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Getting started with TrackMate

45 bytes added, 11:50, 7 August 2014
Standardize keyboard shortcut formatting
What is critical is also to check the dimensionality of the image. In our case, we have a 2D time-lapse of 50 frames. If metadata are not present or cannot be read, ImageJ tends to assume that stack always are Z-stack on a single time-point.
If the calibration or dimensionality of your data is not right, I recommend changing it in the image metadata itself, using ''Image > Properties'' ({{key|Ctrl}}+{{key|Shift}}+{{key|P}}). The press the 'Refresh source' button on the TrackMate start panel to grab changes.
You can also define a 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 source''' 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.
The LoG-based detectors fortunately demand very few parameters to tune them. The only really important one is the ''Estimated blob diameter'''. Just enter the approximate size of the spots you are looking to tracks. Careful: you are expected to enter it in <u>physical units</u>. In our dummy example, there is no calibration (<tt>1 pixel = 1 pixel</tt>), so it does not appear here.
There are extra fields that you can configure also. The '''Threshold''' numerical value aims at helping dealing with situation where a gigantic number of spots can be found. Every spot with a maximal intensity value below this threshold value will not be retained, which can help saving memory. You set this field manually, or by adjusting the threshold using ImageJ: call the ''Image > Adjust > Threshold'' menu item ({{key|Ctrl }}+ Shit {{key|Shift}}+ {{key|T}}), adjust the upper threshold to your liking, the press the '''Refresh threshold''' button on the panel. This will grab the value you just set.
You can check '''Use median filter''': this will apply a 3x3 median filter prior to any processing. This can help dealing with images that have a marked salt & pepper noise which generates spurious spots.
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