# Bioimage Analysis Wiki

### Sidebar

EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

Popularity Ranking

 RT @jytinevez: LimeSeg on bioRXiv: LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation https://t.co/jECl7deOVG About 9 hours, 5 mins ago by: Kota Miura (@cmci_) Impressive and swift moderation @helenajambor ! About 2 days, 14 hours ago by: Kota Miura (@cmci_) RT @LuisDVerde: Now available as a #ggplot2 geom thanks to @naupakaz https://t.co/zOaMWvzd8k https://t.co/AXYBCeGyw6 About 2 days, 14 hours ago by: Kota Miura (@cmci_) RT @helenajambor: awesome, within 2 days .@naupakaz made a code publicly available for anyone wanting to make the half-and-half-plot FYI @… About 2 days, 14 hours ago by: Kota Miura (@cmci_) RT @dgaboriau: Thread on data visualisation: ggplots, boxplots and violin plots https://t.co/QZE7xQtaa3 About 2 days, 19 hours ago by: Kota Miura (@cmci_) RT @christlet: SUSHI from Valentin Nāgerl lab allows super-resolution microscopy of neuronal morphology by STED imaging of extracellular sp… About 2 days, 22 hours ago by: Kota Miura (@cmci_)
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).

## Source

Released under the GNU General Public License v2.

## Requires

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.

## Installation

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

## Description

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

### workflow

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”.

#### MTrackJ file

For loading MTrackJ output file, the file should first be converted using 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.

 ,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