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.
The lower part contains information about LimeSeg state.
Adds image lower part]]
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 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 ====
1. Creating a sphere
Go to the '''Clipped Dots''' tab
, at the right of the makeSphere button, fill in the 4 white boxes. They correspond to the centre of the sphere (x,y,z coordinate in slice number, radius). All units except z are in pixels. 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 ? The
active timepoint is actually another parameter that can be set within LimeSeg. It is written in frame in LimeSeg GUI lower panel. To change this parameter, go to STATE tab and in front of the setCurrentFrame button, type 10 for instance. Now click the '''setCurrentFrame''' button. If you now reclick '''pasteDotsToCellT''', the clipped dots are pasted are the timepoint 10.
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
image sample , and the corresponding segmented