MC Dataset

MC Dataset is an extensive collection of datasets computed with PyXOpto Monte Carlo light propagation models. The readily available datasets are computed for a vast variety of sources, detectors and sample optical properties and include information of reflectance, transmittance, sampling volume and fluence/energy deposition data. The datasets can be easily customized through the dataset module of the PyXOpto project.

Links to the data files of the latest release

Datasets are split into multiple files to reduce the download size and to allow partial downloads. The following table has the links to the dataset files of the latest release. A more detailed description of the individual datasets is given in the following section.

Dataset	Release file	Description
MCML comparison datasets
	mcml_comparison.zip	single layer 100 mm and 1 mm thick, 2-layers 0.1 mm and 1 mm thick
Layered media datasets (MCML)
	mcml_1-layer-semiinfinite_line.zip	Semi-infinite medium, line source
	mcml_1-layer-semiinfinite_collimated-200um.zip	Semi-infinite medium, collimated source with 200 µm diameter
	mcml_1-layer-semiinfinite_gaussian-fwhm-100um.zip	Semi-infinite medium, Gaussian source with 100 µm FWH
	mcml_1-layer-semiinfinite_fiber-200um-0.22na.zip	Semi-infinite medium, fiber source with 200 µm 0.22 NA core
	mcml_1-layer-semiinfinite_six-linear-200um-0_22na.zip	Semi-infinite medium, six-linear array probe, 200 µm 0.22 NA fiber core
	mcml_1-layer-semiinfinite_six-around-one-200um-0_22na.zip	Semi-infinite medium, six-arround-one probe, 200 µm 0.22 NA fiber core
	mcml_1-layer-semiinfinite_six-around-one-400um-0_22na.zip	Semi-infinite medium, six-arround-one probe, 400 µm 0.22 NA fiber core
	mcml_1-layer-semiinfinite_single-fiber-100um-0_22na.zip	Semi-infinite medium, single-fiber probe, 100 µm 0.22 NA fiber core
	mcml_1-layer-semiinfinite_single-fiber-200um-0_22na.zip	Semi-infinite medium, single-fiber probe, 200 µm 0.22 NA fiber core
	mcml_1-layer-semiinfinite_single-fiber-400um-0_22na.zip	Semi-infinite medium, single-fiber probe, 400 µm 0.22 NA fiber core
	mcml_1-layer-semiinfinite_single-fiber-800um-0_22na.zip	Semi-infinite medium, single-fiber probe, 800 µm 0.22 NA fiber core
Voxelized media datasets (MCVOX)
	mcvox.zip	Energy deposition for a voxelized 2-layer skin with an embedded blood vessel at 26 depths]()
	mcvox-2-layer-skin-200um-vessel-500um-depth-deposition.zip	Energy deposition for a voxelized 2-layer skin with an embedded blood vessel at 0.5 mm depth
Sampling volume datasets (SV)
	sv.zip	Sampling volume dataset

Datasets

The following sections provide information on the four groups of datasets:

• MCML comparison datasets
• Layered media datasets (MCML)
• Voxelized media datasets (MCVOX)
• Sampling volume datasets (SV)

At the end of each section there is a breakdown of the directory tree and naming conventions that are used to organize the dataset files.

MCML comparison datasets

This dataset is intended for comparison with the MCML package. Datasets are computed for a 1-layer (1 mm and 100 mm thick) and 2-layer sample (0.1 mm and 1.0 mm thick layers). The optical properties are varied in the top sample layer:

• Absorption coefficient is sampled from [0.0, 2.5, 5.0] cm ^-1.
• Reduced scattering coefficient is sampled from [5.0, 20.0, 35.0] cm ^-1.
• Scattering phase function anisotropy is sampled from [0.1, 0.5, 0.9].
• The refractive index of the sample is set to:
  • 1-layer sample: 1.337,
  • 2-layer sample: 1.462 for the top layer and 1.337 for the bottom layer.
• The refractive index of the surrounding medium is set to 1.0.
• The remaining optical properties of the 2^nd layer are fixed to µ_a=0.5 cm^-1, µ_s'=20.0 cm^-1 and g=0.8.

The datasets are computed with a normally incident infinitely thin source. The reflectance and transmittance are collected through radial detectors with 500 concentric accumulators from 0 to 5 mm.

