Data set: Blood flow simulation and uncertainty quantification in extensive microvascular networks: Application to brain cortical networks

Author: Rasmussen, Peter M

Publisher: Zenodo

DOI: 10.5281/zenodo.15373376

Source: https://zenodo.org/records/15373376/files/dataDescription.pdf

1/8
Da a ﬁles wi h simula ion esul s unde lying ﬁgu es and summa y s a is ics p esen ed in ables
and ﬁgu es in
PM Rasmussen. Blood ﬂow simula ion and unce ain y quan iﬁca ion in ex ensi e mic o ascula
ne wo ks: Applica ion o b ain co ical ne wo ks. Mic oci cula ion, 2025.
Co esponding au ho
Pe e Mond up Rasmussen, Cen e o Func ionally In eg a i e Neu oscience, Depa men o Clinical
Medicine, Aa hus Uni e si y, Aa hus, Denma k. pm @cﬁn.au.dk. ORCID: 0000-0001-6849-0788
Da a se DOI
h ps:// doi.o g/10.5281/zenodo.15373376
Da a se license
Da a ﬁles: CC BY 4.0 license, h ps://c ea i ecommons.o g/licenses/by/4.0/
R analysis sc ip s: GNU GPL 3 license, h ps://www.gnu.o g/licenses/gpl-3.0. x
1. Re e ences
The da a se is published oge he wi h he a icle:
[1] PM Rasmussen. Blood ﬂow simula ion and unce ain y quan iﬁca ion in ex ensi e mic o ascula
ne wo ks: Applica ion o b ain co ical ne wo ks. Mic oci cula ion 2025.
The da a se con ains de i a i es o he ollowing Zenodo sou ces:
[2] F anca Schmid. (2017). A e aged esul s o blood ﬂow simula ions wi h disc e e RBC acking o
mic o ascula ne wo ks [Da a se ]. Zenodo. h ps://doi.o g/10.5281/zenodo.758632
[3] Schmid, F., Con i, G., Jenny, P., & Webe , B. (2021). Time-a e aged simula ions esul s o bi-phasic
blood ﬂow simula ions in ealis ic mic o ascula ne wo ks o a ious single- and mul i-capilla y
occlusion scena ios. [Da a se ]. Zenodo. h ps://doi.o g/10.5281/zenodo.5115639
The da a se con ains alues ha has been ex ac ed om:
[4] Figu e 1 in Taylo ZJ, Hui ES, Wa son AN, Nie X, Dea do RL, Jensen JH, e al. Mic o ascula basis
o g ow h o small in a c s ollowing occlusion o single pene a ing a e ioles in mouse co ex. J Ce eb
Blood Flow Me ab. 2016.
2. Con en
Uncomp ess zenodoDeposi . a .gz.
The di ec o y R con ains R code o c ea ing summa y ﬁgu es and ables om he da a ﬁles. Run he
sc ip main.R. Ins all equi ed R packages i needed – package lis p o ided a he op o he sc ip .
The di ec o y da a con ains . x ﬁles wi h da a unde lying summa y ﬁgu es and ables. Please e e o
he desc ip ions o indi idual ﬁles in he ollowing sec ions. The di ec o y also con ains a subdi ec o y
png, wi h a ious ne wo k plo s used o c ea ing ﬁgu e panels in R. Sou ce da a o hese ne wo k
plo s a e a ailable in he . x ﬁles.
Re .: 2025.09.04.
2/8
3. Segmen da a
File naming:
segmen Expo s_{NW1/NW2}.{ e /cal}.{Da a/Vi o/Vi o/Esl}{“”/.ABC}.{“”,mu*}. x
Da a con en :
Me ics in columns, segmen s in ows, column heade s in ﬁ s ow.
Column
Me ic
Physical uni / no es
nw
Ne wo k name, see [1]
NA
model
Model name, see [1] Table 2
NA
segIdx
Segmen index
In ege : {1, … , numbe O Segmen s}
segType
Segmen ype
In ege : {0,1,2,3,4,5} co esponding o {SA , SV,
DA+A, V+AV, C, UNK }, see [1].
segDia
Segmen diame e
µm
segLen
Segmen Leng h
µm
laye
Analysis laye
AL1-AL6, see [1].
segGen
Segmen gene a ion,
see [1] Figu e 1
Segmen gene a ion ela i e o bounda y node,
see [1].
segP essu e
Mid-segmen p essu e
mmHg
segFlowB
Segmen blood ﬂow a e
(µm)^3/s
segHc
Segmen discha ge hema oc i
F ac ion (be ween 0 and 1)
segShea S ess
Segmen shea s ess
dyn/(cm)^2
segVelB
Segmen blood eloci y
mm/s
segVelC
Segmen RBC eloci y
