Gabriele Cosmo
123 lines
4.2 KiB
Plaintext
123 lines
4.2 KiB
Plaintext
================================
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Geant4 - cellularPhantom example
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================================
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README file
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----------------------
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Authors and contributors:
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P. Barberet, S. Incerti, N. H. Tran, L. Morelli
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LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France
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E-mail: barberet@lp2ib.in2p3.fr or incerti@lp2ib.in2p3.fr
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If you use this code, please cite the following publication:
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Monte-Carlo dosimetry on a realistic cell monolayer geometry exposed to alpha-particle,
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P. Barberet, F. Vianna, M. Karamitros, T. Brun, N. Gordillo, P. Moretto, S. Incerti, H. Seznec,
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Phys. Med. Biol. 57 (2012) 2189-2207
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https://doi.org/10.1088/0031-9155/57/8/2189
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---->0. INTRODUCTION
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The cellularPhantom example shows how to simulate the irradiation of a 3D voxel
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phantom containing biological cells, created from a confocal microscopy 24-bit RGB image.
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The original image was created thanks to:
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- H. De Oliveira, T. Désigaux, N. Dusserre, ART BioPrint, France
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- F. Paris, C. Niaudet, Inserm, France
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These developments were carried out as part of the "Flash'Atlantic" project
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(2023-2024) funded by CNRS-MITI, France, and Inserm, France.
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Two phantom files phantom.dat (low resolution) and phantomHR.dat (high resolution)
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are provided in the phantoms directory.
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They were created using the ImageJ phantom.ijm macro located in the ImageJ directory.
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See the phantoms/Documentation.pdf file for more information
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The low resolution file is used for visualization in the macro vis.mac.
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It contains the following lines:
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54300 20230 17320 16750
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=> total number of voxels, number of red, green and blue voxels
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734.0507 734.0507 90.6372 microns
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=> whole X, Y and Z size of the phantom, with unit
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2.8674 2.8674 2.0142 microns
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=> size of a single voxel, with unit
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And the list of individual voxels, with the format: X, Y and Z positions, type
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(type is 1 for R, 2 for G, 3 for B):
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232.2582 31.5412 0.0000 2
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235.1256 31.5412 0.0000 2
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...
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The low resolution and high resolution files can be used by the run.mac macro.
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---->1. GEOMETRY SET-UP
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The geometry is a 1-mm side cube ("World") made of air, with a thickness of 100 um,
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containing a liquid water medium ("Medium") of side 900 um and thickness 95 um,
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containing itself the phantom ("Phantom").
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The World and Medium dimensions can be changed by UI command.
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---->2. SET-UP
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Make sure $G4LEDATA points to the low energy electromagnetic data files.
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---->3. HOW TO RUN THE EXAMPLE
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In interactive mode, run:
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./cellularPhantom
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this will show the phantom in 3D (requires memory).
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In batch, the macro run.mac can be used:
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./cellularPhantom run.mac
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In this macro, the user can select:
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- the number of threads (MT mode)
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- the phantom file name
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- the World and Medium dimensions
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- the Medium material
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- the phantom voxel density
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- the position (shift in X or Y or Z) of the phantom in the Medium
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- the production cuts outside and inside in the phantom
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- the incident particles (using GPS)
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---->4. PHYSICS
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The PhysicsList class uses Geant4 option4 electromagnetic physics.
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It also contains other physics lists including Geant4-DNA option2,
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which is commented by default.
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---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
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The output results consists in a phantom.root file, containing three ntuples,
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corresponding to the 3 types of voxels (red, green and blue) of the original image.
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The ROOT macro plot.C can be run to extract and display:
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- the cellular phantom
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- the absorbed energy distribution in the 3 types of voxels
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- the absorbed energy 2D map for the 3 types of voxels
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- the absorbed dose 2D map for the 3 types of voxels
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Simply do, after the simulation:
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root plot.C
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In addition, the following quantities are displayed:
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- total number of voxels in phantom
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- total number of RED voxels in phantom
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- total number of GREEN voxels in phantom
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- total number of BLUE voxels in phantom
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- total absorbed energy in RED voxels (MeV)
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- total absorbed energy in GREEN voxels (MeV)
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- total absorbed energy in BLUE voxels (MeV)
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- total absorbed dose in RED voxels (Gy)
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- total absorbed dose in GREEN voxels (Gy)
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- total absorbed dose in BLUE voxels (Gy)
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Results are stored in the results.root file.
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