# SPDX-FileCopyrightText: 2021 Division of Intelligent Medical Systems, DKFZ
# SPDX-FileCopyrightText: 2021 Janek Groehl
# SPDX-License-Identifier: MIT
[docs]class StandardProperties:
"""
This class contains a listing of default parameters that can be used.
These values are sensible default values but are generally not backed up by proper scientific references,
or are rather specific for internal use cases.
"""
AIR_MUA = 1e-10
AIR_MUS = 1e-10
AIR_G = 1.0
GELPAD_MUA = 1e-10
GELPAD_MUS = 1e-10
GELPAD_G = 1.0
# @article{Zhang:09,
# author = {Xiaodong Zhang and Lianbo Hu and Ming-Xia He},
# journal = {Opt. Express},
# number = {7},
# pages = {5698--5710},
# publisher = {OSA},
# title = {Scattering by pure seawater: Effect of salinity},
# volume = {17},
# month = {Mar},
# year = {2009},
# doi = {10.1364/OE.17.005698},
# and https://www.oceanopticsbook.info/view/optical-constituents-of-the-ocean/water
WATER_MUS = 1e-10
WATER_G = 1.0
# @article{Kedenburg:12,
# author = {S. Kedenburg and M. Vieweg and T. Gissibl and H. Giessen},
# journal = {Opt. Mater. Express},
# number = {11},
# pages = {1588--1611},
# publisher = {OSA},
# title = {Linear refractive index and absorption measurements of nonlinear optical liquids in the visible and near-infrared spectral region},
# volume = {2},
# month = {Nov},
# year = {2012},
# url = {http://www.osapublishing.org/ome/abstract.cfm?URI=ome-2-11-1588},
# doi = {10.1364/OME.2.001588},
HEAVY_WATER_MUA = 0.0008
# @book{marx2013rosen,
# title={Rosen's Emergency Medicine-Concepts and Clinical Practice E-Book},
# author={Marx, John and Walls, Ron and Hockberger, Robert},
# year={2013},
# publisher={Elsevier Health Sciences}
# }
BODY_TEMPERATURE_CELCIUS = 37.0
# @techreport{hasgall2018database,
# title = {IT’IS Database for thermal and electromagnetic parameters of biological tissues.
# Version 4.0, May 15, 2018. doi: 10.13099},
# author = {Hasgall, PA and Di Gennaro, F and Baumgartner, C and Neufeld, E and Lloyd, B and Gosselin,
# MC and Payne, D and Klingenb{\"o}ck, A and Kuster, N},
# year = {2018},
# institution = {VIP21000 - 04 - 0.Onl: www.itis.ethz.ch / database}
# }
DENSITY_GENERIC = 1000 # kg/m³
DENSITY_AIR = 1.16
DENSITY_MUSCLE = 1090.4
DENSITY_BONE = 1908 # Cortical Bone
DENSITY_BLOOD = 1049.75
DENSITY_SKIN = 1109
DENSITY_FAT = 911
DENSITY_GEL_PAD = 890
DENSITY_WATER = 1000
DENSITY_HEAVY_WATER = 1107
DENSITY_LYMPH_NODE = 1035
SPEED_OF_SOUND_GENERIC = 1540.0 # m/s
SPEED_OF_SOUND_AIR = 343.0
SPEED_OF_SOUND_MUSCLE = 1588.4
SPEED_OF_SOUND_BONE = 3514.9 # Cortical bone
SPEED_OF_SOUND_BLOOD = 1578.2
SPEED_OF_SOUND_SKIN = 1624.0
SPEED_OF_SOUND_FAT = 1440.2
SPEED_OF_SOUND_GEL_PAD = 1583.0
SPEED_OF_SOUND_WATER = 1482.3
SPEED_OF_SOUND_HEAVY_WATER = 1540
SPEED_OF_SOUND_LYMPH_NODE = 1586
ALPHA_COEFF_GENERIC = 0.02 # dB/cm/MHz
ALPHA_COEFF_AIR = 3.3875e-3
ALPHA_COEFF_MUSCLE = 0.6175
ALPHA_COEFF_BONE = 4.7385 # Cortical bone
ALPHA_COEFF_BLOOD = 0.20
ALPHA_COEFF_SKIN = 0.35
ALPHA_COEFF_FAT = 0.3785
ALPHA_COEFF_GEL_PAD = 0.277
ALPHA_COEFF_WATER = 2.1976e-3
ALPHA_COEFF_LYMPH_NODE = 2.50
[docs]class OpticalTissueProperties:
"""
This class contains a listing of optical tissue parameters as reported in literature.