Illustration of the radial detector that is used to collect the reflectance and transmittance as Radial(Axis(start=0.0, stop=0.005, n=500)). The central and outermost accumulator are highlighted with a gray fill

The energy deposition is collected in a 2D accumulator array along the radial r and z axis. The range of both axis is from 0 to 5 mm and the number of accumulators along each axis is set 500. All the simulations are prepared with 100 million photon packets and simulation termination radius is set to 1000 mm.

Illustration of the radially symmetric energy deposition detector FluenceRz.

Dataset files

Datasets are available as compressed numpy data files that are organized as follows:

data/mcml_comparison/<sample>/line/radial/hg/g-<g>/mua-<mua>-musr-<musr>-invcm.npz

The values of placeholders <> are as follows:

• <sample> can take one of the following values:

  • 1-layer-1mm

    A single layer 1 mm thick medium.

  • 1-layer-100mm

    A single layer 100 mm thick medium.

  • 2-layer-100um-1mm

    A two-layer medium with 0.1 mm thick top layer and 1 mm thick bottom layer

• <g> is the anisotropy formatted with two decimal digits and _ as the decimal separator, e.g 0_10 for g=0.1, 0_50 for g=0.5 or 0_90 for g=0.9.

• <mua> is the absorption coefficient in units of cm ^-1 with formatted with two decimal digits and _ as the decimal separator, e.g 2_50 for µ_a=2.5 cm^-1.

• <musr> is the reduced scattering coefficient in units of cm ^-1 with formatted with two decimal digits and _ as the decimal separator, e.g 25_00 for µ_s'=25.0 cm^-1.

Henyey-Greenstein scattering phase functions used in the MCML comparison dataset.

Layered media datasets (MCML)

The datasets are produced with 100 million photon packets, except for the Spatial Frequency Domain Imaging (SFDI) dataset and all the datasets that use an optical fiber probe with a linear layout of 6 fibers. These datasets are run with 1000 million photon packets. The simulation termination radius is set to 25 mm, except for the spatial frequency domain imaging (SFDI) dataset that uses a 150 mm simulation termination radius. The optical properties of the sample are varied according to the values listed in the following two tables.

Absorption and reduced scattering coefficients

Parameter	From (cm-1)	To (cm-1)	Points
µa	0.0	5.0	21
µs'	5.0	35.0	21

Scattering phase functions

Scattering phase function	Parameter	Values
HG (Henyey-Greenstein)	g	0.1, 0.3, 0.5, 0.7, 0.9
MHG (Modified Henyey-Greenstein)	g	0.1, 0.3, 0.5, 0.7, 0.9
	β	0.0, 0.2, 0.4, 0.6, 0.8, 1.0
GK (Gegenbauer Kernel)	g	0.1, 0.3, 0.5, 0.7, 0.9
	α	-0.5, 0.0, 0.5, 1.0, 1.5
MIE-polystyrene	λ	500 nm
	diameter	0.25, 0.5 1.0, 2.0, 4.0 µm
	nparticle	1.603
	nmedium	1.337
MIE-fused silica	λ	500 nm
	diameter	0.25, 0.5 1.0, 2.0, 4.0 µm
	nparticle	1.462
	nmedium	1.337

The refractive index of the sample is set to 1.337.

Henyey-Greenstein (HG) scattering phase functions as defined in the above table.

Examples of Modified Henyey-Greenstein (MHG) scattering phase functions from the above table.

Examples of Gegenbauer Kernel (GK) scattering phase functions from the above table.

Mie scattering phase functions of water-suspended fused silica particles specified in the above table.

Mie scattering phase functions of water-suspended polystyrene particles specified in the above table.

Datasets are available for the following basic sources that use a laterally uniform boundary between the sample and the surrounding medium.

Basic sources with a uniform sample-source interface and related reflectance detectors

Source	Parameter	Value	Reflectance detector
Line			Radial(Axis(0, 0.005, 500))
UniformBeam	diameter	200 μm	Radial(Axis(0, 0.005, 500))
GaussianBeam	FWHM	100 μm	Radial(Axis(0, 0.005, 500))
UniformFiber	dcore	200 μm	Radial(Axis(0, 0.005, 500))
	dcladding	220 μm
	ncore	1.462
	NA	0.22

The refractive index of the surrounding medium is set to 1.0 except when using the UniformFiber source, when the refractive index of the surrounding medium follows the refractive index of the fiber core 1.462.

The reflectance of basic sources is collected with a radial detector with range from 0 to 5 mm and 500 concentric accumulators, each 5 μm wide. The acceptance angle is unlimited, except for the UniformFiber source for which it is limited by the NA of the fiber core. The acceptance angle within the fiber core.

