Gabriele Cosmo
176 lines
8.0 KiB
Markdown
176 lines
8.0 KiB
Markdown
\page Exampleneuron Example neuron
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\authors M. Batmunkh *(a,b), L. Bayarchimeg (a) \n
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(a) Laboratory of Radiation Biology, Joint Institute for Nuclear Research (JINR),
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6 Joliot-Curie St., 141980 Dubna, Moscow Region, Russia \n
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(b) Division of Natural Sciences, National University of Mongolia (NUM),
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1 University St., 210646 Ulaanbaatar, Mongolia \n
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* Corresponding author, email to batmunkh@jinr.ru \n
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Any report or published results obtained using the Geant4-DNA software shall
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cite the following Geant4-DNA collaboration publications:\n
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Phys. Med. 31 (2015) 861-874 \n
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Med. Phys. 37 (2010) 4692-4708 \n\n
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We also suggest these other references related to this example:\n
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Phys. Part. Nucl. 56 (2025) 1030-1058 \n
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Phys. Part. Nucl. Lett. 16 (2019) 54–62 \n
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Physica Medica. 57 (2019) 88-94 \n
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EPJ Web Conf. 173 (2018) 05005 \n
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Physica Medica. 32 (2016) 1510-1520 \n
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Radiat Res Appl Sci. V (2015) 498-507 \n\n
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## INTRODUCTION
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The NEURON example allows for the modelling of neuron cell irradiation, including physical,
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physico-chemical and chemical processes (eg. production of oxidative radical species in the
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vicinity of neurons). It uses realistic geometrical models of neurons generated from a
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standardized SWC file representing neuron morphology.
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A typical neuron cell is composed of a cell body (soma), a single axon, a dendritic tree,
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and thousands of dendritic spines. In the example, individual compartments of a neuron cell
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are simulated by spherical and cylindrical voxels.
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The soma is represented by combination of several spheres, while the dendritic tree is described with combinations of cylinders.
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Each voxel is represented as interconnection of two tracing points of the neuron model.
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A standardized neuromorphometric format (SWC) is an output file representing individual neuron
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morphology generated by digitally tracing tools based on 3D confocal microscopy images.
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In the SWC file, different numerical markers (e.g. from 1 to 6) describe different types of tracing points:
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- 1 - soma
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- 2 - axon
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- 3 - apical dendrite
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- 4 - basal dendrite
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- 5+ - custom (5 – spines, 6 – terminals, etc.).
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Details are available in the NeuronLoadDataFile class.
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In order to simulate a neural network, user can create his own file containing
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a combination of several individual neurons (see NeuralNETWORK.dat sample file
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describing a network of 10 pyramidal neurons).
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Geant4-DNA models are activated in the neuron model, which is declared as a G4Region.
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Geant4 condensed EM models are used outside the neuron structure.
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The example package contains:
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- source files (src, include, neuron.cc)
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- README
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- .in, plotDend.C and visualization macro files
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- GranuleCell-Nr2.CNG.swc (Sample file describing a single granule neuron is loaded by default)
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- NeuralNETWORK.dat (Sample file describing a network of 10 pyramidal neurons)
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To run the example: see section HOW TO RUN THE EXAMPLE of this README. \n
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To simulation output: see section SIMULATION OUTPUT AND RESULT ANALYSIS of this README.
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The code can be compiled with cmake.
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It works in MT mode.
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## GEOMETRY SET-UP
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The geometry is cube (World) made of galactic material.
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Before computation, user loads a standardized SWC file of a neuron and generates
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a bounding volume and a homogeneous spherical medium of liquid water.
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Dimensions of the target volume are automatically extrapolated using SWC file describing
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3D coordinates of a neuron. The homogeneous medium contains volumes of neuronal cell and a bounding slice.
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The side cube (World) is again represented as overall dimensions of neuronal cell
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that is equal to the diameter of the homogeneous medium.
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The construction of whole geometry of neuron morphology is set in the
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DetectorConstruction class.
