| Geant4 Cross Reference |
1 ================================
2 Geant4 - cellularPhantom example
3 ================================
4
5 README file
6 --------------------
7
8 Authors and contribut
9
10 P. Barberet, S. Incerti, N. H. Tran, L. Morell
11 LP2i, IN2P3 / CNRS / Bordeaux University, 3317
12 E-mail: barberet@lp2ib.in2p3.fr or incerti@lp2
13
14 If you use this code, please cite the followin
15 Monte-Carlo dosimetry on a realistic cell mono
16 P. Barberet, F. Vianna, M. Karamitros, T. Brun
17 Phys. Med. Biol. 57 (2012) 2189-2207
18 https://doi.org/10.1088/0031-9155/57/8/2189
19
20 ---->0. INTRODUCTION
21
22 The cellularPhantom example shows how to simul
23 phantom containing biological cells, created f
24
25 The original image was created thanks to:
26 - H. De Oliveira, T. Désigaux, N. Dusserre, A
27 - F. Paris, C. Niaudet, Inserm, France
28
29 These developments were carried out as part of
30 (2023-2024) funded by CNRS-MITI, France, and I
31
32 Two phantom files phantom.dat (low resolution)
33 are provided in the phantoms directory.
34
35 They were created using the ImageJ phantom.ijm
36 See the phantoms/Documentation.pdf file for mo
37
38 The low resolution file is used for visualizat
39 It contains the following lines:
40
41 54300 20230 17320 16750
42 => total number of voxels, number of red, gree
43
44 734.0507 734.0507 90.6372 micron
45 => whole X, Y and Z size of the phantom, with
46
47 2.8674 2.8674 2.0142 microns
48 => size of a single voxel, with unit
49
50 And the list of individual voxels, with the fo
51 (type is 1 for R, 2 for G, 3 for B):
52 232.2582 31.5412 0.0000
53 235.1256 31.5412 0.0000
54 ...
55
56 The low resolution and high resolution files c
57
58 ---->1. GEOMETRY SET-UP
59
60 The geometry is a 1-mm side cube ("World") mad
61 containing a liquid water medium ("Medium") of
62 containing itself the phantom ("Phantom").
63
64 The World and Medium dimensions can be changed
65
66 ---->2. SET-UP
67
68 Make sure $G4LEDATA points to the low energy e
69
70 ---->3. HOW TO RUN THE EXAMPLE
71
72 In interactive mode, run:
73 ./cellularPhantom
74 this will show the phantom in 3D (requires mem
75
76 In batch, the macro run.mac can be used:
77 ./cellularPhantom run.mac
78
79 In this macro, the user can select:
80 - the number of threads (MT mode)
81 - the phantom file name
82 - the World and Medium dimensions
83 - the Medium material
84 - the phantom voxel density
85 - the position (shift in X or Y or Z) of the p
86 - the production cuts outside and inside in th
87 - the incident particles (using GPS)
88
89 ---->4. PHYSICS
90
91 The PhysicsList class uses Geant4 option4 elec
92
93 It also contains other physics lists including
94 which is commented by default.
95
96 ---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
97
98 The output results consists in a phantom.root
99 corresponding to the 3 types of voxels (red, g
100
101 The ROOT macro plot.C can be run to extract an
102 - the cellular phantom
103 - the absorbed energy distribution in the 3 ty
104 - the absorbed energy 2D map for the 3 types o
105 - the absorbed dose 2D map for the 3 types of
106
107 Simply do, after the simulation:
108 root plot.C
109
110 In addition, the following quantities are disp
111 - total number of voxels in phantom
112 - total number of RED voxels in phantom
113 - total number of GREEN voxels in phantom
114 - total number of BLUE voxels in phantom
115 - total absorbed energy in RED voxels (MeV)
116 - total absorbed energy in GREEN voxels (MeV)
117 - total absorbed energy in BLUE voxels (MeV)
118 - total absorbed dose in RED voxels (Gy)
119 - total absorbed dose in GREEN voxels (Gy)
120 - total absorbed dose in BLUE voxels (Gy)
121
122 Results are stored in the results.root file.