Datasets are also prepared for optical fiber probe sources that use a surface layout to more accurately describe the interface between the optical fiber probe tip and the sample. All the probe sources launch the photon packets with the UniformFiber source.

Optical fiber probe sources with a detailed sample-source interface and related reflectance detectors

Probe	Parameter	Value	Description	Reflectance detector
SixAroundOne	dcore	200 μm	six-around-one layout	SixAroundOne
	dcladding	220 μm
	ncore	1.462
	NA	0.22
	diameter	6.0 mm
	reflectivity	0.6
SixAroundOne	dcore	400 μm	six-around-one layout	SixAroundOne
	dcladding	420 μm
	ncore	1.462
	NA	0.22
	diameter	6.0 mm
	reflectivity	0.6
LinearArray	dcore	200 μm	linear layout of 6 fibers	LinearArray
	dcladding	220 μm
	ncore	1.462
	NA	0.22
	n	6
	diameter	6.0 mm
	reflectivity	0.6
LinearArray	dcore	100 μm	single fiber layout	LinearArray
	dcladding	120 μm
	ncore	1.462
	NA	0.22
	n	1
	diameter	6.0 mm
	reflectivity	0.6
LinearArray	dcore	200 μm	single fiber layout	LinearArray
	dcladding	220 μm
	ncore	1.462
	NA	0.22
	n	1
	diameter	6.0 mm
	reflectivity	0.6
LinearArray	dcore	400 μm	single fiber layout	LinearArray
	dcladding	420 μm
	ncore	1.462
	NA	0.22
	n	1
	diameter	6.0 mm
	reflectivity	0.6
LinearArray	dcore	800 μm	single fiber layout	LinearArray
	dcladding	820 μm
	ncore	1.462
	NA	0.22
	n	1
	diameter	6.0  mm
	reflectivity	0.6

Illustration of the surface layouts for the two six-around-one optical fiber probes (SixAroundOne) with 200 and 400 μm fiber cores.

Illustration of the surface layout for the linear array probe (LinearArray) with 6 optical fibers.

Illustration of the surface layouts for the single fiber probes (LinearArray) with 100, 200, 400 and 800 μm fiber cores.

The reflectance of optical fiber probe sources is collected only through the individual optical fibers of the probe.

SFDI source-detector arrangements

The SFDI datasets are computed for two source-detector configurations and include raw reflectance and the corresponding frequency-domain reflectance, which is computed for spatial frequencies from 0.00 to 0.80 mm^-1 in 0.01 mm^-1 steps:

• A normally incident Line source and a radial Radial(Axis(0.0, stop=0.15, n=4000, logscale=True), cosmin=0.98481) reflectance detector that uses 4000 logarithmically spaced concentric accumulators from 0 to 150 mm. The acceptance angle is limited to 10°. Hankel transform is used to compute the spatial frequency-domain reflectance. Note that this transform produces real values.

A Radial detector with logarithmically spaced accumulators. The outermost accumulator is highlighted with a gray fill

• A normally incident Line source and a tilted linear detector with 20° incidence (along the x axis). The accumulators of the detector extend to infinity along the positive and negative y axis and follow a logarithmic spacing along the positive and negative direction of the x axis SymmetricX(SymmetricAxis(center=0.0, range=0.15, n_half=4000, logscale=True), cosmin=0.98480). The described detector uses 8000 (4000 in each direction along the :math:x axis) logarithmically spaced accumulators x=-150 to x=150; mm. The acceptance angle of the detector is limited to 10° around the tilted detector axis. Fourier transform is used to compute the spatial frequency-domain reflectance. Note that this transform produces complex values with amplitude and phase information.

A SymmetricX detector with logarithmically spaced accumulators around the central axis. The first and last accumulators are highlighted with a gray fill.

Note that the SFDI datasets are run with 1000 million photon packets and that the simulation termination radius is set to 150 mm.

Dataset files

Datasets are available as compressed numpy data files that are organized as follows:

data/mcml/<sample>/<source>/<detector>/<pf>/<pf_param_1>/<pf_param_2>/mua-<mua>-musr-<musr>-invcm.npz

The values of placeholders <> are as follows:

• <sample> can take the following values:

  • 1-layer-semiinfinite

    A single sample layer of infinite thickness.

• <source> is the type of the photon packet source / probe used in the datasets:

  • line

    Infinitely narrow line source (Line).

  • collimated-200um

    A 200  µm beam diameter (UniformBeam).

