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Getting started with TrackMate

783 bytes added, 10:00, 15 January 2012
The start panel
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 sub-region for processing: if you are only interested in finding spots in a defined region of the image, you can use any of the ROI tools of ImageJ to draw a closed area on the image. Once you are happy with it, press the '''Refresh''' button on the panel to pass it to TrackMate. You should see that the '''X''' '''Y''' start and end values change to reflect the bounding box of the ROI you defined. The ROI needs not to be a square. It can be any closed shape.  If you want to define the min and max '''Z''' and/ or '''T''', you have to edit manually the fields on the panel.  Defining a smaller area to analyze can be very beneficial to test and inspect for correct parameters, particularly for the segmentation step. In this tutorial, the image is so small and parse that we need not worrying about it.
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