Révision 26 README_LSM.txt
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Level Set Methods (LSM) |
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- lsm3d - |
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Tools for segmenting 3D images of plant tissues |
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at multiple scales using the level set method¶ |
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Methods to improve image segmentation |
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Images are save in .inr.gz |
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**** 1 : lsm to detect the exterior contour image -> contour |
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Download |
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-------- |
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svn --username $USER checkout http://forge.cbp.ens-lyon.fr/svn/levelsetmethod/lsm3D |
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Standard version = ./lsm_contour.exe image t_up t_down beta smooth |
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image : grayscale, 8bit, .inr or .inr.gz |
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t_up, t_down : linear threshold (int) |
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beta : curvature term (0:none) |
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smooth : amount of gaussian blur (float) |
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source code : lsm_detect_contour.cpp |
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Compile |
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-------- |
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cd lsm3D |
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./lsm3D_compile.sh |
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Change stop criteria = ./lsm_contour_SC.exe image t_up t_down beta smooth perUp perDown |
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every iteration, the percentage of background growth is measure |
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the algorithm stop after 10 succesive iterations between perDown and perUp |
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in the standart version perUp=0.002 and perDown=-0.002 |
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source code : lsm_detect_contour_stopCriteria.cpp |
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Start with a contour = ./lsm_start.exe image contour beta smooth
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contour : binary image with background=1
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.inr or .inr.gz
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source code : lsm_detect_startContour.cpp
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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_cells --> used to cellular segmentation or nuclei detection
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**** 2 : improved watershed on image + contour -> watershed |
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**** lsm_contour --> detects the outer surface of the tissue |
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./segmentation_amelioration.py image contour |
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Usage : lsm_detect_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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Upper threshold : t_up = 20 |
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Down threshold : t_down = 5 |
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Area term : a = 0 (0.5, 1) |
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Curvature term : b = 0 (1) |
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Gaussian filter : smooth = 1 (0, if image already filtered) |
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Stop criteria : the contour evolution is in [perDown,perUp] for 10 consecutive iterations |
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perUp = 0.002, perDown = -0.002 |
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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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**** 3 : lsm to detect cells image + contour + watershed -> segmentation |
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------------------------------------------------------- |
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Standard version = ./lsm_cells.exe image wat contour erosion |
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image : grayscale, 8bit, .inr or .inr.gz |
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wat : 16bit, .inr or .inr.gz |
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contour : binary with background=1 |
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erosion : amount of erosion for each cell (int) |
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source code : lsm_cells_para.cpp |
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**** lsm_cells --> for cellular segmentation or nuclei detection |
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Only do a list of cells = ./lsm_cells_list.exe image wat contour erosion list |
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list : .txt file with one number per row |
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number = cell label on watershed |
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source code : lsm_cells_para_list.cpp |
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keep watershed for other cells |
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Usage : lsm_cells img img_wat img_contour erosion [a b smooth lsm_type] |
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----------------- |
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img : grayscale image of cells, (.inr or .inr.gz) |
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img_wat : image of seeds, (.inr or .inr.gz) |
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img_contour : mask, where cells do not evolve, (.inr or .inr.gz) |
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if 'None', then cells can evolve on the whole image |
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erosion : amount of erosion of seeds for initialisation (uint8) --> -2, 0, 2 |
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if 0, then no erosion or dilation |
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if negative, then a dilation is performed |
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a : area term (float) --> 0 or 0.5 or 1 (the default is 0.5) |
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if negative, the object retracts |
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if positive, the object inflates |
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b : curvature term (float) --> 0 or 1 (the default is 0) |
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gamma : scale parameter (float>0) --> 0.5 or 1 (the default is 1) |
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smooth : gaussian blur to apply to the image (int) --> 0 or 1 (the default is 0) |
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lsm_type : image, gradient or hessien based evolution --> 'i', 'g' or 'h' (the default is g) |
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Restart at the final step = ./lsm_cells_step.exe image evoEdge contour
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evoEdge : 2nd step from standart lsm_cells
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source code : lsm_cells_para_finalstep.cpp
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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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Change curvature terms = ./lsm_cells_beta.exe image wat contour erosion beta betabis |
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beta : curvature term for the 2nd step (evoEdge) |
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betabis : curvature term for the final step |
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Known issues |
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----------------------------------------------------------- |
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Fiji is not able to read correctly the 16 bits watershed images : the labels are wrong |
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You can use "./display.exe image" to visualize the result correctly |
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------------------------------------------------------------ |
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C++ version implement by Typhaine Moreau based on the work of Annamaria Kiss |
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C++ version implemented by Typhaine Moreau based on the work of Annamaria Kiss |
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Formats disponibles : Unified diff