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Getting started with MaMuT

23 bytes added, 09:02, 15 March 2017
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Now is a good time to talk a little bit on how we control the look of spots on the MaMuT viewer. All the MaMuT are in sync and they share common display settings. It is not possible to separately tune the display of each view. Display settings for spots can be tuned on the main GUI window, in the top part of the '''Views''' tab. Here you can toggle the visibility of all spots, make their name appear. The display radius simple change their apparent radius on the MaMuT viewer. This display setting has no impact on subsequent analysis and apart from visibility tidiness, it will have its utility later.
The spot coloring colouring uses the notion of ''numerical features''. In MaMuT, and as in TrackMate, each annotation object can have several numerical, scalar features associated. For instance a spot can have features like X, Y, Z for its position, etc. The drop-box menu \textbf{'''Set color by} ''' lets you choose the feature you want to use for the spot color. The color range below the menu shows you the min and max value for the feature you picked over all the dataset and interpolate from blue to red with a jet color-map. If you scroll through the menu, you can see that the features available are sorted in three categories: <tt style="font-size: 1.25em;">spot features</tt>, <tt style="font-size: 1.25em;">default</tt> and <tt style="font-size: 1.25em;">track features</tt>. <tt style="font-size: 1.25em;">Spot features</tt> is the category where you can find all the numerical features that relate to single spots, like their position, radius, ''etc.'' In <tt style="font-size: 1.25em;">default</tt>, colors colours are not picked from a numerical feature, but either all the same (uniform color) or set manually (we will see later how). The <tt style="font-size: 1.25em;">track feature category</tt> is special: it gives to spots the color taken from the feature of the ''track'' they belong to.
[[Image:bdv-MaMuT_ConfigureSpotDisplay.png]]
We propagate the identity of a cell over time using several spots in several time-points, connected from one to its successor by ''links''. Particle-linking algorithms are algorithms that find automatically what are the right links from one time-point to another given a set of spots spread over several time-points. Of course, the definition of "right" depends on the specificity of the algorithm. Tracking is the process of finding automatically all spots in an 2D+T or 3D+T image, and linking them. MaMuT does not do fully automatic tracking. It is a tool that specializes in manual or semi-automatic tracking, privileging data exploration and manual annotation on very large images. However, we will show in another tutorial how to import the results of automated tracking algorithms in MaMuT, so that they can be verified and curated. Here, we limit ourselves to manual and semi-automatic tracking.
A link is a directed relationship from a spot, called the source, to another spot, called the target. The source spot is always the predecessor in time, so links always point towards increasing time. All the spots that can be reached from a spot by crossing links form what is called a ''track''. In our case, a track represents a lineage from a single starting (founder) cell lineage.
The actual data structure behind the annotations in MaMuT (and TrackMate) is a ''simple directed graph''. A graph is a mathematical structure made of vertices (in our case, spots representing cells) connected by edges (in our case, links representing propagation of identify identity across several time-points). The graph is ''simple'' because it is forbidden to have more than one link between two spots, and that a link cannot link a spot to itself. It is ''directed'' because links have a direction, following increasing time. In MaMuT, we added an extra constraint that forbids the existence of a link between two spots belonging to the same time-point, but otherwise this data structure is very standard.
So a link can be created between any two spots, provided they do not belong to the same time-point. There is no other restriction. For instance, a spot can be the source of several links. If there is two outgoing links from a spot, they may represent a cell division (mother cell linked to its two daughters). Several source spots can be linked to a single common target spot, though the biological meaning of this is less evident. MaMuT does not put constraints on the number of links going from or to a spot. We reasoned that MaMuT is to be used to build generic graph-like annotations, and that the subsequent analysis should be specific to the biological context. For instance, for cell lineaging there should be at most two outgoing links from a source spot, and at most one ingoing link on a target spot.
* Press {{key press|L}} to add a link between these two spots, or to remove it already exists.
So here are the two new useful bindings for \textbf{'''editing links}''':
* {{key press|Shift-Left Click}} add and remove spots from the selection.
[[Image:bdv-MaMuT_DesiredTracking_1.PNG|500px]]
Note that when you create a link with this method, after link creating the selection is set to be made of only the last spot added. To create the next link, you just have to add the target spot to the selection, the source spot is already in. But still, after creating links over only 10 time-points, lets recognize let us admit that this is probably not the best quickest way to quickly create a lineage. This method is probably best suited to edit an existing annotation.
=== The auto-linking mode. ===
Press {{key press|Shift-L}} with a MaMuT viewer window active. A message should appear in the MaMuT viewer that states the auto-linking mode is now on. In this mode, a link is automatically created when you create a new spot between this spot and the last one in the selection. Then the selection is changed to be the last spot added. Using this, you can quickly create lineage by moving forward in time with the keyboard and creating spots by typing {{key press|A}}. You can also use {{key press|Double Click}} to create spots, but because a simple click would clear the selection, you have to hold the {{key press|Shift}} key down to use auto-linking with mouse clicks.
Try to use the auto-linking mode to create the cell lineage of the dividing cell above, this time following the other daughter cell. Move back to the first time-point, select the mother cell, move to the second time-point {{key press|M}} and add a spot {{key press|A}} or {{key press|Shift-Double Click}} on the cell location. Repeat by following the right daughter cell. You should end up with an annotation that resembles the following:
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