mm/s
DAR
Di ec ion ag eemen a e
%
No es:
Segmen me ics o he calib a ion models, *.cal.*.ABC. x , a e a e ages ac oss 1000 MCMC i e a ions,
see [1]. SegVelC o he e e ence models, *. e .*.*. x is NaN, see [1]. The *. e .Vi o.ABC.mu*. x ﬁles
con ain segmen me ics o a ious p essu e de iance o se s, see Figu e 12 in File S3 in [1].
3/8
4. Pa h da a
File naming:
pa hsExpo s_{NW1/NW2}.{ e /cal}.{Da a/Vi o/Vi o/Esl}{“”/.ABC}. x
Da a con en :
Me ics in columns, pa hs in ows, column heade s in ﬁ s ow.
Column
Me ic
Physical uni / no es
nw
Ne wo k name, see [1]
NA
model
Model name, see [1] Table 2
NA
idxPa h
Pa h index
In ege : {1, … , numbe O Pa hs}
laye
Analysis laye assigned o
pa h, see [1]
AL1-AL6, see [1]
ﬂowB
Blood ﬂow a e along pa h
(µm)^3/s
ﬂowC
RBC ﬂow a e along pa h
(µm)^3/s
dpSA
P essu e d op ac oss essel
ca ego y SA
mmHg
dpA
P essu e d op ac oss essel
ca ego y DA+A
mmHg
dpC
P essu e d op ac oss essel
ca ego y C
mmHg
dpV
P essu e d op ac oss essel
ca ego y AV+V
mmHg
dpSV
P essu e d op ac oss essel
ca ego y SV
mmHg
zCapIn
Capilla y inpu dep h
µm
zCapOu
Capilla y ou pu dep h
µm
da SA
Di ec ion ag eemen a e
a e aged ac oss pa h SA
segmen s
%
da A
Di ec ion ag eemen a e
a e aged ac oss pa h DA+A
segmen s
%
da C
Di ec ion ag eemen a e
a e aged ac oss pa h C
segmen s
%
da V
Di ec ion ag eemen a e
a e aged ac oss pa h AV+V
segmen s
%
da SV
Di ec ion ag eemen a e
a e aged ac oss pa h SV
segmen s
%
No es:
Pa hs o calib a ion models, *.cal.*. ABC. x , we e ﬁ s accumula ed ac oss 1000 MCMC samples, see
[1]. Pa h ﬂow a es and p essu e d ops ep esen pa h a e ages ac oss 1000 MCMC samples o he
espec i e se s o accumula ed pa hs. FlowC o he e e ence models, *. e .*.*. x , is 0, see [1].
4/8
5. Da a used o eloci y ﬁ s
File naming:
{emp/ e }VelCDa a. x
Da a con en :
Me ics in columns, da a poin s in ows, column heade s in ﬁ s ow.
Column
Me ic
Physical uni / no es
segDia
Segmen diame e
µm
segVelC
Segmen RBC eloci y
mm/s
segType
Segmen ype, see [1]
A o Ven
No es:
Da a in he empVelCDa a. x was ex ac ed om Figu e 1 in Taylo ZJ, Hui ES, Wa son AN, Nie X,
Dea do RL, Jensen JH, e al. Mic o ascula basis o g ow h o small in a c s ollowing
occlusion o single pene a ing a e ioles in mouse co ex. J Ce eb Blood Flow Me ab. 2016.
Da a in e VelCDa a. x was de i ed om he e e ence da a se , e Da a, om essels
ca ego ies A ( esp. Ven) co esponding o essel ca ego ies [0,2] ( esp. [1,3]) wi h diame e <30
µm and in AL1, see [1].
5/8
6. Calib a ion ﬁ s and mean squa ed e o s
File naming:
modelFi _{NW1/NW2}.cal.{Vi o/Vi o/Esl}.ABC. x
Da a con en :
Me ics in columns, da a poin s in ows, column heade s in ﬁ s ow.
Column
Me ic
Physical uni / no es
nw
Ne wo k name, see [1]
NA
model
Model name, see [1] Table 2
NA
segIdx
Segmen index
In ege
segType
Segmen ype
In ege : {0,1,2,3} co esponding o {SA, SV,
DA+A, V+AV }, see [1].
me ic
P edic ed me ic
S ing { elC}
yTa ge
Ta ge RBC eloci y
mm/s
yHa
P edic ed RBC eloci y
mm/s
No es:
P edic ed RBC eloci ies a e a e ages ac oss 1000 MCMC samples.
File naming:
modelFi Mse_{NW1/NW2}.cal.{Vi o/Vi o/Esl}.ABC. x
Da a con en :
Me ics in columns, da a poin s in ows, column heade s in ﬁ s ow.
Column
Me ic
Physical uni / no es
nw
Ne wo k name, see [1]
NA
model
Model name, see [1] Table 2
NA
mseVelC
Mean squa ed RBC eloci y
e o
(mm/s)^2
No es:
Rows con ain mean squa ed RBC eloci y e o (a e aged ac oss essel segmen s) o indi idual
MCMC samples, 1000 ows in o al.

