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LimeSeg

505 bytes added, 20:40, 21 January 2018
LimeSeg I/O
3D objects generated by LimeSeg can be saved and retrieved. The structure choice was done with several convention that LimeSeg uses, in order to simplify objects manipulation outside of FIJI.
TODOIf you download and unzip the sample file https://raw.githubusercontent.com/NicoKiaru/TestImages/master/LimeSegOutput/DubSeg.zip, you will see that the folder contains an xml file which contains the last segmentation parameters (LimeSegParams.xml) and one folder per Cell object. In each folder, named according to the Cell id object, a CellParams.xml file contains the parameters specific to the Cell object, and CellT objects (Cell at a specific timepoint), consists of files T_x.ply where x is the timepoint number and where ply is the standard 3D format used. [https://en.wikipedia.org/wiki/PLY_(file_format) PLY] file format is standard and can be used in many other 3D software.
To save the current objects of LimeSeg, choose an EMPTY folder in LimeSeg GUI I/O Tab, with the button '''WriteTo:''', then click on the '''saveStateToXmlPly ''' button.
  The "State" of LimeSeg basically represents on which 3D image LimeSeg is currently working on. It consists of :1. A working imageTo open previously saved data, which can be set within State>setWorkingImage2. A current frame, (LimeSeg.currentFrame)3. A current channel, (LimeSeg.currentChannel), however its structure needs to understand a bit more select the folder with the core structure of LimeSegLoadFrom: button then click loadStateFromXmlPly button. Each tab provided on the left of LimeSeg correspond to specific actions that will be detailed below, but before the structure of This erases all previous data contained in LimeSeg will be developed.
== LimeSeg groovy scripting with examples ==
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