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1
2 =========================================================
3 Geant4 - NEURON
4 =========================================================
5
6 README file
7 ----------------------
8
9
10 Authors: M. Batmunkh *(a,b), O.V. Belov *(a), L. Bayarchimeg (a), O. Lkhagva (b)
11
12 (a) Laboratory of Radiation Biology, Joint Institute for Nuclear Research (JINR), 6 Joliot-Curie St., 141980 Dubna, Moscow Region, Russia
13 (b) Division of Natural Sciences, National University of Mongolia (NUM), 1 University St., 210646 Ulaanbaatar, Mongolia
14 * Corresponding authors, email to batmunkh@jinr.ru, dem@jinr.ru
15
16 Paper: O.V. Belov, M. Batmunkh, S. Incerti, O. Lkhagva. Radiation damage to
17 neuronal cells: Simulating the energy deposition and water radiolysis
18 in a small neural network. Physica Medica. 2016. 32. 1510-1520.
19
20 ---->1. INTRODUCTION.
21
22 The NEURON example allows for the modelling of neuron cell irradiation, including physical,
23 physico-chemical and chemical processes (eg. production of oxidative radical species in the
24 vicinity of neurons). It uses realistic geometrical models of neurons generated from a
25 standardized SWC file representing neuron morphology.
26 // A typical neuron cell is composed of a cell body (soma), a single axon, a dendritic tree,
27 // and thousands of dendritic spines. In the example, individual compartments of a neuron cell
28 // are simulated by spherical and cylindrical voxels.
29 // The soma is represented by combination of several spheres, while the dendritic tree is described with combinations of cylinders.
30 // Each voxel is represented as interconnection of two tracing points of the neuron model.
31
32 // A standardized neuromorphometric format (SWC) is an output file representing individual neuron
33 // morphology generated by digitally tracing tools based on 3D confocal microscopy images.
34 // In the SWC file, different numerical markers (e.g. from 1 to 6) describe different types of tracing points:
35 // 1 - soma
36 // 2 - axon
37 // 3 - apical dendrite
38 // 4 - basal dendrite
39 // 5+ - custom (5 – spines, 6 – terminals, etc.).
40 // Details are available in the NeuronLoadDataFile class.
41
42 // In order to simulate a neural network, user can create his own file containing
43 // a combination of several individual neurons (see NeuralNETWORK.dat sample file
44 // describing a network of 10 pyramidal neurons).
45
46 Geant4-DNA models are activated in the neuron model, which is declared as a G4Region.
47 Geant4 condensed EM models are used outside neuron structure.
48
49 The example package contains:
50 - source files (src, include, neuron.cc)
51 - README
52 - .in, plotDend.C and visualization macro files
53 - GranuleCell-Nr2.CNG.swc (Sample file describing a single granule neuron is loaded by default)
54 - NeuralNETWORK.dat (Sample file describing a network of 10 pyramidal neurons)
55
56 To run the example: see section 5 of this README
57 To simulation output: see section 6 of this README
58
59 The code can be compiled with cmake.
60 It works in MT mode.
61
62 ---->2. GEOMETRY SET-UP.
63
64 The geometry is cube (World) made of galactic material.
65 Before computation, user loads a standardized SWC file of a neuron and generates
66 a bounding volume and a homogeneous spherical medium of liquid water.
67 Dimensions of the target volume are automatically extrapolated using SWC file describing
68 3D coordinates of a neuron. The homogeneous medium contains volumes of neuronal cell and a bounding slice.
69 The side cube (World) is again represented as overall dimensions of neuronal cell
70 that is equal to the diameter of the homogeneous medium.
