**Manual Tracking**

+-----------+----------------------------------------------------------+
| **        | Fabrice Cordelières, Institut Curie, Orsay (France).     |
| Author:** |                                                          |
|           | fabrice.cordelieres at curie.u-psud.fr                   |
+-----------+----------------------------------------------------------+
| **H       | 2004/06/25: First version                                |
| istory:** |                                                          |
|           | 2005/06/15: New features: 2D centring correction,        |
|           | Directionality check, Previous track files may be        |
|           | reloaded, 3D features added (retrieve z coordinates,     |
|           | quantification and 3D representation as VRML file).      |
+-----------+----------------------------------------------------------+
| **Requir  | ImageJ 1.34k or later                                    |
| ements:** |                                                          |
+-----------+----------------------------------------------------------+
| **        | Manual_Tracking.java                                     |
| Source:** |                                                          |
+-----------+----------------------------------------------------------+
| **Instal  | Download Manual_Tracking.class to the plugins folder and |
| lation:** | restart ImageJ. Documentation in pdf format may be       |
|           | downloaded here.                                         |
+-----------+----------------------------------------------------------+
| **Descr   | This plug-in allows the user to quantify movement of     |
| iption:** | objects between frames of a temporal stack, in 2D and    |
|           | 3D.                                                      |
|           |                                                          |
|           | ***[Results table:]{.underline}***                       |
|           |                                                          |
|           | This plug-in provides a way to retrieve in a table       |
|           | (figure 1) XY and XYZ coordinates as well as velocity,   |
|           | distance covered between two frames and intensity of the |
|           | selected pixel or volume, by simply clicking on the      |
|           | structure of interest.                                   |
|           |                                                          |
|           | Figure 1:                                                |
|           |                                                          |
|           | ![](media/image1.jpeg){width="3.0125in"                  |
|           | height="2.625in"}                                        |
|           |                                                          |
|           | Note: as the first velocity value can\'t be calculated   |
|           | (first tracked frame where time interval equals zero),   |
|           | its first displayed value will be -1, as in most of the  |
|           | commercial software.                                     |
|           |                                                          |
|           | ***[Interface:]{.underline}***                           |
|           |                                                          |
|           | Figure 2:                                                |
|           |                                                          |
|           | ![](media/image2.jpeg){width="3.161111111111111in"       |
|           | height="3.767361111111111in"}                            |
|           |                                                          |
|           | The interface is composed of 5 parts:                    |
|           |                                                          |
|           | -   *Tracking buttons:*                                  |
|           |                                                          |
|           |     -   To start recording one track, the user has to    |
|           |         click on \"add track\".                          |
|           |                                                          |
|           |     -   The tracking is done by clicking on the          |
|           |         structure on the image. After each mouse click,  |
|           |         the following image of the temporal stack is     |
|           |         activated until the last image is reached or the |
|           |         \"End track\" button is pressed.                 |
|           |                                                          |
|           |     -   \"Delete last point\" is used to erase the last  |
|           |         recorded coordinates.                            |
|           |                                                          |
|           |     -   \"End track\" button should be used to stop the  |
|           |         tracking procedure in case the structure         |
|           |         disappeared from the image.                      |
|           |                                                          |
|           |     -   By selecting the number in the list next to the  |
|           |         \"Delete track n°\" button, the user is allowed  |
|           |         to erase one track from the result table. This   |
|           |         choice should be validated by clicking on the    |
|           |         \"Delete track n°\" button.                      |
|           |                                                          |
|           |     -   \"Delete all tracks\" is used to clean up the    |
|           |         results table.                                   |
|           |                                                          |
|           | ```{=html}                                               |
|           | <!-- -->                                                 |
|           | ```                                                      |
|           | -   *Centring correction:* helps the user to point the   |
|           |     right pixel.                                         |
|           |                                                          |
|           | -   *Directionality:* retrieves information on whether   |
|           |     the movement is retrograde or anterograde.           |
|           |                                                          |
|           | -   *Drawing:* this section deals with the ways to get a |
|           |     visual representation of the coordinates recorded in |
|           |     the results table. Several displays are available:   |
|           |     each button\'s function is illustrated in the        |
|           |     following section                                    |
|           |                                                          |
|           | -   *Parameters:* this section contains all required     |
|           |     calibration values and drawing settings.             |
|           |                                                          |
|           | ***[Display:]{.underline}***                             |
|           |                                                          |
|           | The Manual Tracking module has display capacities aiming |
|           | to provide either a synthetic vision of the tracked      |
|           | points and/or their paths (figure 3, top), or an overlay |
|           | of one of the synthetic representations and the original |
|           | image (figure 3, bottom).                                |
|           |                                                          |
|           | Figure 3:                                                |
|           |                                                          |
|           | ![](media/image3.gif){width="5.125in"                    |
|           | height="3.4270833333333335in"}                           |
|           |                                                          |
|           | ***[Retrieve z coordinates:]{.underline}***              |
|           |                                                          |
|           | The Manual Tracking module was improved to allow a       |
|           | simple retrieval of z coordinates. This operation may be |
|           | monitored by generating a VRML file of the 3D+time       |
|           | dataset (Figure 4) which can be viewed in any web        |
|           | browser equipped with the appropriate plug-in (see       |
|           | documentation for more details).                         |
|           |                                                          |
|           | Figure 4:                                                |
|           |                                                          |
|           | ![](media/image4.gif){width="2.7708333333333335in"       |
|           | height="2.772222222222222in"}                            |
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