Laboratoire RDP » Biophysics Team » lsm3d

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			   Level Set Methods (LSM)

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Methods to improve image segmentation

Images are save in .inr.gz

**** 1 : lsm to detect the exterior contour           image -> contour

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Standard version = ./lsm_contour.exe image t_up t_down beta smooth

		 image : grayscale, 8bit, .inr or .inr.gz

		 t_up, t_down : linear threshold (int)

		 beta : curvature term (0:none)

		 smooth  : amount of gaussian blur (float)

		 source code : lsm_detect_contour.cpp

Change stop criteria = ./lsm_contour_SC.exe image t_up t_down beta smooth perUp perDown

		     every iteration, the percentage of background growth is measure

		     the algorithm stop after 10 succesive iterations between perDown and perUp

		     in the standart version perUp=0.002 and perDown=-0.002

		     source code : lsm_detect_contour_stopCriteria.cpp

Start with a contour = ./lsm_start.exe image contour beta smooth

		     contour : binary image with background=1

		     .inr or .inr.gz

		     source code : lsm_detect_startContour.cpp

**** 2 : improved watershed on                         image + contour -> watershed

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./segmentation_amelioration.py image contour

**** 3 : lsm to detect cells                           image + contour + watershed -> segmentation

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Standard version = ./lsm_cells.exe image wat contour erosion

	 	 image : grayscale, 8bit, .inr or .inr.gz

		 wat : 16bit, .inr or .inr.gz

		 contour : binary with background=1

		 erosion : amount of erosion for each cell (int)

		 source code : lsm_cells_para.cpp

Only do a list of cells = ./lsm_cells_list.exe image wat contour erosion list

     	       	  	list : .txt file with one number per row

			number = cell label on watershed

			source code : lsm_cells_para_list.cpp

			keep watershed for other cells

Restart at the final step = ./lsm_cells_step.exe image evoEdge contour

	       	     	  evoEdge : 2nd step from standart lsm_cells

			  source code : lsm_cells_para_finalstep.cpp

Change curvature terms = ./lsm_cells_beta.exe image wat contour erosion beta betabis

       		       beta : curvature term for the 2nd step (evoEdge)

		       betabis : curvature term for the final step

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         Known issues

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 Fiji is not able to read correctly the 16 bits watershed images : the labels are wrong

  You can use "./display.exe image" to visualize the result correctly

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C++ version implement by Typhaine Moreau based on the work of Annamaria Kiss