FNTD processing, Fluorescent Nuclear Track Detectors, Alpha
microdosimetry, Spheroid simulation dataset
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Code files
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/Java-library
Java code library which, after compiling, yields a .jar file to
be placed in the /R-Package/inst/java folder.
For further description of the library: https://github.com/FNTD/
Exceptions:
/Java-library/CellHitStatistics.java
Class for extrapolation of measured tracks in FNTDs into 3D
cell images. Also contains functions for spheroid calculations.
/R-package
R library for FNTD processing and track analysis and dosimetry.
For further description of the library: https://github.com/FNTD/
Exceptions:
/R-package/R/FNTD.find.depth.R
Function for FNTD surface plane determination based on the
expected average particle penetration.
/R-package/R/FNTD.real.cell.hits.R
Function for extrapolation of measured tracks in FNTDs into 3D
cell images. Calls /Java-library/CellHitStatistics.java
/R-package/R/FNTD.simulate.cell.hits.R
Function for extrapolation of measured tracks in FNTDs through
simulated cells with variable nucleus and cytoplasm diameter.
/R-package/R/FNTD.get.proc.track.length.R
Function for determination of the Continuous Slowing Down
Approximation procedural track length of tracks in FNTDs.
/R-package/R/FNTD.get.macro.dose.R
Function for calculation of the dose deposited in the given
scenario's.
/R-package/R/FNTD.spheroid.simulation.R
Function for simulation of alpha emitters in spheroids.
Calls /Java-library/CellHitStatistics.java
/R
Collection of scripts for processing and analyzing FNTDs.
Relies heavily on the accompanying R-package library. Also contains
code for calculation and simulation of microdosimetric spectra in
cells.
/R/Add.Scan.To.DB.R
Script for adding FNTD scans to the database. Requires surface
plane equation and an ID.
/R/CellHit/Cell.LET.distribution.R
Calculates the LET distribution given a cell image and a
collection of FNTD images. Only works for alpha particles.
/R/CellHit/Cell.microdosimetry.R
Calculates the expected survival of a monoloyer using the macro-
and microdosimetry approach.
/R/CellHit/Cell.multi.hit.distribution.R
Plots nucleus dose spectra of cells given a corresponding
macrodose.
/R/CellHit/Cell.processing.R
Calls /Java-library/CellHitStatistics.java to calculate the
amount of alpha particles hitting energy and the corresponding
dose deposition given a cell image and a collection of alpha
tracks in FNTDs.
/R/CellHit/Cell.single.hit.distribution.R
Plots nucleus dose spectra of cells given a corresponding
number of particles hitting the nucleus.
/R/CellHit/Spheroid.cyto.ratio.R
Plots the nucleus-cytoplasm dose ratio as found in spheroid
simulations.
/R/CellHit/Spheroid.LET.distribution.R
Calculates the LET distribution in a spheroid simulation
and plots it.
/R/CellHit/Spheroid.show.spatial.distribution.R
Plots the spatial distribution of locations from which an
alpha decay event hit the center nucleus in spheroid
simulations.
/R/CellHit/Spheroid.simulation.java.R
Calls /Java-library/CellHitStatistics.java to calculate the
amount of alpha particles hitting energy and the corresponding
dose deposition in a virtual spheroid for the given alpha
particle energy.
/R/CellHit/Spheroid.single.hit.distribution.R
Plots nucleus dose spectra of cells in spheroids given a
corresponding number of particles hitting the nucleus.
/R/CellHit/Spheroid.survival.R
Calculates the expected survival in spheroid for various
isotope distributions.
/R/Data/CSV/Angular_spectrum_1800.csv
Expected angular distribution of alpha particles hitting
FNTDs irradiated above the 1800 um collimator.
/R/Data/CSV/Angular_spectrum_2600.csv
Expected angular distribution of alpha particles hitting
FNTDs irradiated above the 2600 um collimator.
/R/Data/CSV/Energy_spectrum_1800.csv
Expected energy distribution of alpha particles hitting
FNTDs irradiated above the 1800 um collimator.
/R/Data/CSV/Energy_spectrum_2600.csv
Expected energy distribution of alpha particles hitting
FNTDs irradiated above the 2600 um collimator.
/R/Data/CSV/Samples.csv
Sample information for FNTD images in the database.
/R/Data/CSV/table_*.csv
Conversion tables for energy, range and LET in various (*)
materials.
/R/Data/Plots
Folder for plot files
/R/Data/Spheroids
Simulation data files for spheroids. Generated by
/R/CellHit/Spheroid.simulation.java.R
/R/Data/Tracks
Data files for track storage as found in FNTD images in the
database.
/R/E3/FNTD.Processing.R
General FNTD processing and track reconstruction. Stores
resulting tracks in /R/Data/Tracks.
/R/E3/Plane.Intercept.optimization.R
Find the surface plane of a FNTD given the average expected
alpha energy. Calls /R-package/R/FNTD.find.depth.R.
/R/Include/default.R
Include file for used libraries and global variables.
/R/Plots
Plot routines for various variables and statistics for tracks
found in FNTDs.