Warning, /geant4/examples/extended/medical/dna/neuron/README is written in an unsupported language. File is not indexed.
0001
0002 =========================================================
0003 Geant4 - NEURON
0004 =========================================================
0005
0006 README file
0007 ----------------------
0008
0009
0010 Authors: M. Batmunkh *(a,b), O.V. Belov *(a), L. Bayarchimeg (a), O. Lkhagva (b)
0011
0012 (a) Laboratory of Radiation Biology, Joint Institute for Nuclear Research (JINR), 6 Joliot-Curie St., 141980 Dubna, Moscow Region, Russia
0013 (b) Division of Natural Sciences, National University of Mongolia (NUM), 1 University St., 210646 Ulaanbaatar, Mongolia
0014 * Corresponding authors, email to batmunkh@jinr.ru, dem@jinr.ru
0015
0016 Paper: O.V. Belov, M. Batmunkh, S. Incerti, O. Lkhagva. Radiation damage to
0017 neuronal cells: Simulating the energy deposition and water radiolysis
0018 in a small neural network. Physica Medica. 2016. 32. 1510-1520.
0019
0020 ---->1. INTRODUCTION.
0021
0022 The NEURON example allows for the modelling of neuron cell irradiation, including physical,
0023 physico-chemical and chemical processes (eg. production of oxidative radical species in the
0024 vicinity of neurons). It uses realistic geometrical models of neurons generated from a
0025 standardized SWC file representing neuron morphology.
0026 // A typical neuron cell is composed of a cell body (soma), a single axon, a dendritic tree,
0027 // and thousands of dendritic spines. In the example, individual compartments of a neuron cell
0028 // are simulated by spherical and cylindrical voxels.
0029 // The soma is represented by combination of several spheres, while the dendritic tree is described with combinations of cylinders.
0030 // Each voxel is represented as interconnection of two tracing points of the neuron model.
0031
0032 // A standardized neuromorphometric format (SWC) is an output file representing individual neuron
0033 // morphology generated by digitally tracing tools based on 3D confocal microscopy images.
0034 // In the SWC file, different numerical markers (e.g. from 1 to 6) describe different types of tracing points:
0035 // 1 - soma
0036 // 2 - axon
0037 // 3 - apical dendrite
0038 // 4 - basal dendrite
0039 // 5+ - custom (5 – spines, 6 – terminals, etc.).
0040 // Details are available in the NeuronLoadDataFile class.
0041
0042 // In order to simulate a neural network, user can create his own file containing
0043 // a combination of several individual neurons (see NeuralNETWORK.dat sample file
0044 // describing a network of 10 pyramidal neurons).
0045
0046 Geant4-DNA models are activated in the neuron model, which is declared as a G4Region.
0047 Geant4 condensed EM models are used outside neuron structure.
0048
0049 The example package contains:
0050 - source files (src, include, neuron.cc)
0051 - README
0052 - .in, plotDend.C and visualization macro files
0053 - GranuleCell-Nr2.CNG.swc (Sample file describing a single granule neuron is loaded by default)
0054 - NeuralNETWORK.dat (Sample file describing a network of 10 pyramidal neurons)
0055
0056 To run the example: see section 5 of this README
0057 To simulation output: see section 6 of this README
0058
0059 The code can be compiled with cmake.
0060 It works in MT mode.
0061
0062 ---->2. GEOMETRY SET-UP.
0063
0064 The geometry is cube (World) made of galactic material.
0065 Before computation, user loads a standardized SWC file of a neuron and generates
0066 a bounding volume and a homogeneous spherical medium of liquid water.
0067 Dimensions of the target volume are automatically extrapolated using SWC file describing
0068 3D coordinates of a neuron. The homogeneous medium contains volumes of neuronal cell and a bounding slice.
0069 The side cube (World) is again represented as overall dimensions of neuronal cell
0070 that is equal to the diameter of the homogeneous medium.
