Warning, /geant4/examples/advanced/dna/cellularPhantom/README is written in an unsupported language. File is not indexed.
0001 ================================
0002 Geant4 - cellularPhantom example
0003 ================================
0004
0005 README file
0006 ----------------------
0007
0008 Authors and contributors:
0009
0010 P. Barberet, S. Incerti, N. H. Tran, L. Morelli
0011 LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France
0012 E-mail: barberet@lp2ib.in2p3.fr or incerti@lp2ib.in2p3.fr
0013
0014 If you use this code, please cite the following publication:
0015 Monte-Carlo dosimetry on a realistic cell monolayer geometry exposed to alpha-particle,
0016 P. Barberet, F. Vianna, M. Karamitros, T. Brun, N. Gordillo, P. Moretto, S. Incerti, H. Seznec,
0017 Phys. Med. Biol. 57 (2012) 2189-2207
0018 https://doi.org/10.1088/0031-9155/57/8/2189
0019
0020 ---->0. INTRODUCTION
0021
0022 The cellularPhantom example shows how to simulate the irradiation of a 3D voxel
0023 phantom containing biological cells, created from a confocal microscopy 24-bit RGB image.
0024
0025 The original image was created thanks to:
0026 - H. De Oliveira, T. Désigaux, N. Dusserre, ART BioPrint, France
0027 - F. Paris, C. Niaudet, Inserm, France
0028
0029 These developments were carried out as part of the "Flash'Atlantic" project
0030 (2023-2024) funded by CNRS-MITI, France, and Inserm, France.
0031
0032 Two phantom files phantom.dat (low resolution) and phantomHR.dat (high resolution)
0033 are provided in the phantoms directory.
0034
0035 They were created using the ImageJ phantom.ijm macro located in the ImageJ directory.
0036 See the phantoms/Documentation.pdf file for more information
0037
0038 The low resolution file is used for visualization in the macro vis.mac.
0039 It contains the following lines:
0040
0041 54300 20230 17320 16750
0042 => total number of voxels, number of red, green and blue voxels
0043
0044 734.0507 734.0507 90.6372 microns
0045 => whole X, Y and Z size of the phantom, with unit
0046
0047 2.8674 2.8674 2.0142 microns
0048 => size of a single voxel, with unit
0049
0050 And the list of individual voxels, with the format: X, Y and Z positions, type
0051 (type is 1 for R, 2 for G, 3 for B):
0052 232.2582 31.5412 0.0000 2
0053 235.1256 31.5412 0.0000 2
0054 ...
0055
0056 The low resolution and high resolution files can be used by the run.mac macro.
0057
0058 ---->1. GEOMETRY SET-UP
0059
0060 The geometry is a 1-mm side cube ("World") made of air, with a thickness of 100 um,
0061 containing a liquid water medium ("Medium") of side 900 um and thickness 95 um,
0062 containing itself the phantom ("Phantom").
0063
0064 The World and Medium dimensions can be changed by UI command.
0065
0066 ---->2. SET-UP
0067
0068 Make sure $G4LEDATA points to the low energy electromagnetic data files.
0069
0070 ---->3. HOW TO RUN THE EXAMPLE
0071
0072 In interactive mode, run:
0073 ./cellularPhantom
0074 this will show the phantom in 3D (requires memory).
0075
0076 In batch, the macro run.mac can be used:
0077 ./cellularPhantom run.mac
0078
0079 In this macro, the user can select:
0080 - the number of threads (MT mode)
0081 - the phantom file name
0082 - the World and Medium dimensions
0083 - the Medium material
0084 - the phantom voxel density
0085 - the position (shift in X or Y or Z) of the phantom in the Medium
0086 - the production cuts outside and inside in the phantom
0087 - the incident particles (using GPS)
0088
0089 ---->4. PHYSICS
0090
0091 The PhysicsList class uses Geant4 option4 electromagnetic physics.
0092
0093 It also contains other physics lists including Geant4-DNA option2,
0094 which is commented by default.
0095
0096 ---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
0097
0098 The following results are displayed at the end of the simulation:
0099 - total number of voxels in phantom
0100 - total number of RED voxels in phantom
0101 - total number of GREEN voxels in phantom
0102 - total number of BLUE voxels in phantom
0103 - total absorbed energy in RED voxels (MeV)
0104 - total absorbed energy in GREEN voxels (MeV)
0105 - total absorbed energy in BLUE voxels (MeV)
0106 - total absorbed dose in RED voxels (Gy)
0107 - total absorbed dose in GREEN voxels (Gy)
0108 - total absorbed dose in BLUE voxels (Gy)
0109
0110 A phantom.root result file contain three ntuples,
0111 corresponding to the 3 types of voxels (red, green and blue) of the original image.
0112 The following voxel information is available in these ntuples:
0113 - x, y, z position
0114 - energy deposition
0115 - absorbed dose
0116 - voxel number (ID)
0117
0118 The ROOT macro plot.C can be run to display:
0119 - the cellular phantom
0120 - the absorbed energy distribution in the 3 types of voxels
0121 - the absorbed energy 2D map for the 3 types of voxels
0122 - the absorbed dose 2D map for the 3 types of voxels
0123
0124 Simply do, after the simulation:
0125 root plot.C
