Track3D - 9 Running 3D Analysis
Last updated: Jul 25, 2026
9 Running 3D analysis
9 Running 3D Analysis
Overview
In this chapter you find the procedure for importing the 2D data in the Track3D software and obtaining the results, both graphical and numerical. What you need now is: The input data files (*.xls, *.xlsx, .txt) - Containing the X,Y (2D) coordinates from the two camera views. The calibration file (.xls, .xlsx) - Containing the calibration data (see page 39). Make sure that the EthoVision XT hardware key is plugged in one of the USB ports of your computer. At the end of this procedure, for each pair of input data files you obtain: An output file (.xls). A 3D chart (that you can export as a picture file). Figure 18 Track3D receives the input files from EthoVision XT and the Calibration file from CentroidFinder. 9 Running 3D analysis
Analysis Procedure
- Start Track3D. The Track3D window opens.
Together with the Track3D window, another (DOS command)
window appears. Do not close this window. 2. Make sure that the settings in Track3D correspond to what you require (see Settings in Track3D on page 64). 3. Under Analysis, select: - New calibration if you want to use a calibration file different from that used the last time you ran analysis. 9 Running 3D analysis - Old calibration to retain the last used calibration.
To be able to use the Old calibration option, make sure that the
old calibration file is stored where Track3D is installed (C:\MCR). Next, click Start calculations. 4. If you have selected New calibration, the Select calibration file window opens. Select the calibration file (this is the file created with the procedure on page 31) and click Open. Result - Three windows appear one on top, named with
progressive numbers (Figure 1, Figure 2, etc.). Those images
illustrate the quality of calibration (see page 124 for details). If you have selected Old calibration, go to the next step. 5. The One or two input files window appears. - Click One combined file if you combined the track files from the two cameras into one. - Click Two separate files if you use the original track files exported from EthoVision XT. 6. The Select input from camera 1 window opens. Select the file you require (available formats: *.xls, *.xlsx, *.txt) and click Open.
Next, the Select input from camera 2 window opens. Select the file
you require and click Open. Make sure that the camera view of the first file corresponds to that of the first calibration image, and that the camera view of the second file corresponds to that of the second calibration image. 9 Running 3D analysis
If you selected One combined file in the previous step, you are
asked to select the combined input file (available formats: *.xls, *.xlsx, *.txt). 7. The Save file window opens. In this window you can specify where to save the results data file (see page 85). Browse to destination folder and enter a name for the file, then click Save.
By default, the file name is out_3d.xls and is saved in the same
folder as that of the Track3D software. 8. The Statistics window appears. This lists the percentage of missing samples found in the input data for camera 1 and camera 2 and in total (camera 1 OR camera 2). 9. Click OK. A new window "Figure n" appears showing the subject's trajectory in 3D.
Notes
If you encounter issues and error messages, see the Troubleshooting section for Track3D on page 127. The Track3D output file is saved in Excel format (*.xls) or text format if Excel is not installed on the PC. If the results file with that name already exists in the destination folder, the program asks whether you want to replace it with the new version. The name of the chart window is "Figure n" where n is an increasing number.
In the Statistics window the total percentage of missing samples
may be higher than the sum of the values for camera 1 and 2. This 9 Running 3D analysis can be due to the clean up input settings. A low Maximum intersection error (page 74) results in excluding several (non- missing) data points.
What next?
Look at the 3D chart and animate the track (see page 76). Create a video of the track (see page 82). Open the results file (see page 85). 10 Settings in Track3D
10 Settings In Track3D
Lenses
Additional lenses correction (optional)
Under Lenses, select Perform lens correction if you want to correct for
lens distortion (see page 120). If you do not want to perform lens correction, clear this option. Lens correction is necessary if the lenses you use have a significant barrel distortion ("fish-eye" effect). If you use rectilinear lenses, keep this option de-selected.
Air Speed
Click the Air speed button.
Under Air speed, enter the estimated speed (in mm/s) of the air flow in
the test chamber (if known), otherwise enter 0. 10 Settings in Track3D
Odour Plume
Click the Odour plume button. If the test is performed with an odour plume, and you want to analyze
the data of the subject relative to the odour plume, select Include
odour plume.
Under Cone top position, enter the X, Y and Z coordinates of the
vertex of the cone (the release point of the odour; see Figure 19).
Under Axis point position, enter the X, Y, and Z coordinates of the
point that, together with the top position (vertex), defines the axis (and therefore the orientation) of the cone.
Next to Cone angle (degrees), enter the angle in degrees that
determines the aperture of the cone.
Enter the Number of circles you want to visualize in the 3D chart
(see Figure 19).
Next to Buffer zone width, enter the width in mm of the buffer
area. This generates a second cone external to the main one. 10 Settings in Track3D Selecting this option results in the test chamber being divided in three spaces: (a) a cone representing the odour plume in the test chamber, (b) a buffer zone around the cone, and (c) the remaining space. The coordinates' origin and axis orientation are those indicated by your calibration (see Calibration on page 26). Figure 19 Representation of the odour plume in 3D. To draw the cone, enter the coordinates of the Cone top position and the Axis position points. Those points define the cone axis. You can also define a buffer zone around the cone by entering the zone width. The points of the 3D track will be displayed in different colors depending on in which zone they are: within the cone, in the buffer zone or outside the buffer zone. In this example the cone's main axis is placed horizontally. If you want the cone's axis to be oblique, for example when the odour plume points upward, then follow the note on page 122. 10 Settings in Track3D
3d Zones
Use this option to analyze the data in relation to the position of the subject in one or more three-dimensional zones of the tracking chamber. Click the Zone indication button.
In the Zone indication box, select one or more of the following:
Note that the axes and the position of the origin point are those defined by your calibration.