  • gaussian-fwhm-100um

    A Gaussian beam with 100 µm FWHM (GaussianBeam).

  • fiber-200um-0_22na

    A 200 µm, 0.22 NA fiber source (UniformFiber).

  • six-around-one-200um-0_22na

    A six-around-one layout optical fibers (200 µm core, 220 µm cladding, 0.22 NA) (SixAroundOne) with the central optical fiber used as the source (UniformFiber). The fibers are tightly packed.

  • six-around-one-400um-0_22na

    For a six-around-one layout optical fibers (400 µm core, 420 µm cladding, 0.22 NA) (SixAroundOne) with the central optical fiber used as the source (UniformFiber). The fibers are tightly packed.

  • six-linear-array-200um-0_22na

    For a linear layout of 6 optical fibers (200 µm core, 220 µm cladding, 0.22 NA) (LinearArray) with the leftmost optical fiber used as the source (UniformFiber). The fibers are tightly packed.

  • single-fiber-100um-0_22na

    A single fiber layout (100 µm core, 120 µm cladding, 0.22 NA) (LinearArray).

  • single-fiber-200um-0_22na

    A single fiber layout (200 µm core, 220 µm cladding, 0.22 NA) (LinearArray).

  • single-fiber-400um-0_22na

    A single fiber layout (400 µm core, 420 µm cladding, 0.22 NA) (LinearArray).

  • single-fiber-400um-0_22na

    A single fiber layout (800 µm core, 820 µm cladding, 0.22 NA) (LinearArray).

• <detector> is the type of detector used by the datasets:

  • radial

    For simple sources with laterally uniform source-sample boundary,

  • probe

    For optical fiber probes with surface layout.

• <pf> is the type of scattering phase function used in the datasets:

  • hg for HG.

  • mhg for MHG.

  • gk for GK.

  • mie-polystyrene for MIE - a water suspension of polystyrene spheres.

  • mie-fusedsilica for MIE - a water suspension of fused silica spheres.

• pf_param_1: is the first parameter of the scattering phase function formatted with two decimal digits and using _ as the decimal separator:

  • g-<g> for HG, e.g. g-0_10 for g=0.1.

  • g-<g> for MHG, e.g. g-0_50 for g=0.5.

  • g-<g> for GK, e.g. g-0_90 for g=0.9.

  • diameter-<d>um MIE, e.g. diameter-0_25 for d=0.25 µm.

• pf_param_2: is the second parameter of the scattering phase function formatted with two decimal digits and using _ as the decimal separator. An exception to this rule is the wavelength parameter of the MIE scattering phase function that is converted to nm and formatted as an integer. This placeholder is not used with the HG scattering phase function.

  • b-<b> for MHG, e.g. b-0_60 for β=0.6.

  • a-<a> for GK, e.g. a-0_50 for α=0.5.

  • wavelength-<w>nm for MIE, e.g. wavelength-500nm for w=500 nm.

• <mua> is the absorption coefficient in units of cm^-1 with two decimal digits and _ as the decimal separator, e.g 2_50 for µ_a=2.5 ^-1.

• <musr> is the reduced scattering coefficient in units of cm^-1 with two decimal digits and _ as a decimal separator, e.g 20_00 for µ_a=20.0 cm^-1.

Voxelized media datasets (MCVOX)

These datasets include fluence/energy deposition data simulated with the MC kernel for voxelized media. A two-layer skin model with an embedded blood vessel is used. The depth/position of the blood vessel along the z axis is varied from 0.2 to 0.8 mm in steps of 0.025 mm. The refractive index of the surrounding medium is set to 1.337. The simulations are run with 1000 million photon packets.

A two-layer skin model with an embedded blood vessel

	Parameter	Value	Description
Line			normally incident
Material	µa	16.5724 cm-1	epidermis
	µs	375.9398 cm-1
	n	1.337
	pf	HG(0.9)
Material	µa	45.85 cm-1	dermis
	µs	356.5406 cm-1
	n	1.337
	pf	HG(0.9)
Material	µa	230.5427 cm-1	blood vessel
	µs	93.985 cm-1
	n	1.337
	pf	HG(0.9)
Fluence	xaxis	Axis(start=-502.5e-6, stop=502.5e-6, n=201)	energy deposition detector
	yaxis	Axis(start=-502.5e-6, stop=502.5e-6, n=201)
	zaxis	Axis(start=0.0, stop=0.001, n=200)
Cartesian	xaxis	Axis(start=-502.5e-6, stop=502.5e-6, n=201)	reflectance/transmittance detector
	yaxis	Axis(start=-502.5e-6, stop=502.5e-6, n=201)
Blood vessel	diameter	200.0 μm	in dermis
	position	(x, y) = (0, 0)
	z	from 0.2 to 0.8 in 0.025 mm steps
	direction	(x, y, z) = (0, 1, 0)
Epidermis	thickness	100 μm

Illustration of the Cartesian detector that is used to collect the reflectance and transmittance.