0071
0072 The construction of whole geometry of neuron morphology is set in the
0073 DetectorConstruction class.
0074
0075 User can choose between single-neuron simulation and modelling a neural network. Single-neuron
0076 simulation is set by default. To switch simulation to neural network, the following command should be used:
0077 > ./neuron -network FileName.dat
0078
0079 ---->3. EVENT: THE PRIMARY GENERATOR
0080
0081 The primary kinematic consists of a single particle starting at the random positions
0082 on the sphere surface. Then, the particle beam is directed towards the bounding slice volume,
0083 and traverses the individual neurons (default option). The type of the particle and its energy are set in the
0084 PrimaryGeneratorAction class, and can be changed via the G4 build-in commands of G4ParticleGun class.
0085 We included the following options for particle directions:
0086 a) Particles are directed to "square" on the XY plane of bounding slice (or YZ, XZ)
0087 ./neuron -mac myMacro.mac -sXY
0088 b) Particles are directed to "disk" on the XY plane of bounding slice (or YZ, XZ)
0089 ./neuron -mac myMacro.mac -dXY
0090 c) Particles are directed towards the bounding slice (default option)
0091 ./neuron -mac myMacro.mac
0092
0093 ---->4. PHYSICS
0094
0095 The following options of physical and chemical processes are included:
0096 Default Livermore physics
0097 ./neuron -mac myMacro.mac
0098
0099 a) Livermore + DNAphysics with extended Rudd ionisation model.
0100 ./neuron -mac myMacro.mac -dnaliv
0101 b) Livermore + DNAPhysics + DNAChemistry
0102 ./neuron -mac myMacro.mac -dnachemON
0103 c) Combination of DNA- and Livermore- physics with hadronic physics.
0104 ./neuron -mac myMacro.mac -dnahad
0105
0106 NOTE, that it requires more memory or computing resources when chemistry is ON (b) and
0107 also long computational time when dnaphysics activated. Conversely, it can works faster when default.
0108
0109 Look at the src/PhyscisList.cc files.
0110
0111
0112 ---->5. HOW TO RUN THE EXAMPLE
0113
0114 To get help, run:
0115
0116 > ./neuron -h
0117
0118 In visualization and interactive mode, run:
0119
0120 > ./neuron -gui
0121 ( OGL used by default)
0122 or you may use your own visualization driver, for instance:
0123 ./neuron -vis "DAWNFILE"
0124
0125 "GranuleCell-Nr2.CNG.swc" is the default file and it should be placed into same directory as the executable.
0126 You can download it here:
0127 http://neuromorpho.org/neuron_info.jsp?neuron_name=GranuleCell-Nr2
0128 You can change neuron`s file name using the following command:
0129
0130 > ./neuron -swc newFileName.swc
0131
0132 In batch mode , run:
0133
0134 > ./neuron(.exe) [-mac neuron.in] [-mt numberofThreads]
0135 > ./neuron -mac ../neuron.in -mt 3 > neuron.out
0136
0137 To get visualization, make sure to uncomment the #/control/execute vis.mac line in the macro.
0138 User can start a visualization of the chemical track evolution in time and space
0139 using SetEndTime (default-10 ps) and SetVerbose setting in src/ActionInitialization.cc file.
0140
0141
0142 ---->6. SIMULATION OUTPUT AND RESULT ANALYSIS
0143
0144 The simulation outputs appears in terminal display.
0145 - the energy deposit in the bounding slice and each structure of neuron (in kiloelectronVolt)
0146 - the scored energy deposit within hitting compartment of neuron structure (in kiloelectronVolt)
0147 - the number of particles inside and outside neuron
0148 - the number of radiolytic species inside neuron when chemistry is activated
0149
0150 The main output results are stored in OutputPerEvent.out file, containing for each event.
0151 Dend3DEdep.out, Axon3DEdep.out and Soma3DEdep.out files for given dose:
0152 - the position (x, y, z in micrometre) of compartments traversed by particle track.
0153 - the Axon and Dendrite (basal and apical) distance of compartments from Soma (in micrometre).
0154 - the energy deposition in compartments (in kiloelectronVolt).
0155
0156 This file can be easily analysed using for example the provided ROOT macro
0157 file plotDend.C; to do so:
0158 * be sure to have ROOT installed on your machine
0159 * be sure to be in the neuron directory
0160 * launch ROOT by typing root
0161 * under your ROOT session, type in : .X plotDend.C to execute the macro file
0162 * alternatively you can type directly under your session : root plotDend.C
0163 ---------------------------------------------------------------------------
0164 If you have any questions or wish to notify of updates and/or modification please contact:
0165 batmunkh@jinr.ru, dem@jinr.ru
