 
Centre for Molecular and Cellular Imaging (CMCI)\\
EMBL Heidelberg\\ 
miura at embl dot de\\ 
Tel: +49 6221 387 404

===== History =====

  * 2012-04-23 First Version
  * 2012-07-11 2nd version
    * 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}}

===== Source =====

Released under the [[http://www.gnu.org/licenses/gpl-2.0.html|GNU General Public License v2]]. 

===== Requires =====

Most recent Fiji ([[http://fiji.sc| >> Fiji site]]). Definitely requires 3DViewer plugin installed, and for this, Fiji will be a easy choice than installing multiple plugins for ImageJ. 

===== Installation =====

Download the plugin using this link: 
  * [[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]. 

===== 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 (see the example below):

index - trackID - frame - x - y - z - scaled x - scaled y - scaled z  - particleID

[{{ :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>