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Getting started with MaMuT

337 bytes removed, 10:02, 20 March 2018
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This page contains a tutorial for the [[MaMuT]] plugin. It describes and document all its features using a publication related dataset.
 
== Publication. ==
If you find MaMuT useful for your research, please cite it:
''Reconstruction of cell lineages and behaviors underlying arthropod limb outgrowth with multi-view light-sheet imaging and tracking'', Carsten Wolff, Jean-Yves Tinevez, Tobias Pietzsch, Evangelia Stamataki, Benjamin Harich, Stephan Preibisch, Spencer Shorte, Philipp J Keller, Pavel Tomancak, Anastasios Pavlopoulos '''bioRxiv''' 112623; doi: https://doi.org/10.1101/112623{{Publication | MaMuT}}
If you are on a time-point not a multiple of the time-step, the next key-press will move to the closest multiple. The goal of these commands is to quickly generate a lineage that extends deeply in time by skipping some frames. But the time-points we reach with these commands are always the same multiples, so the annotated frames are all the same when using the stepwise time browsing.
Below is an example from an actual annotation, peeking ahead the lineage visualizer we will describe in the next section. Inn In this view , cells are arranged by lineage, time running from top to bottom. Time-points are lines of alternating color. You can see that except when cells are dividing or when there is an ambiguity, this user only annotated time-points multiples of 5. This leads to a sparser annotation, generated faster.
[[Image:bdv-MaMuT_TrackSchemeStepwiseTimeBrowsing.png|500px]]
* <tt style="font-size: 1.25em;">Show all entire tracks</tt> is the default and display all the whole tracks with no time cue.
* <tt style="font-size: 1.25em;">Show local tracks</tt> only shows a portion of the track which extend shortly before and after the current time-point. As the time distance increases, the track display fades in the image using transparency. You can control how much time context you want to display using the \textbf{'''Limit frame depth} ''' checkbox and the '''Frame depth''' field.
* <tt style="font-size: 1.25em;">Show local tracks, backward</tt> is similar, but only extends tracks backward in time (this mode is sometimes nicknamed 'dragon tail' in other softwares).
* <tt style="font-size: 1.25em;">Show local tracks, forward</tt> is the same thing, but forward in time.
=== Managing a selection in TrackScheme. ===
[[TrackScheme]] is useful to build a selection and query its properties. As we said above, \TrackScheme does not abide any visibility setting. Spots and links are always visible, which is useful to build a selection. Spots and links are added to the current selection in a classical way:
* {{key press|Left-Click}} on a spot or link to set the selection with this spot or link. The selection is cleared before.
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