71
72 The construction of whole geometry of neuron morphology is set in the
73 DetectorConstruction class.
74
75 User can choose between single-neuron simulation and modelling a neural network. Single-neuron
76 simulation is set by default. To switch simulation to neural network, the following command should be used:
77 > ./neuron -network FileName.dat
78
79 ---->3. EVENT: THE PRIMARY GENERATOR
80
81 The primary kinematic consists of a single particle starting at the random positions
82 on the sphere surface. Then, the particle beam is directed towards the bounding slice volume,
83 and traverses the individual neurons (default option). The type of the particle and its energy are set in the
84 PrimaryGeneratorAction class, and can be changed via the G4 build-in commands of G4ParticleGun class.
85 We included the following options for particle directions:
86 a) Particles are directed to "square" on the XY plane of bounding slice (or YZ, XZ)
87 ./neuron -mac myMacro.mac -sXY
88 b) Particles are directed to "disk" on the XY plane of bounding slice (or YZ, XZ)
89 ./neuron -mac myMacro.mac -dXY
90 c) Particles are directed towards the bounding slice (default option)
91 ./neuron -mac myMacro.mac
92
93 ---->4. PHYSICS
94
95 The following options of physical and chemical processes are included:
96 Default Livermore physics
97 ./neuron -mac myMacro.mac
98
99 a) Livermore + DNAphysics with extended Rudd ionisation model.
100 ./neuron -mac myMacro.mac -dnaliv
101 b) Livermore + DNAPhysics + DNAChemistry
102 ./neuron -mac myMacro.mac -dnachemON
103 c) Combination of DNA- and Livermore- physics with hadronic physics.
104 ./neuron -mac myMacro.mac -dnahad
105
106 NOTE, that it requires more memory or computing resources when chemistry is ON (b) and
107 also long computational time when dnaphysics activated. Conversely, it can works faster when default.
108
109 Look at the src/PhyscisList.cc files.
110
111
112 ---->5. HOW TO RUN THE EXAMPLE
113
114 To get help, run:
115
116 > ./neuron -h
117
118 In visualization and interactive mode, run:
119
120 > ./neuron -gui
121 ( OGL used by default)
122 or you may use your own visualization driver, for instance:
123 ./neuron -vis "DAWNFILE"
124
125 "GranuleCell-Nr2.CNG.swc" is the default file and it should be placed into same directory as the executable.
126 You can download it here:
127 http://neuromorpho.org/neuron_info.jsp?neuron_name=GranuleCell-Nr2
128 You can change neuron`s file name using the following command:
129
130 > ./neuron -swc newFileName.swc
131
132 In batch mode , run:
133
134 > ./neuron(.exe) [-mac neuron.in] [-mt numberofThreads]
135 > ./neuron -mac ../neuron.in -mt 3 > neuron.out
136
137 To get visualization, make sure to uncomment the #/control/execute vis.mac line in the macro.
138 User can start a visualization of the chemical track evolution in time and space
139 using SetEndTime (default-10 ps) and SetVerbose setting in src/ActionInitialization.cc file.
140
141
142 ---->6. SIMULATION OUTPUT AND RESULT ANALYSIS
143
144 The simulation outputs appears in terminal display.
145 - the energy deposit in the bounding slice and each structure of neuron (in kiloelectronVolt)
146 - the scored energy deposit within hitting compartment of neuron structure (in kiloelectronVolt)
147 - the number of particles inside and outside neuron
148 - the number of radiolytic species inside neuron when chemistry is activated
149
150 The main output results are stored in OutputPerEvent.out file, containing for each event.
151 Dend3DEdep.out, Axon3DEdep.out and Soma3DEdep.out files for given dose:
152 - the position (x, y, z in micrometre) of compartments traversed by particle track.
153 - the Axon and Dendrite (basal and apical) distance of compartments from Soma (in micrometre).
154 - the energy deposition in compartments (in kiloelectronVolt).
155
156 This file can be easily analysed using for example the provided ROOT macro
157 file plotDend.C; to do so:
158 * be sure to have ROOT installed on your machine
159 * be sure to be in the neuron directory
160 * launch ROOT by typing root
161 * under your ROOT session, type in : .X plotDend.C to execute the macro file
162 * alternatively you can type directly under your session : root plotDend.C
163 ---------------------------------------------------------------------------
164 If you have any questions or wish to notify of updates and/or modification please contact:
165 batmunkh@jinr.ru, dem@jinr.ru
