Révision 31 README_LSM.txt
| README_LSM.txt (revision 31) | ||
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Typhaine Moreau, Annamaria Kiss (Laboratoire RDP, ENS Lyon) |
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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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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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Formats disponibles : Unified diff