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User can choose between single-neuron simulation and modelling a neural network. Single-neuron
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simulation is set by default. To switch simulation to neural network, the following command should be used:
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> ./neuron -network FileName.dat
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## EVENT: THE PRIMARY GENERATOR
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The primary kinematic consists of a single particle starting at the random positions
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on the sphere surface. Then, the particle beam is directed towards the bounding slice volume,
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and traverses the individual neurons (default option). The type of the particle and its energy are set in the
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PrimaryGeneratorAction class, and can be changed via the G4 build-in commands of G4ParticleGun class.
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We included the following options for particle directions:
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a) Particles are directed to "square" on the XY plane of bounding slice (or YZ, XZ)
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> ./neuron -mac myMacro.mac -sXY
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b) Particles are directed to "disk" on the XY plane of bounding slice (or YZ, XZ)
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> ./neuron -mac myMacro.mac -dXY
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c) Particles are directed towards the bounding slice (default option)
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> ./neuron -mac myMacro.mac
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## PHYSICS
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The following options of physical and chemical processes are included:
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Default Livermore physics
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> ./neuron -mac myMacro.mac
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a) Livermore + DNAphysics when use DNARegion in myMacro.mac file
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> ./neuron -mac myMacro.mac
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b) Livermore + DNAPhysics + DNAChemistry
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> ./neuron -mac myMacro.mac -dnachemON
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c) Combination of DNA- and Livermore- physics with hadronic physics.
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> ./neuron -mac myMacro.mac -dnahad
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NOTE, that it requires more memory or computing resources when chemistry is ON (b) and
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also long computational time when dnaphysics activated. Conversely, it can works faster when default.
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Look at the src/PhyscisList.cc files.
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## HOW TO RUN THE EXAMPLE
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To get help, run:
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> ./neuron -h
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In visualization and interactive mode, run:
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> ./neuron -gui
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( OGL used by default)
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or you may use your own visualization driver, for instance:
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> ./neuron -vis "DAWNFILE"
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"GranuleCell-Nr2.CNG.swc" is the default file and it should be placed into same directory as the executable.
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You can download it here:
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http://neuromorpho.org/neuron_info.jsp?neuron_name=GranuleCell-Nr2
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You can change neuron`s file name using the following command:
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> ./neuron -gui -swc newFileName.swc
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In batch mode , run:
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> ./neuron(.exe) [-mac neuron.in] [-mt numberofThreads]
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> ./neuron -mac ../neuron.in -mt 3 > neuron.out
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To get visualization, make sure to uncomment the #/control/execute vis.mac line in the macro.
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User can start a visualization of the chemical track evolution in time and space
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using SetEndTime (default-10 ps) and SetVerbose setting in src/ActionInitialization.cc file.
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## SIMULATION OUTPUT AND RESULT ANALYSIS
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The simulation outputs appears in terminal display.
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- the energy deposit in the bounding slice and each structure of neuron (in kiloelectronVolt)
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- the scored energy deposit within hitting compartment of neuron structure (in kiloelectronVolt)
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- the number of particles inside and outside neuron
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- the number of radiolytic species inside neuron when chemistry is activated
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The main output results are stored in OutputPerEvent.out file, containing for each event.
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Dend3DEdep.out, Axon3DEdep.out and Soma3DEdep.out files for given dose:
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- the position (x, y, z in micrometre) of compartments traversed by particle track.
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- the Axon and Dendrite (basal and apical) distance of compartments from Soma (in micrometre).
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- the energy deposition in compartments (in kiloelectronVolt).
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- the dose deposition in compartments (in Gray).
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This file can be easily analysed using for example the provided ROOT macro
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file plotDend.C; to do so:
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- be sure to have ROOT installed on your machine
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- be sure to be in the neuron directory
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- launch ROOT by typing root
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- under your ROOT session, type in : .X plotDend.C to execute the macro file
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- alternatively you can type directly under your session : root plotDend.C
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---------------------------------------------------------------------------
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If you have any questions or wish to notify of updates and/or modification please contact:
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batmunkh@jinr.ru \n
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