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14:57, 21 January 2018
LimeSeg optimizer usage
=== LimeSeg optimizer usage ===
To allow for a proper usage of LimeSeg optimizer, the way it can function is modular.
To make it work without commands, here are the steps that should be followed:
* Select the 3D image to work with:
** STATE tab > Select the image with the Img: button then click on setWorkingImage
** Choose the correct Timepoint with setCurrentFrame button
** Choose the correct Channel with the setCurrentChannel button
* Set the ratio of Z spacing versus XY spacing. ( For instance 5 for 200 nm per pixel and 1 um per slice).
** Goto the Otimizer tab.
** In the first right box next to setOptimizerParameter, put 'Z_scale'
** In the second, put the correct numeric parameter (1 for isotropic acquisition)
** Click the setOptimizerParameter button (compulsory)
We now suppose that you already have created 3D objects that you want to optimize. Object creation is succintly explained in 3D object manipulation section.
* Now the optimizer knows which image it should use, but there are no 3D objects into it. 3D Objects are called CellT objects in LimeSeg (for cell timepoint). To add such objects into the optimizer, you need, for each object you want to put in:
** Set the current or active Cell as the one you want to use
** Set the current Frame parameter you are working
** Go to the Current CellT tab, and click 'putCurrentCellTToOptimizer
** Notice in the GUI down panel, the number of dots in Optimizer #dots: should increase
* You now need to run the optimizer
** In the Optimizer tab, set the number of optimization step you want to perform (-1 means until convergence), then click '''runOptimisation'''
=== LimeSeg I/O ===
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