The listing is not the result of a meta analysis, but rather uses the best fitting paper at
the time pf implementation.
Each of the fields is annotated with a literature reference or a descriptions of how the particular
values were derived for tissue modelling.
"""
# Background oxygenation assumed arbitrarily, to cover a large range of oxygenation values
BACKGROUND_OXYGENATION = 0.5
BACKGROUND_OXYGENATION_VARIATION = 0.5
# Venous blood parameters taken from the referenced literature. <60% SvO2 were reported as critical. Normal values
# are reported as 70%.
# @article{molnar2018monitoring,
# title={Monitoring of tissue oxygenation: an everyday clinical challenge},
# author={Molnar, Zsolt and Nemeth, Marton},
# journal={Frontiers in medicine},
# volume={4},
# pages={247},
# year={2018},
# publisher={Frontiers}
# }
VENOUS_OXYGENATION = 0.7
VENOUS_OXYGENATION_VARIATION = 0.1
# Arterial blood parameters taken from the referenced literature.
# @article{merrick1976continuous,
# title={Continuous, non-invasive measurements of arterial blood oxygen levels},
# author={Merrick, Edwin B and Hayes, Thomas J},
# journal={Hewlett-packard J},
# volume={28},
# number={2},
# pages={2--9},
# year={1976}
# }
ARTERIAL_OXYGENATION = 0.95
ARTERIAL_OXYGENATION_VARIATION = 0.05
# Tissue Property derived from the meta analysis by Steve Jacques in 2013:
# @article{jacques2013optical,
# title={Optical properties of biological tissues: a review},
# author={Jacques, Steven L},
# journal={Physics in Medicine \& Biology},
# volume={58},
# number={11},
# pages={R37},
# year={2013},
# publisher={IOP Publishing}
# }
MUS500_BACKGROUND_TISSUE = 191.0 # Table 2: Average over all other soft tissue
FRAY_BACKGROUND_TISSUE = 0.153 # Table 2: Average over all other soft tissue
BMIE_BACKGROUND_TISSUE = 1.091 # Table 2: Average over all other soft tissue
MUS500_MUSCLE_TISSUE = 161.0 # Table 2: Average over all other soft tissue
FRAY_MUSCLE_TISSUE = 0.21 # Table 2: Average over all other soft tissue
BMIE_MUSCLE_TISSUE = 1.5 # Table 2: Average over all other soft tissue
MUS500_EPIDERMIS = 93.01 # Bashkatov et al. 2011 but adjusted for epidermis anisotropy
FRAY_EPIDERMIS = 0.29 # Table 1; Salomatina et al 2006; One value for epidermis
BMIE_EPIDERMIS = 2.8 # Table 1; Salomatina et al 2006; One value for epidermis
MUS500_DERMIS = 175.0 # Bashkatov et al. 2011 but adjusted for DERMIS_ANISOTROPY
FRAY_DERMIS = 0.1 # Table 1; Salomatina et al 2006; One value for dermis
BMIE_DERMIS = 3.5 # Table 1; Salomatina et al 2006; One value for dermis
MUS500_FAT = 193.0 # Table 2 average fatty tissue
FRAY_FAT = 0.174 # Table 2 average fatty tissue
BMIE_FAT = 0.447 # Table 2 average fatty tissue
MUS500_BLOOD = 1170 # Table 1 Alexandrakis et al 2005
FRAY_BLOOD = 0.0 # Table 1 Alexandrakis et al 2005
BMIE_BLOOD = 0.93 # Table 1 Alexandrakis et al 2005
MUS500_BONE = 153.0 # Table 2 Mean for bone
FRAY_BONE = 0.022 # Table 2 Mean for bone
BMIE_BONE = 0.326 # Table 2 Mean for bone
STANDARD_ANISOTROPY = 0.9 # Average anisotropy of measured values presented in paper
DERMIS_ANISOTROPY = 0.715
BLOOD_ANISOTROPY = 0.98
