Page 1 o 12
Da aTools4Hea
A Eu opean Heal h Da a Toolbox o Enhancing Ca diology Da a In e ope abili y, Reusabili y and P i acy
Miles one MS12:
Documen a ion and use manuals o he oolbox
and VAs a ailable o esea che s, ca diologis s,
and da a manage s
Re e ence MS12_ Da aTools4Hea _AT_30092025
Lead Bene icia y ATH
Au ho (s) Kons an inos Kechagias (ATH), Laia Codó, Ca les
He nandez-Fe e
(BSC), Jo ge Fabila, C is ian
Izquie do (UB)
Dissemina ion le el Public
Means o e i ica ion A ailable a he pla o m and p ojec ’s web-si e
O icial Deli e y Da e 30/09/2025
Da e o alida ion o he WP leade 29/09/2025
Da e o alida ion by he P ojec
Coo dina o
30/09/2025
P ojec Coo dina o Signa u e
Da aTools4Hea is unded by he Eu opean Union’s Ho izon Eu ope
F amewo k Unde G an Ag eemen No. 101057849.
Page 2 o 12
Ve sion Log
Issue Da e Ve sion In ol ed Commen s
18/08/2025
0.1
Kons an inos Kechagias
Ini ial D a & ToC S uc u e
16/09/2025
0.2
Kons an inos Kechagias, Laia
Codó, Ca les He nandez-Fe e ,
Jo ge Fabila, C is ian Izquie do
Fi s Documen Re iew
29/09/2025
0.3
Kons an inos Kechagias, Ca les
He nandez-Fe e , Jo ge Fabila,
C is ian Izquie do
Final D a Re iew
30/09/2025
Final
C is ian Izquie do, Xènia Puig,
Ka im Lekadi
Re ised and co ec ed inal
e sion
Execu i e Summa y
Miles one MS12 es ablishes he a ailabili y o use -o ien ed documen a ion and manuals o he
Da aTools4Hea (DT4H) oolbox and Vi ual Assis an s (VAs). The objec i e is o p o ide end-use s,
namely esea che s, ca diologis s, and da a manage s, wi h s uc u ed guidance on how o na iga e
and in e ac wi h DT4H componen s in hei espec i e con ex s.
The manuals ocus on use lows, ou lining he s eps and in e ac ions equi ed o pe o m ypical asks
wi h he oolbox and VAs. Fo esea che s, he documen a ion p o ides pa hways o explo e da a and
analy ical unc ionali ies; o ca diologis s, i demons a es he in eg a ion o VAs wi hin clinical decision
suppo wo k lows; and o da a manage s, i speci ies how he oolbox suppo s da a access,
go e nance, and compliance.
P epa ed in a concise, accessible, and ole-speci ic manne , he documen a ion enables s akeholde s
o quickly iden i y he unc ionali ies mos ele an o hei ac i i ies. To ensu e usabili y and
dissemina ion, he manuals a e consolida ed in he DT4H documen a ion hub hos ed on Gi Hub, which
se es as he cen al access poin o all componen s and ools.
The means o e i ica ion o his miles one is he con i med a ailabili y o hese use guides and
manuals in he DT4H eposi o ies. This miles one ensu es ha he DT4H oolbox and VAs a e no only
echnically ope a ional bu also p ac ically usable and aligned wi h he wo k lows o he in ended end-
use communi ies.
Page 3 o 12
Table o Con en s
Ve sion Log ................................................................................................................................. 2
Execu i e Summa y .................................................................................................................... 2
Ac onyms .................................................................................................................................... 3
Lis o igu es .............................................................................................................................. 3
1 In oduc ion .............................................................................................................................. 4
1.1 Pu pose o he Miles one (ATH) ...................................................................................... 4
1.2 Rela ion o P ojec Objec i es and Wo k Packages (ATH) ............................................... 4
2 Me hodology ............................................................................................................................ 4
2.1 Documen a ion De elopmen P ocess (BSC, UB) ........................................................... 5
2.2 Ta ge Use G oups (Resea che s, Ca diologis s, Da a Manage s) (BSC, UB) ............... 6
3 Documen a ion and Use Manuals (ATH) ................................................................................. 6
3.1 Pla o m Documen a ion ( echnical manuals) (BSC, UB) ................................................. 6
3.2 Vi ual Assis an Documen a ion (ATH) ........................................................................... 6
3.3 Me ada a Ca alogue ........................................................................................................ 7
3.4 MIP Documen a ion ......................................................................................................... 7
3.5 FLCo e ............................................................................................................................ 7
4 Accessibili y, Dissemina ion, and Ve i ica ion ......................................................................... 12
4.1 A ailabili y in DT4H Reposi o ies (BSC, UB, ATH) ........................................................ 12
5 Conclusion ............................................................................................................................. 12
Ac onyms
FEM: Fede a ed Execu ion Manage
VA: Vi ual Assis an
Lis o igu es
Figu e 1. S uc u e o he cen alized documen a ion eposi o y on Gi Hub Pages
Page 4 o 12
1 In oduc ion
The Da aTools4Hea (DT4H) p ojec deli e s a oolbox o p i acy-p ese ing componen s o
ede a ed ca diology da a analysis, oge he wi h a Vi ual Assis an (VA) o suppo in ui i e use. To
ensu e hese ools can be e ec i ely adop ed, clea documen a ion is equi ed.
