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Geant4/examples/advanced/dna/cellularPhantom/README

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  1 ================================
  2 Geant4 - cellularPhantom example
  3 ================================
  4 
  5                                 README file
  6                           ----------------------
  7 
  8                          Authors and contributors:
  9 
 10 P. Barberet, S. Incerti, N. H. Tran, L. Morelli
 11 LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France
 12 E-mail: barberet@lp2ib.in2p3.fr or incerti@lp2ib.in2p3.fr
 13 
 14 If you use this code, please cite the following publication:
 15 Monte-Carlo dosimetry on a realistic cell monolayer geometry exposed to alpha-particle,
 16 P. Barberet, F. Vianna, M. Karamitros, T. Brun, N. Gordillo, P. Moretto, S. Incerti, H. Seznec,
 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 simulate the irradiation of a 3D voxel
 23 phantom containing biological cells, created from a confocal microscopy 24-bit RGB image.
 24 
 25 The original image was created thanks to:
 26 - H. De Oliveira, T. Désigaux, N. Dusserre, ART BioPrint, France
 27 - F. Paris, C. Niaudet, Inserm, France
 28 
 29 These developments were carried out as part of the "Flash'Atlantic" project
 30 (2023-2024) funded by CNRS-MITI, France, and Inserm, France.
 31 
 32 Two phantom files phantom.dat (low resolution) and phantomHR.dat (high resolution)
 33 are provided in the phantoms directory.
 34 
 35 They were created using the ImageJ phantom.ijm macro located in the ImageJ directory.
 36 See the phantoms/Documentation.pdf file for more information
 37 
 38 The low resolution file is used for visualization in the macro vis.mac.
 39 It contains the following lines:
 40 
 41 54300   20230   17320   16750
 42 => total number of voxels, number of red, green and blue voxels
 43 
 44 734.0507        734.0507        90.6372 microns
 45 => whole X, Y and Z size of the phantom, with unit
 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 format: X, Y and Z positions, type
 51 (type is 1 for R, 2 for G, 3 for B):
 52 232.2582        31.5412         0.0000          2
 53 235.1256        31.5412         0.0000          2
 54 ...
 55 
 56 The low resolution and high resolution files can be used by the run.mac macro.
 57 
 58 ---->1. GEOMETRY SET-UP
 59 
 60 The geometry is a 1-mm side cube ("World") made of air, with a thickness of 100 um,
 61 containing a liquid water medium ("Medium") of side 900 um and thickness 95 um,
 62 containing itself the phantom ("Phantom").
 63 
 64 The World and Medium dimensions can be changed by UI command.
 65 
 66 ---->2. SET-UP
 67 
 68 Make sure $G4LEDATA points to the low energy electromagnetic data files.
 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 memory).
 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 phantom in the Medium
 86 - the production cuts outside and inside in the phantom
 87 - the incident particles (using GPS)
 88 
 89 ---->4. PHYSICS
 90 
 91 The PhysicsList class uses Geant4 option4 electromagnetic physics.
 92 
 93 It also contains other physics lists including Geant4-DNA option2,
 94 which is commented by default.
 95 
 96 ---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
 97 
 98 The output results consists in a phantom.root file, containing three ntuples,
 99 corresponding to the 3 types of voxels (red, green and blue) of the original image.
100 
101 The ROOT macro plot.C can be run to extract and display:
102 - the cellular phantom
103 - the absorbed energy distribution in the 3 types of voxels
104 - the absorbed energy 2D map for the 3 types of voxels
105 - the absorbed dose 2D map for the 3 types of voxels
106 
107 Simply do, after the simulation:
108 root plot.C
109 
110 In addition, the following quantities are displayed:
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.