# Water content of bone:
# @article{timmins1977bone,
# title={Bone water},
# author={Timmins, PA and Wall, JC},
# journal={Calcified tissue research},
# volume={23},
# number={1},
# pages={1--5},
# year={1977},
# publisher={Springer}
# }
WATER_VOLUME_FRACTION_BONE_MEAN = 0.19
WATER_VOLUME_FRACTION_BONE_STD = 0.01
# Adult body composition derived values
# @article{forbes1953composition,
# title={The composition of the adult human body as determined by chemical analysis},
# author={Forbes, RM and Cooper, AR and Mitchell, HH and others},
# journal={J Biol Chem},
# volume={203},
# number={1},
# pages={359--366},
# year={1953}
# }
WATER_VOLUME_FRACTION_SKIN = 0.58
WATER_VOLUME_FRACTION_HUMAN_BODY = 0.68
# Muscle tissue blood volume fraction:
# @article{vankana1998mechanical,
# title={Mechanical blood-tissue interaction in contracting muscles: a model study},
# author={Vankana, WJ and Huyghe, Jacques M and van Donkelaar, Corrinus C and Drost, Maarten R and Janssen,
# Jan D and Huson, A},
# journal={Journal of Biomechanics},
# volume={31},
# number={5},
# pages={401--409},
# year={1998},
# publisher={Elsevier}
# }
BLOOD_VOLUME_FRACTION_MUSCLE_TISSUE = 0.01 # Value of arterial bvf at t0 in fig 3.
BLOOD_PLASMA_FRACTION = 0.55 # This value seems to be widely accepted.
# Mean and spread calculated from europeans from figure 2C, averaged over both
# photoexposed and photoprotected simpa_examples.
# @article{alaluf2002ethnic,
# title={Ethnic variation in melanin content and composition in photoexposed and photoprotected human skin},
# author={Alaluf, Simon and Atkins, Derek and Barrett, Karen and Blount, Margaret and Carter,
# Nik and Heath, Alan},
# journal={Pigment Cell Research},
# volume={15},
# number={2},
# pages={112--118},
# year={2002},
# publisher={Wiley Online Library}
# }
MELANIN_VOLUME_FRACTION_MEAN = 0.014
MELANIN_VOLUME_FRACTION_STD = 0.003
# Approximated mean of figure 3
# @inproceedings{antunes2019optical,
# title = {Optical Properties on Bone Analysis: An Approach to Biomaterials},
# author = {Antunes, Andrea and Pontes, Jos{\'e} HL and Monte, Adamo FG and Barbosa, Alcimar and Ferreira,
# Nuno MF},
# booktitle = {Multidisciplinary Digital Publishing Institute Proceedings},
# volume = {27},
# number = {1},
# pages = {36},
# year = {2019}
# }
BONE_ABSORPTION = 1.8
# Approximated table 2 with gaussian fit
# @article{bugter2021detecting,
# title={Detecting head and neck lymph node metastases with white light reflectance spectroscopy; a pilot study},
# author={Bugter, Ois{\'\i}n and Aaboubout, Yassine and Algoe, Mahesh and de Bruijn, Henri{\"e}tte S and Keereweer, Stijn and Sewnaik, Aniel and Monserez, Dominiek A and Koljenovi{\'c}, Senada and Hardillo, Jose AU and Robinson, Dominic J and others},
# journal={Oral Oncology},
# volume={123},
# pages={105627},
# year={2021},
# publisher={Elsevier}
# }
BLOOD_VOLUME_FRACTION_LYMPH_NODE = 0.14
BLOOD_VOLUME_FRACTION_LYMPH_NODE_VARIATION = 0.07
LYMPH_NODE_OXYGENATION = 0.73
LYMPH_NODE_OXYGENATION_VARIATION = 0.15
[docs]class MorphologicalTissueProperties:
"""
This class contains a listing of morphological tissue parameters as reported in literature.
