root / README_LSM.txt @ 3
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| 1 | 1 | akiss | ---------------------------------------------------------------------- |
|---|---|---|---|
| 2 | 1 | akiss | - lsm3d - |
| 3 | 1 | akiss | Tools for segmenting 3D images of plant tissues |
| 4 | 1 | akiss | at multiple scales using the level set method¶ |
| 5 | 1 | akiss | ---------------------------------------------------------------------- |
| 6 | 1 | akiss | Copyright 2016 ENS de Lyon, see accompanying file LICENSE.txt |
| 7 | 1 | akiss | |
| 8 | 1 | akiss | Authors : |
| 9 | 1 | akiss | Typhaine Moreau, Annamaria Kiss <annamaria.kiss@ens-lyon.fr.fr> |
| 10 | 1 | akiss | (Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France) |
| 11 | 1 | akiss | ---------------------------------------------------------------------- |
| 12 | 1 | akiss | |
| 13 | 1 | akiss | The "lsm3d" tools |
| 14 | 1 | akiss | ----------------- |
| 15 | 1 | akiss | - lsm_contour --> detects the outer surface of the tissue |
| 16 | 1 | akiss | - lsm_cells --> used to cellular segmentation or nuclei detection |
| 17 | 1 | akiss | |
| 18 | 1 | akiss | Dependencies |
| 19 | 1 | akiss | ------------- |
| 20 | 1 | akiss | The levelset tools make use of the CImg image processing C++ library, which in turn needs Xlib library. |
| 21 | 1 | akiss | Furthermore, the lsm_cells tool is parallelized using OpenMP. |
| 22 | 1 | akiss | |
| 23 | 1 | akiss | In particular, if you do not have Xlib on your computer, you may add it: |
| 24 | 1 | akiss | - on Ubuntu: |
| 25 | 1 | akiss | sudo apt-get install libx11-dev |
| 26 | 1 | akiss | - on MacOS X: |
| 27 | 1 | akiss | install xQuartz from www.xquartz.org |
| 28 | 1 | akiss | |
| 29 | 1 | akiss | Download |
| 30 | 1 | akiss | -------- |
| 31 | 1 | akiss | In a terminal go to the directory where you wish to download and install the tool |
| 32 | 1 | akiss | cd Path_to_your_directory |
| 33 | 1 | akiss | svn checkout http://forge.cbp.ens-lyon.fr/svn/lsm3d |
| 34 | 1 | akiss | |
| 35 | 1 | akiss | Compile |
| 36 | 1 | akiss | -------- |
| 37 | 3 | akiss | cd lsm3d |
| 38 | 3 | akiss | ./lsm3d_compile.sh |
| 39 | 1 | akiss | |
| 40 | 1 | akiss | Troubleshooting if problems with compilation : |
| 41 | 3 | akiss | In lsm3d_compile.sh |
| 42 | 1 | akiss | - you might have to choose an appropriate compiler, which supports OpenMP. |
| 43 | 1 | akiss | - you might need to precise the location of the X11 library in the compilation options. |
| 44 | 1 | akiss | |
| 45 | 1 | akiss | |
| 46 | 1 | akiss | The following binaries will be generated in the bin directory : |
| 47 | 1 | akiss | -------------------------------------------------------------- |
| 48 | 1 | akiss | - lsm_contour --> detects the outer surface of the tissue |
| 49 | 1 | akiss | - lsm_cells --> used to cellular segmentation or nuclei detection |
| 50 | 1 | akiss | |
| 51 | 1 | akiss | |
| 52 | 1 | akiss | **** lsm_contour --> detects the outer surface of the tissue |
| 53 | 1 | akiss | ------------------------------------------------------- |
| 54 | 1 | akiss | |
| 55 | 1 | akiss | Usage : lsm_contour img t_up t_down a b smooth perUp perDown |
| 56 | 1 | akiss | Examples for parameter values: |
| 57 | 1 | akiss | ------------------------------ |
| 58 | 1 | akiss | img : grayscale image of cells, (.inr or .inr.gz) |
| 59 | 1 | akiss | Upper threshold : t_up = 20 |
| 60 | 1 | akiss | Down threshold : t_down = 5 |
| 61 | 1 | akiss | Area term : a = 0 (0.5, 1) |
| 62 | 1 | akiss | Curvature term : b = 0 (1) |
| 63 | 1 | akiss | Gaussian filter : smooth = 1 (0, if image already filtered) |
| 64 | 1 | akiss | Stop criteria : the contour evolution is in [perDown,perUp] for 10 consecutive iterations |
| 65 | 1 | akiss | perUp = 0.002, perDown = -0.002 |
| 66 | 1 | akiss | |
| 67 | 1 | akiss | Test : |
| 68 | 1 | akiss | ------ |
| 69 | 1 | akiss | lsm_detect_contour sample-stack.inr.gz 20 10 0 0 1 0.002 -0.002 |
| 70 | 1 | akiss | |
| 71 | 1 | akiss | |
| 72 | 1 | akiss | **** lsm_cells --> for cellular segmentation or nuclei detection |
| 73 | 1 | akiss | ------------------------------------------------------------- |
| 74 | 1 | akiss | |
| 75 | 1 | akiss | Usage : lsm_cells img img_wat img_contour erosion [a b smooth lsm_type] |
| 76 | 1 | akiss | ----------------- |
| 77 | 1 | akiss | img : grayscale image of cells, (.inr or .inr.gz) |
| 78 | 1 | akiss | img_wat : image of seeds, (.inr or .inr.gz) |
| 79 | 1 | akiss | img_contour : mask, where cells do not evolve, (.inr or .inr.gz) |
| 80 | 1 | akiss | if 'None', then cells can evolve on the whole image |
| 81 | 1 | akiss | erosion : amount of erosion of seeds for initialisation (uint8) --> -2, 0, 2 |
| 82 | 1 | akiss | if 0, then no erosion or dilation |
| 83 | 1 | akiss | if negative, then a dilation is performed |
| 84 | 1 | akiss | a : area term (float) --> 0 or 0.5 or 1 (the default is 0.5) |
| 85 | 1 | akiss | if negative, the object retracts |
| 86 | 1 | akiss | if positive, the object inflates |
| 87 | 1 | akiss | b : curvature term (float) --> 0 or 1 (the default is 0) |
| 88 | 1 | akiss | gamma : scale parameter (float>0) --> 0.5 or 1 (the default is 1) |
| 89 | 1 | akiss | smooth : gaussian blur to apply to the image (int) --> 0 or 1 (the default is 0) |
| 90 | 1 | akiss | lsm_type : image, gradient or hessien based evolution --> 'i', 'g' or 'h' (the default is g) |
| 91 | 1 | akiss | |
| 92 | 1 | akiss | Test : |
| 93 | 1 | akiss | ------ |
| 94 | 1 | akiss | lsm_cells sample-satck.inr.gz sample-satck-wat.inr.gz 'None' 2 0.3 0 0.2 1 'h' |
| 95 | 1 | akiss | or |
| 96 | 1 | akiss | 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' |
| 97 | 1 | akiss |