6/8
7. I e a ion s a s, hema oc i i e a ions
File naming:
i e S a .{NW1/NW2}.cal.{Vi o/Vi o/Esl}.ABC.{“”,w10}. x
Da a con en :
Me ics in columns, da a poin s in ows, column heade s in ﬁ s ow.
Column
Me ic
Physical uni / no es
nI e
I e a ions a con e gence
In ege
nBi u SubTh
Numbe o bi u ca ions below
h eshold φ3 (0.9) a
con e gence.
See Sec ion 3.3 in File S1 in [1].
nBi u SupTh
Numbe o bi u ca ions abo e
h eshold φ3 (0.9) a
con e gence.
See Sec ion 3.3 in File S1 in [1].
No es:
None.
7/8
8. Segmen blood ﬂow a es and hema oc i s in indi idual hema oc i i e a ions
File naming:
NW1.cal.ESL.ABC{“ ”, .w 1 0}_{ﬂow,hc }I e a ions_idxSample42. x
Da a con en :
Me ic iden iﬁe {segFlowB, segHc } in he ﬁ s column and alues in emaining columns (numbe o
segmen s +1 columns in o al). Indi idual i e a ions in ows. Blood ﬂow a es (segFlowB) a e in
(µm)^3/s and discha ge hema oc i s (segHc ) a e be ween 0 and 1.
No es:
None.
8/8
9. Segmen in o ma ion and node in o ma ion
File naming:
segmen In o_{NW1/NW2/NW1.noT im/NW2.noT im}. x
Da a con en :
Me ics in columns, alues in ows, column heade s in ﬁ s ow.
Column
Me ic
Physical uni / no es
nw
Ne wo k name, see [1]
NA
segIdx
Segmen index
In ege : {1, … , numbe O Segmen s}
segType
Segmen ype
S ing: {SA, SV, DA+A, V+AV, C, UNK}, see [1]
segS a Node
Segmen s a node
In ege
segEndNode
Segmen end node
In ege
segDia
Segmen diame e
µm
segLen
Segmen leng h
µm
laye
Analysis laye
AL1-AL6, see [1].
segGen
Segmen gene a ion,
see [1] Figu e 1
Segmen gene a ion ela i e o bounda y node,
see [1].
segIdxO ig
Segmen index in sou ce [2]
In ege . Segmen (edge) index in sou ce [2].
No es:
noT im a e non- immed ne wo k a ian s, see Figu e 1 in File S3 in [1].
File naming:
nodeIn o_{NW1/NW2/ NW1.noT im/NW2.noT im}. x
Da a con en :
Me ics in columns, alues in ows, column heade s in ﬁ s ow.
Column
Me ic
Physical uni / no es
nw
Ne wo k name, see [1]
NA
nodeIdx
Node index
In ege : {1, … , numbe O Nodes}
laye
Analysis laye o node
AL1-AL6, see [1].
segType
Segmen ype, only p o ided o
bounda y nodes.
S ing: {SA, SV, DA+A, V+AV, C, UNK} o
bounda y nodes. Emp y s ing o in e io
nodes.
bndNode
I node is a bounda y node.
In ege : 1 i bounda y node. 0 o he wise.
bndNodeABC
I bounda y node was go e ned by
he adap i e me hod o p essu e
bounda y condi ions, see [1].
In ege : 1 i bounda y node and he
adap i e me hod was used o his node. 0
o he wise.
e NodeABC
I in e io node was used as a
e e ence node in he adap i e
me hod o p essu e bounda y
condi ions, see [1].
In ege : 1 i in e io node and he node
was used as a e e ence node in he
adap i e me hod.
g oupIdxABC
G oup membe ship o bounda y
nodes and e e ence nodes in he
adap i e me hod o p essu e
bounda y condi ions, see [1].
In ege : Posi i e in ege co esponding o
g oup index. 0 o he wise.
posX
Node X coo dina e
µm
posY
Node Y coo dina e
µm
posZ
Node Z coo dina e
µm
No es:
noT im a e non- immed ne wo k a ian s, see Figu e 1 in File S3 in [1].

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