The listing is not the result of a meta analysis, but rather uses the best fitting paper at
the time pf implementation.
Each of the fields is annotated with a literature reference or a descriptions of how the particular
values were derived for tissue modelling.
"""
# @article{ashraf2010size,
# title={Size of radial and ulnar artery in local population},
# author={Ashraf, Tariq and Panhwar, Ziauddin and Habib, Sultana and Memon, Muhammad Anis and Shamsi,
# Fahad and Arif, Javed},
# journal={JPMA-Journal of the Pakistan Medical Association},
# volume={60},
# number={10},
# pages={817},
# year={2010}
# }
RADIAL_ARTERY_DIAMETER_MEAN_MM = 2.25
RADIAL_ARTERY_DIAMETER_STD_MM = 0.4
ULNAR_ARTERY_DIAMETER_MEAN_MM = 2.35
ULNAR_ARTERY_DIAMETER_STD_MM = 0.35
# Accompanying veins diameter reference. They specifically only mention the ulnar accompanying vein properties.
# We assume a non-significant similarity for the radial accompanying vein.
# @incollection{yang_ulnar_2018,
# title = {Ulnar {Artery} to {Superficial} {Arch} {Bypass} with a {Vein} {Graft}},
# booktitle = {Operative {Techniques}: {Hand} and {Wrist} {Surgery}},
# author = {Yang, Guang and Chung, Kevin C.},
# year = {2018},
# doi = {10.1016/B978-0-323-40191-3.00081-0},
# pages = {732--737},
# }
RADIAL_VEIN_DIAMETER_MEAN_MM = 1.0
RADIAL_VEIN_DIAMETER_STD_MM = 0.2
ULNAR_VEIN_DIAMETER_MEAN_MM = 1.0
ULNAR_VEIN_DIAMETER_STD_MM = 0.2
# Median artery diameter reference (at the P2 point):
# @article{hubmer2004posterior,
# title={The posterior interosseous artery in the distal part of the forearm. Is the term ‘recurrent branch of
# the anterior interosseous artery’justified?},
# author={Hubmer, Martin G and Fasching, Thomas and Haas, Franz and Koch, Horst and Schwarzl, Franz and Weiglein,
# Andreas and Scharnagl, Erwin},
# journal={British journal of plastic surgery},
# volume={57},
# number={7},
# pages={638--644},
# year={2004},
# publisher={Elsevier}
# }
MEDIAN_ARTERY_DIAMETER_MEAN_MM = 0.6
MEDIAN_ARTERY_DIAMETER_STD_MM = 0.25
# TODO CITE
# Assumption: about half the size of the radial and ulnar accompanying veins due to size of the respective
# artery in comparison to the radial and ulna artery
MEDIAN_VEIN_DIAMETER_MEAN_MM = 0.5
MEDIAN_VEIN_DIAMETER_STD_MM = 0.1
# Thickness of the dermis and epidermis approximated with values for the hand. Averaged for
# @article{oltulu2018measurement,
# title={Measurement of epidermis, dermis, and total skin thicknesses from six different body regions
# with a new ethical histometric technique},
# author={Oltulu, Pembe and Ince, Bilsev and Kokbudak, Naile and Findik, Sidika and Kilinc, Fahriye and others},
# journal={Turkish Journal of Plastic Surgery},
# volume={26},
# number={2},
# pages={56},
# year={2018},
# publisher={Medknow Publications}
# }
DERMIS_THICKNESS_MEAN_MM = 2.3