Zones separated by planes perpendicular to x axis
Choose this option to divide the tracking chamber in two or more regions, separated by planes perpendicular to the x axis (wind direction). 10 Settings in Track3D Enter the values of distance D from the x axis, separated by blank spaces.
For example, entering 100 and 200 will define three zones:
A - Within 100 mm from the vertical plane passing through the
origin. B - Between 100 mm and 200 mm from the same vertical plane.
C - Between 200 mm from the same vertical plane and the other
end of the tracking chamber. 10 Settings in Track3D
Zones separated by planes perpendicular to y axis
Choose this option to divide the tracking chamber in two or more regions, separated by horizontal planes. Enter the values of distance D along the y axis, separated by blank spaces. For example, entering 200 and 400 will define three zones:
A - Within 200 mm from the vertical plane passing through the
origin. B - Between 200 mm and 400 mm from the same vertical plane.
C - Between 400 mm from the same vertical plane and the other
end of the tracking chamber.
Zones separated by planes perpendicular to z axis
Choose this option to divide the tracking chamber in two or more regions, separated by planes perpendicular to the z axis. Enter the values of distance D from the x axis, separated by blank spaces.
For example, entering 200 and 400 mm will define three zones:
A - Within 200 mm from the horizontal plane passing through the
origin *(this is usually the bottom of the wind tunnel). B - Between 200 mm and 400 cm from the same plane. 10 Settings in Track3D
C - Between 400 cm from the same plane and the other end of the
tracking chamber.
Note - Track 3D marks each 3D data point depending on in which zone
it is located. It does not analyze or visualize those points based on the 3D zones. To analyze the data points in this way, filter the results file with Excel using the zone codes (see page 116).
Cylindric zones
Choose this option to divide the tracking chamber in concentric cylinders.Enter the coordinates of the center of the cylinder (Point on axis), the Slope relative to the x axis (in degrees; default = 0, which means that the cylinders are parallel the x axis), and the values of diameter of each cylinder, separated by blank spaces (Diameters, in mm). For example, entering 200 and 400 mm will define three zones: A - A cylinder with diameter 200 mm.
B - A zone between two cylinders of 200 mm and 400 mm
diameter. C - A zone including all space out of zone B. 10 Settings in Track3D
Interpolation
Click the Interpolation button.
Select Perform interpolation if you want to replace missing samples in
the input file (with 2D data) with values obtained by interpolation using adjacent valid samples. Enter the maximum number of successive missing samples acceptable within a block. 10 Settings in Track3D
Notes
Interpolation is applied after clean up input (page 74). Missing samples are missing X,Y coordinate values in the input data files. They occur when EthoVision cannot detect an object using the current detection settings. For example, when the animal is out of the camera view. Here you can choose whether to replace missing samples with interpolated data. If you decide not to perform interpolation, the missing bits of the track are visualized as blue dashed lines. If missing samples occur in trains, with one missing sample immediately following another, performing interpolation makes little sense as the longer time between adjacent valid samples reduces the predictive power. You can prevent this from happening by entering the maximum number of successive samples to be interpolated.
Example - An input data file contains three consecutive missing
samples for camera 1. To interpolate those samples, enter 3 or a higher value. If you enter a value smaller then 3, the missing samples will not be interpolated. The data before and after those samples will be considered in two different blocks. Missing samples that are not interpolated are not included in the output file. 10 Settings in Track3D
Filtering (track Smoothing)
Click the Filtering button.
Select Perform filtering if you want to replace the raw coordinates with
values obtained with a lowpass Butterworth filter (see page 123). Note that Filtering does not reduce the number of samples in your input data set
Select 2D if you want to smooth the 2D data, that is, the X and Y
coordinate values obtained from EthoVision.
Select 3D if you want to smooth the 3D data, that is, the calculated
X, Y, Z coordinates values (that is, the values you find in the output file). If you select this option, the output file always contains the smoothed data, not the original 3D data. For both options specify: - Filter order - Enter the order of the spline interpolation function. - Cut off - Enter the cut off frequency (in Hz). Apparent movements with frequency higher then the value you enter are 10 Settings in Track3D smoother out. The lower the cutoff value, the smoother the resulting line.
By default, 2D and 3D are selected with filter options: Filter order =
2, and Cut off = 8.
Next to Frame rate (fps), enter the sample rate you used for
tracking with EthoVision. More details on page 123.
Clean Up Input
Choose this option to remove artifacts and less reliable data points. Click the Clean up input button. Enter the following:
Maximum change of any coordinate in successive frames is -
Enter the maximum distance (in pixels) between two successive samples that you want to consider as valid. Use this function for example to exclude samples that are so far from each that they likely result from bad detection (see an example below).
Maximum intersection error is - The program checks whether
Ethovision tracked the same object at every sample. This is done by comparing the ideal lines that join each camera lens and the tracked object. If the EthoVision tracked different objects from the two cameras (for example, the actual animal from Camera 1 and a 10 Settings in Track3D reflection from Camera 2), the two lines do not intersect. You can remove such instances entering a maximum distance (in pixels) between the two lines.
Notes
Clean up input removes samples from your input data set. Because interpolation (see page 71) is applied after removing those samples, a different clean up setting (for example a lower Maximum intersection error) results in different values of x,y,z coordinates and output parameters. If you enter a small Maximum intersection error value, you take the risk of excluding good samples. A high value makes it more likely to include false detections in the 3D tracks. Run analysis a few times, each with a different maximum intersection error and compare the charts. If you need to enter a large maximum intersection error to obtain good results, it could be due to the fact that the calibration is not valid anymore, for example a camera may have been moved in the meantime. Make a new calibration and specify this in analysis (page 60).
Source: Track3D 2 - Reference Manual (March 2025)