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Getting started with MaMuT

333 bytes removed, 05:02, 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]]
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