DERMIS_THICKNESS_STD_MM = 1.2
EPIDERMIS_THICKNESS_MEAN_MM = 0.22
EPIDERMIS_THICKNESS_STD_MM = 0.1
# Distance of radius and ulnar at resting position, when bones are not crossed
# @article{christensen1968study,
# title={A study of the interosseous distance between the radius and ulna during rotation of the forearm},
# author={Christensen, John B and Adams, John P and Cho, KO and Miller, Lawrence},
# journal={The Anatomical Record},
# volume={160},
# number={2},
# pages={261--271},
# year={1968},
# publisher={Wiley Online Library}
# }
RADIUS_ULNA_BONE_SEPARATION_MEAN_MM = 32.0
RADIUS_ULNA_BONE_POSITION_STD_MM = 2.0
# Subcutaneous veins depth measurements are extrapolated from graphs in table 3.
# The diameter measurement are supposed to resemble the approximate range from figure 15.
# @article{goh2017subcutaneous,
# title={Subcutaneous veins depth measurement using diffuse reflectance images},
# author={Goh, CM and Subramaniam, R and Saad, NM and Ali, SA and Meriaudeau, F},
# journal={Optics express},
# volume={25},
# number={21},
# pages={25741--25759},
# year={2017},
# publisher={Optical Society of America}
# }
SUBCUTANEOUS_VEIN_DEPTH_MEAN_MM = 1.5
SUBCUTANEOUS_VEIN_DEPTH_STD_MM = 0.7
SUBCUTANEOUS_VEIN_DIAMETER_MEAN_MM = 0.8
SUBCUTANEOUS_VEIN_DIAMETER_STD_MM = 0.6
# The following properties were experimentally determined based on data sets provided by Janek Groehl
# (Photoacoustic forearm images) and André Klein (Forearm CT images from full body CTs)
RADIAL_ARTERY_DEPTH_MEAN_MM = 6.0
RADIAL_ARTERY_DEPTH_STD_MM = 0.5
ULNAR_ARTERY_DEPTH_MEAN_MM = 6.0
ULNAR_ARTERY_DEPTH_STD_MM = 0.5
DISTANCE_RADIAL_AND_ULNA_ARTERY_MEAN_MM = 30
DISTANCE_RADIAL_AND_ULNA_ARTERY_STD_MM = 5
RADIUS_BONE_DIAMETER_MEAN_MM = 20.0
RADIUS_BONE_DIAMETER_STD_MM = 2.0
ULNA_BONE_DIAMETER_MEAN_MM = 15.0
ULNA_BONE_DIAMETER_STD_MM = 2.0
MEDIAN_ARTERY_DEPTH_MEAN_MM = 19.0
MEDIAN_ARTERY_DEPTH_STD_MM = 1.0
ACCOMPANYING_VEIN_MEDIAN_DISTANCE_MEAN_MM = 1.0
ACCOMPANYING_VEIN_MEDIAN_DISTANCE_STD_MM = 0.2
ACCOMPANYING_VEIN_DISTANCE_MEAN_MM = 2.5
ACCOMPANYING_VEIN_DISTANCE_STD_MM = 0.4
ACCOMPANYING_VEIN_DEPTH_STD_MM = 1.5
RADIUS_BONE_DEPTH_MEAN_MM = 22.0
RADIUS_BONE_DEPTH_STD_MM = 2.0
ULNA_BONE_DEPTH_MEAN_MM = 22.0
ULNA_BONE_DEPTH_STD_MM = 2.0
# Arbitrary position constants based on the respective coordinate systems
RADIAL_ARTERY_X_POSITION_MEAN_MM = 7.5
ULNAR_ARTERY_X_POSITION_MEAN_MM = RADIAL_ARTERY_X_POSITION_MEAN_MM + DISTANCE_RADIAL_AND_ULNA_ARTERY_MEAN_MM
MEDIAN_ARTERY_X_POSITION_MEAN_MM = RADIAL_ARTERY_X_POSITION_MEAN_MM + DISTANCE_RADIAL_AND_ULNA_ARTERY_MEAN_MM / 2
ARTERY_X_POSITION_UNCERTAINTY_MM = DISTANCE_RADIAL_AND_ULNA_ARTERY_STD_MM / (2**(1/2))