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Getting started with TrackMate

473 bytes added, 03:48, 1 August 2013
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== Selecting a displayer view ==
[[Image:TrackMate DisplayerChoice.png|right|border|]]
Honestly, choose the HyperStack displayer. Unless you have a very specific and complicated case that needs to inspect results in 3D immediately, you do not need the 3D viewer. The HyperStack displayer is simpler, lighter, allow to manually edit spots, and you will be able to launch a 3D viewer at the end of the process and still get the benefits.
<br style="clear: both" /> == Computing spot feature and rendering displayer == [[Image:TrackMate ComputeSpotFeatures.png|right|border|]] We are now back to the log panel. As When you pressed press the '''Next''' button, two process startedstarts:
* the features of all spots (well, those you left after the initial filtering step) are calculated;
* the displayer selected does everything it needs to prepare displaying them.
So nothing much. When the Let'''Next''' button is re-enabled, press it to move to the spot filtering steps carry on.
<br style="clear: both" />
Let us try it to play with it to find the best feature to filter out spurious spots.
By default , when the combo-box is on '''DefaultUniform color''', all spots are purple. By clicking on it, you see that you can select amongst all the possible features calculated. For instance, if you select '''X''', the spots will be colored according to their X position. A colored bar below the combo-box indicates the range the color gradient corresponds to.
'''X''' does not seem to be a good feature to select relevant spots. We know that '''Quality''' should be, by construction, but let us pick '''Mean intensity'''. By scrolling through the time slide you should be able to see that now all the spurious spots have a blue to turquoise color, whether the real one stands forward in red or yellow.
To move the threshold, simply click and drag inside the histogram window. Notice how the overlay is updated to display only the remaining spots after filtering.
 
<u>Interlude</u>: A word on the GUI: I put some effort into having a GUI that can be navigated almost solely with the keyboard. Any of the small filter panel can be controlled with the keyboard. For instance: give the histogram the focus by either pressing the Tab key or clicking into it.
<ul>
<li> The floating threshold value should turn from orange to dark red. You can now type a numerical value (including decimals using the dot '.' as separator); wait two seconds, and the threshold value will be updated to what you just typed.
<li> Ot use the arrow keys: the left and right arrow keys will change the threshold value by 10%, the up and down arrow will set it to the max and min value respectively.
</ul>
A filter can be set to be above or below the given threshold. You change this behavior using the radio buttons below the histogram window. In our case, we want it to be above of course. The '''Auto''' button uses [http://en.wikipedia.org/wiki/Otsu%27s_method Otsu's method] to determine automatically a threshold. In our case, we will put it manually around 33.
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