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LimeSeg

55 bytes added, 16:23, 19 January 2018
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=== Single object segmentation ======= Sphere Seg command ====
The command Sphere Seg ('''Plugins>LimeSeg>Sphere Seg''') is the easiest way to use LimeSeg. It allows to segment a 3D object starting from a spherical seed. Here's an example to show how to use it:
* "the segmentation goes crazy and I'd like to stop it". You can either execute the command '''Plugins>LimeSeg>Stop Optimisation''', or you can set a value different from -1 in the number of optimisation steps parameter (10000 steps is enough for this demo case).
==== Refining a segmentation result ====
It is possible to refine a segmentation by decreasing D_0 after a first roughly defined shape is found. Doing a first segmentation at a high D_0 and then decreasing it by refinement is usually faster than starting the segmentation at a low D_0 value. This can be done after a first segmentation by using the '''Plugins>LimeSeg>Coarsen/Refine''' command.
[[File:LimeSeg_2D3DViews_Refined_Vesicle.png]]
==== Alternative ways to segment a single object: multiple spheres and skeletons ====
If the object you want to segment is tortuous or big, starting with a single spherical may not give good results. Here are two alternative ways to segment a single object.
[[File:LimeSeg_CElegans_Global.png]]
=== Multiple objects segmentation ===
It is possible to segment multiple non overlapping objects with LimeSeg. The most basic way to do this is through the Sphere Seg command. In order too to an example, you can open the test image fo C Elegans with File>Import>URL..
The output table also displays the surface and volume of the segmented cells.
=== Others commands ======= Cancelling a segmentation result ====
To cancel the last launched segmentation command, you can launch the command : '''Plugins > LimeSeg > Cancel Last Optimisation'''
The segmentation needs to be stopped before applying this command.
==== Clearing all segmented objects ====
* launch the command : '''Plugins > LimeSeg > Clear all'''
Should be used cautiously : this erases all objects segmented by LimeSeg so far.
==== Stopping a segmentation in progress ====
* Command '''Plugins>LimeSeg>Stop optimization'''
= 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.
3. A current channel, (LimeSeg.currentChannel)
== Groovy Scripting ==
TODO
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