Energy deposition mean along the y axis for the above configuration of a 2-layer skin with an embedded blood vessel

Dataset files

Datasets are available as compressed numpy data files that are organized as follows:

data/mcvox/fluence/2-layer-skin-<diameter>um-vessel-<depth>um-depth-deposition.npz

The values of placeholders <> are as follows:

• <diameter> is the diameter of the blood vessel in units of μm, formatted as an integer value, e.g 200 for a 200 μm blood vessel.

• <depth> is the z coordinate (depth) of the blood vessel in units of μm, formatted as an integer value, e.g 500 for z=500 μm.

Sampling volume datasets (SV)

The sampling volume dataset is computed for a semi-infinite homogeneous medium for an optical fiber probe with two optical fibers placed at a distance of 0.5 mm. The refractive index of the surrounding medium is set to 1.0. Simulations are run in batches until 1,000,000 photon packet traces that reach the detector fiber are collected and converted to sampling volume information. The trace capacity is limited to 1000 events. The simulation termination radius is set to 25 mm.

Sampling volume for a probe with two optical fibers

	Parameter	Value	Description
LinearArray	dcore	200 μm	linear layout of 2 fibers
	dcladding	220 μm
	ncore	1.462
	NA	0.22
	spacing	500 μm
	diameter	6.0 mm
	reflectivity	0.6
Trace	maxlen	1000	packet trace configuration
SamplingVolume	xaxis	Axis(start=-0.00075, stop=0.00075, n=300)
	yaxis	Axis(start=-0.00075, stop=0.00075, n=300)
	zaxis	Axis(start=0.0, stop=0.001, n=200)	sampling volume voxelization
Layer	μa	2.0 cm-1	sample layer
	μs	500 cm-1
	n	1.337
	pf	HG(0.95)

Sampling volume mean along the y axis for the above configuration of optical probe with two optical fibers

Dataset files

Datasets are available as compressed numpy data files that are organized as follows:

data/mcml/1-layer-semiinfinite/sv/reflectance/fiber-200um-0_22na/sds-<sds>um/hg/g-<g>/um-mua-<mua>-musr-<musr>-invcm.npz

The values of placeholders <> are as follows:

• <sds> is the distance between the centers of the source and detector fibers in units of μm, formatted as an integer value, e.g 500 for a 500 μm distance.

• <g> is the anisotropy formatted with two decimal digits and _ as the decimal separator, e.g 0_15 for g=0.15.

• <mua> is the absorption coefficient in units of cm^-1 with two decimal digits and _ as the decimal separator, e.g 2_50 for μ_a=2.5 cm^-1.

• <musr> is the reduced scattering coefficient in units of cm^-1 with two decimal digits and _ as a decimal separator, e.g 20_00 for μ_s'=20.0 cm^-1.

Citing MC Dataset

We, the authors of MC Dataset, expect that the package is used in accordance with the GPL3+ license and that any work using the MC Dataset package also cites the project and at least one of the following references:

• M. Bürmen, F. Pernuš, and P. Naglič, MCDataset: a public reference dataset of Monte Carlo simulated quantities for multilayered and voxelated tissues computed by massively parallel PyXOpto Python package, J. Biomed. Opt., 27 (8), 083012 (2022), https://doi.org/10.1117/1.JBO.27.8.083012.

• P. Naglič, F. Pernuš, B. Likar, and M. Bürmen, Limitations of the commonly used simplified laterally uniform optical fiber probe-tissue interface in Monte Carlo simulations of diffuse reflectance, Biomed. Opt. Expres, 6 (10), 3973-3988 (2015), https://doi.org/10.1364/BOE.6.003973.

• P. Naglič, F. Pernuš, B. Likar, and M. Bürmen, Lookup table-based sampling of the phase function for Monte Carlo simulations of light propagation in turbid media, Biomed. Opt. Expres, 8 (3), 1895-1910 (2017), https://doi.org/10.1364/BOE.8.001895.

For alternative licensing options of MC Dataset please contact us at [email protected].