Révision 31

lsm3D_compile.sh (revision 31)
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#! /bin/bash
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# 1. Choose an appropriate C++ compiler, that supports OpenMP.


  		





  
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# ============================================================


  		





  
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# For Linux (Default choice):


  		





  
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# --------------------------


  		





  
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CCPP='g++'


  		





  
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# For MacOS X:


  		





  
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# ---------------------------


  		





  
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#CCPP='g++-mp-6'


  		





  
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#CCPP='clang++'  


  		





  
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#CCPP='gcc-4.6'


  		





  
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#For Windows:


  		





  
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# -----------------


  		





  
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# 2. Compiling options, including link to X11 library


  		





  
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# ====================================================


  		





  
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compiling_options='-O2 -lm -lpthread -lX11 -I/usr/X11R6/include -L/usr/X11R6/lib -L/opt/X11/lib -I/opt/X11/include'


  		





  
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# 3. Path to binaries


  		





  
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# ====================


  		





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bin_directory='../bin'


  		





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compiling_options=' -O2 -lm -lpthread -lX11 -I/usr/X11R6/include -L/usr/X11R6/lib -L/opt/X11/lib -I/opt/X11/include'


  		





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# 4. Compile


  		





  
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# ==========


  		





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cd src


  		





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echo '------------------------------------'


  		





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echo 'compiling lsm_contour...'


  		





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g++ -o $bin_directory/lsm_contour lsm_contour.cpp $compiling_options


  		





  
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$CCPP -o $bin_directory/lsm_contour lsm_contour.cpp $compiling_options


  		





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echo 'compiling lsm_cells...'


  		





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g++ -o $bin_directory/lsm_cells lsm_cells.cpp $compiling_options -fopenmp


  		





  
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$CCPP -o $bin_directory/lsm_cells lsm_cells.cpp $compiling_options -fopenmp 


  		





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echo 'Done!'


  		





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cd ..


  		












  

    
      README_LSM.txt	(revision 31)
    
  






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Typhaine Moreau, Annamaria Kiss (Laboratoire RDP, ENS Lyon)


  		





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----------------------------------------------------------------------


  		





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The "lsm3d" tools


  		





  
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-----------------


  		





  
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- lsm_contour --> detects the outer surface of the tissue


  		





  
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- lsm_cells --> used to cellular segmentation or nuclei detection


  		





  
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Dependencies


  		





  
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-------------


  		





  
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The levelset tools make use of the CImg image processing C++ library, which in turn needs Xlib library.


  		





  
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Furthermore, the lsm_cells tool is parallelized using OpenMP.


  		





  
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In particular, if you do not have Xlib on your computer, you may add it:


  		





  
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- on Ubuntu:


  		





  
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    sudo apt-get install libx11-dev


  		





  
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- on MacOS X:


  		





  
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    install xQuartz from www.xquartz.org


  		





  
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Download


  		





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--------


  		





  
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In a terminal go to the directory where you wish to download and install the tool


  		





  
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cd Path_to_your_directory


  		





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svn --username $USER checkout http://forge.cbp.ens-lyon.fr/svn/levelsetmethod/lsm3D


  		





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Compile


  		





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cd lsm3D


  		





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./lsm3D_compile.sh


  		





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Troubleshooting if problems with compilation :


  		





  
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In lsm3D_compile.sh


  		





  
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- you might have to choose an appropriate compiler, which supports OpenMP.


  		





  
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- you might need to precise the location of the X11 library in the compilation options.


  		





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The following binaries will be generated in the bin directory :


  		





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--------------------------------------------------------------


  		





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- lsm_contour --> detects the outer surface of the tissue


  		





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**** lsm_contour --> detects the outer surface of the tissue


  		





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-------------------------------------------------------


  		





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Usage : lsm_detect_contour img t_up t_down a b smooth perUp perDown


  		





  
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Usage : lsm_contour img t_up t_down a b smooth perUp perDown


  		





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Examples for parameter values:


  		





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------------------------------


  		





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img : grayscale image of cells, (.inr or .inr.gz)


  		





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Test :


  		





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------


  		





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lsm_detect_contour t3_cut.inr.gz 20 10 0 0 1 0.002 -0.002


  		





  
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lsm_detect_contour sample-stack.inr.gz 20 10 0 0 1 0.002 -0.002


  		





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**** lsm_cells --> for cellular segmentation or nuclei detection


  		





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Test :


  		





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------


  		





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lsm_cells t3_cut.inr.gz t3_cut_wat.inr.gz t3_cut_LSMcont20-10a0b0s1/t3_cut_LSMcont20-10a0b0s1.inr.gz 2 0.3 0 0.2 1 'h'


  		





  
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lsm_cells sample-satck.inr.gz sample-satck-wat.inr.gz 'None' 2 0.3 0 0.2 1 'h'


  		





  
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or


  		





  
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lsm_cells sample-satck.inr.gz sample-satck-wat.inr.gz sample-satck_LSMcont20-10a0b0s1/sample-satck_LSMcont20-10a0b0s1.inr.gz 2 0.3 0 0.2 1 'h'


  		





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