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Getting started with TrackMate

2,111 bytes added, 07:15, 15 January 2012
Also, if you look carefully, you will see that there are two splitting events - where a spot seems to divide in two spots in the next frame, one merging event - the opposite, and a gap closing event - where a spot disappear for one frame then reappear a bit further. TrackMate is made to handle these events, and we will see how.
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== Starting TrackMate ==
[[Image:TrackMate MainButtons.png|right|border|]]
With this image selected, launch TrackMate from the menu ''Plugins > Tracking > Track Mate'' or from the [[Using the Command Launcher|Command launcher]]. The Track Mate GUI appears next to the image, displaying the starting dialog panel.
But first, just a few words about its look. The user interface is a single frame divided in a main panel, that displays context-dependent dialogs, and a permanent bottom panel containing the four main buttons depicted right.
The '''Next''' button allows to step through the tracking process. It might be disabled depending on the current panel content. For instance, if you do not select a valid image in the first panel, it will be disabled. The '''Previous''' button steps back in the process, without executing actions. For instance, if you go back on the segmentation panel, segmentation will not be re-executed.
Pressing the '''Load''' button opens a dialog asking you for a TrackMate file (they are plain XML files). Depending on when in the process you saved it, it will load all of its data and put you at the adequate step to pursue or inspect tracking results. The '''Save''' button does of course the converse.
Now is a good time to speak strategy when it comes to saving/restoring. You can save at anytime in TrackMate. If you save just before the tracking process, you will be taken there with the data you generated so far upon loading. TrackMate saves a <u>link to the image file</u> (as an absolute file path) but not the image itself. When loading a TrackMate file, it tries first to retrieve and open this file in ImageJ. So it is a good idea to pre-process, crop, edit metadata and massage the target image first in Fiji, then save it as a .tif, then launch TrackMate. Particularly if you deal with a multi-series file, such as Leica .lif files.
The advantage of this approach is that you can launch TrackMate, immediately press the load button, and everything you need will be loaded and displayed. However, if you need to change with the target file of if it cannot be retrieved, you will have to open the TrackMate XML file and edit its 4th line.
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== The start panel ==
[[Image:TrackMate StartPanel.png|right|border|]]
This first panel allows you to check the spatial and temporal calibration of your data. It is very important to get it right, since everything afterwards will be based on physical units and not in pixel units (for instance μm and minutes, and not pixels and frames). In our case, that does not matter actually, since our test image has a dummy calibration (1 pixel = 1 pixel).
If the calibration or dimensionality of your data is not right, I recommend changing it in the image metadata itself, using ''Image > Properties'' (Ctrl+Shift+P). The press the 'Refresh' button on the TrackMate start panel to grab changes.
You can also define a drop cube for processing.
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