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LimeSeg

26 bytes added, 16:32, 19 January 2018
Advanced usage
=== Stopping a segmentation in progress ===
* Command '''Plugins>LimeSeg>Stop optimization'''
 
== LimeSeg 3D Viewer (basic) ==
So far LimeSeg provides its own 3D vizualizer. The 3D viewer looks at a specific point in 3D. Mouse dragging allows to rotate around this point. Zoom/zoom out can be done with the mouse wheel.
= Advanced usage=
== LimeSeg architecture ==
== Graphical user interface ==
The command Plugins>LimeSeg> Show GUI displays LimeSeg GUI. This graphical interface allows to do almost almost everything in LimeSeg, however its structure needs to understand a bit more the core structure of LimeSeg. Each tab provided on the left of LimeSeg correspond to specific actions that will be detailed below, but before the structure of LimeSeg will be developed.
 
LimeSeg mainly consists of:
* A "State"
2. A current frame, (LimeSeg.currentFrame)
3. A current channel, (LimeSeg.currentChannel)
, however its structure needs to understand a bit more the core structure of LimeSeg. Each tab provided on the left of LimeSeg correspond to specific actions that will be detailed below, but before the structure of LimeSeg will be developed.
 
== Groovy Scripting LimeSeg groovy scripting with examples ==
TODO
== Graphical user interface ==
The command '''Plugins>LimeSeg> Show GUI''' displays LimeSeg GUI. This graphical interface allows to do almost almost everything in LimeSeg.
     == LimeSeg 3D Viewer (advanced) ==So far LimeSeg provides its own 3D vizualizer. In LimeSeg GUI, several options are available for the 3D Viewer. The 3D view can be moved with arrows, rotated with mouse dragging, and zoomed/unzoomed with the mouse wheel.
* Image synchronization
First of all, the LimeSeg 3D viewer is synchronized with a selected ImageJ imagethe workingImage of LimeSeg state. This image is automatically set by the user selection during a command launch. However, it can also be set with LimeSeg GUI (Plugins>within the LimeSeg>Show GUI). To select this image, go to the STATE tab, then choose the proper image by clicking on img, then click on "setWorkingImage" button (do not forget this, otherwise the image selection has no effect).
The synchronization occurs since the current slice is highlighted (downlighted...) in the 3D view in synchronization with the selected slice in the 2D view. Also change frame will change the 3D object displayed in case of a multiframe image.
== 3D objects handling in LimeSeg ==
 
Each time a command is performed which is generating objects, these objects are stored within a global array variable (LimeSeg.allCells). Manipulation of these objects with LimeSeg commands is very basic (they can all be erased with clear all command, or the last created objects can be erased with the cancel last optimization command).
== Groovy scripting : advanced usage ==
 
[TODO]
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