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

• 2012-04-23 First Version

• recent log

• Debugging for compile finished. still errors with tests (2016/04/26 22:14)
• precious refactoring (2016/04/26 14:33)
• updates in javadoc (2016/04/26 14:31)
• pom updated to the latest (2016/04/26 14:26)
• a small fix with imports (2013/11/27 17:38)
• Merge branch 'simple' of github.com:cmci/3Dviewer_TrackVisualization … (2013/11/27 17:29)
• small change commits before pull (2013/11/27 17:27)
• removed Ant build files. (2013/11/27 16:24)
• mavenization for simple branch done, pom.xml with all required (2013/11/27 16:21)
• mavenization, file structure changed, pom.xml added, package name (2013/11/26 14:43)

Released under the GNU General Public License v2.

Most recent Fiji ( >> Fiji site). Definitely requires 3DViewer plugin installed, and for this, Fiji will be a easy choice than installing multiple plugins for ImageJ.

Download the plugin using this link:

• Plot_4D.jar

The plugin will appear under the following menu tree: [Plugins → EMBLTools → 4D track Plotter].

This 3D visualization tool is an extended functionality for 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

3D track viewer, GUI

1. Click “Choose Track File” and select your csv file with track data.
2. Decide if you would like to visualize tracks as a static 3D path, or dynamic 4D path (“Dynamic”).
   1. 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.
3. Decide if you want to also see path nodes.
4. Activate the checkbox according to your decision.
   1. 4D path / nodes cannot be visualized together with 3D path and vice versa.
5. click “plot”.

 ,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