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LimeSeg

316 bytes added, 21:18, 20 January 2018
LimeSeg structure
The GUI consists of an upper panel that can apply different actions on LimeSeg.
Tabs separate the different kinds of objects where actions can be applied.
 
[[Adds image upper part]]
 
The lower part contains information about LimeSeg state.
[[Adds image lower partFile:LimeSegGUI.png]]
To load the sample dataset onto LimeSeg, do the following actions:
==== Vizualizing 3D Objects ====
In LimeSeg GUI, go to 3D View, click '''make3DViewVisible''', then '''putAllCellsTo3DDisplay'''. This displays the C Elegans embryo, but only at the first timepoint (timepoint 1 by convention in ImageJ1). However as seen in the table, many more objects exist. To be able to see the evolution of the embryo over time, LimeSeg has to be linked to an ImageJ image (ImagePlus). To link LimeSeg with the proper image, download the image sample (https://raw.githubusercontent.com/NicoKiaru/TestImages/master/CElegans/dub-0.5xy-TP1-22.tif) and open it in Fiji.
Now you need to link the Image with LimeSeg. To do that:
1. Click '''Img:''' in the STATE tab of LimeSeg GUI, and select the image. Click OK. '''This has no effect at this step'''.
==== 'Populating' a Cell ====
The newly Created cell_0 is empty, as you can see in the Cells explorer windows. Two ways can be used to populate the cell. Both implies the use of Clipped Dots 'buffer' object. Also, a A prerequisite to act of this on a specific cell is to make sure that it is the current cell (or active cell). The current or active cell name is played in the LimeSeg state panel (Cells: current=...) and it its column is highlighted in blue in the Cells explorer window. To change the current Cell of LimeSeg you caneither* Double click on it on the Cells explorer table* Use the '''selectCellById''' button in the STATE pane (fill in the parameter before clicking)* Use the '''selectCellByNumber''' button in the STATE pane (fill in the parameter before clicking)
* double click on Make sure the current Cell is cell_0. It should be empty. You can check this in the Cells explorer* or by using '''selectCellById''' in windows. Two ways can be used to populate the STATE pane (fill in cell. Both implies the parameter before clicking)* or by using use of Clipped Dots 'buffer''selectCellByNumber''' in the STATE pane (fill in the parameter before clicking)object that will contain either simple shapes or copies of existing CellT objects.
1. Creating a sphere
Go to the '''Clipped Dots''' tab, at . At the right of the makeSphere button, fill in the 4 white boxes. They correspond to the centre center of the sphere (x,y,z coordinate in slice number, radius). All units are in pixel except for z are which is in pixelsnumber of slice. Enter 180, 130, 19, 100 for instance. Then click the '''makeSphere''' button. A sphere object has been created in the clipped dots buffer objects. This can be vizualized in the lower panel of LimeSeg GUI (Clipped dots: #dots=).
2. Pasting the sphere into a Cell Object
To put the sphere into the current Cell, go to the Current CellT tab, and click '''pasteDotsToCellT'''. Notice that the Cells explorer now displays C(7906) for the currentCell at the TimePoint 1. And the 3D viewer is updated. Now this sphere was pasted at the TimePoint 1, why ? Because LimeSeg has an active or a current frame parameter which is 1 by default. The active timepoint current frame is actually another parameter that can be set within LimeSeg. It Its current value is written in frame displayed in the lower panel of LimeSeg GUI lower panel. To change this parameter, go to the STATE tab and in front of the setCurrentFrame button, type 10 for instance. Now click the '''setCurrentFrame''' button. The active frame is now 10. If you now reclick click again on '''pasteDotsToCellT''', the clipped dots (i.e. the sphere) are pasted are the timepoint 10of the current Cell.
3. Deleting a Cell Timpepoint (CellT object)
==== Deleting a Cell ====
As an example, we will delete the newly created Cell '''cell_0'''. First of all, you need to set the cell that you want to delete as the '''currentCell''' of LimeSeg. To do this, several options are possible Click in the tab '''Current Cell''' the button '''clearCurrentCell'''
image sample , and the corresponding segmented
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