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downloads:3dtrackviewer [2012/07/11 08:10]
127.0.0.1 external edit
downloads:3dtrackviewer [2016/05/24 05:46] (current)
Line 1: Line 1:
 +~~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>​
 + 
downloads/3dtrackviewer.txt ยท Last modified: 2016/05/24 05:46 (external edit)