Miles one MS12 con i ms he a ailabili y o use manuals o a selec ed se o oolbox componen s
and he VA. These manuals ocus on use lows and ask-o ien ed guidance, enabling esea che s,
ca diologis s, and da a manage s o apply he ools in p ac ice wi hou deep echnical expe ise.
1.1 Pu pose o he Miles one
The pu pose o MS12 is o e i y ha accessible use documen a ion is p o ided o he DT4H oolbox
componen s and he VA. The manuals ou line ypical wo k lows o di e en use g oups and a e
published on bo h he DT4H pla o m and he p ojec websi e, ensu ing anspa ency, usabili y, and
wide up ake o p ojec esul s.
1.2 Rela ion o P ojec Objec i es and Wo k Packages
Miles one MS12 con ibu es o he p ojec ’s objec i es o usabili y, anspa ency, and adop ion by
p o iding ole-speci ic documen a ion o he DT4H oolbox and he Vi ual Assis an . The manuals
enable esea che s, ca diologis s, and da a manage s o ollow clea use lows, ensu ing ha
echnical ou comes can be e ec i ely applied in p ac ice.
This miles one is closely linked o:
● WP6 – In eg a ed Pla o m, Vi ual Assis an s, and Sus ainabili y, which deli e s he oolbox
componen s and he VA add essed in he manuals.
● WP7 – Clinical Use Cases: Design, Implemen a ion and Valida ion, whe e use documen a ion
suppo s es ing and alida ion in clinical se ings.
● WP8 – Coo dina ion, Managemen , Dissemina ion, Communica ion and Exploi a ion, h ough
he publica ion and dissemina ion o manuals ia he DT4H pla o m and p ojec websi e.
Th ough hese connec ions, MS12 ensu es ha echnical de elopmen s a e complemen ed by
accessible documen a ion, acili a ing clinical alida ion and long- e m sus ainabili y.
2 Me hodology
To ensu e ha he documen a ion and use manuals a e easily accessible and consis en ly
main ained, a cen alized documen a ion hub has been es ablished using Gi Hub Pages
(h ps://gi hub.com/Da aTools4Hea /documen a ion-hub). By consolida ing all ma e ials in one place,
he hub p o ides a single-en y poin o esea che s, ca diologis s, and da a manage s, a oiding
agmen a ion and acili a ing in ui i e na iga ion ac oss he pla o m’s esou ces.
The eposi o y has been designed wi h a clea and modula s uc u e ha suppo s bo h anspa ency
and long- e m scalabili y. A he oo le el, each o he main pla o m componen s is alloca ed a
dedica ed olde , namely ai-dashboa d, me ada a-ca alogue, and i ual-assis an , each con aining i s
espec i e documen a ion. Complemen ing hese, a ools-manuals di ec o y has been c ea ed o hos
sub olde s o e e y ool ha can be igge ed ia he main pla o m, wi h each ool main aining i s own
documen a ion space. In addi ion, an asse s olde is included o s o e supplemen a y ma e ials such
as igu es, images, and con igu a ion iles ha en ich he manuals and imp o e use unde s anding.
Page 5 o 12
All manuals a e au ho ed in Ma kdown (.md), a ligh weigh ma kup o ma ha ensu es bo h human
eadabili y and compa ibili y wi h Gi Hub Pages. This choice no only enables s aigh o wa d
collabo a i e edi ing and e sion con ol h ough Gi Hub bu also gua an ees ha upda es and
ex ensions can be in eg a ed wi hou dis up ing he exis ing s uc u e. The Ma kdown-based wo k low
u he suppo s modula g ow h, as new componen s and ools can be added seamlessly while
main aining consis ency in s yle and o ma .
The o e all eposi o y s uc u e is illus a ed in Figu e 1, which p esen s he olde o ganiza ion o he
documen a ion hub. This igu e highligh s he hie a chical a angemen o componen s, ools, and
suppo ing asse s, he eby o e ing use s a clea o e iew o whe e o loca e he documen a ion o
in e es . By combining s uc u ed o ganiza ion, web accessibili y, and collabo a i e edi ing ea u es,
he me hodology ensu es ha he documen a ion emains a eliable, scalable, and use - iendly
esou ce o all a ge s akeholde s.
Figu e 1. S uc u e o he cen alized documen a ion eposi o y on Gi Hub Pages.
2.1 Documen a ion De elopmen P ocess
The de elopmen o documen a ion o indi idual ools ollows a s anda dized wo k low designed o
ensu e consis ency and main ainabili y ac oss he documen a ion hub. Tool de elope s a e equi ed
o use he s anda d “ o k and pull eques ” model, wo king di ec ly wi h he Gi Hub eposi o y a
h ps://gi hub.com/Da aTools4Hea /documen a ion-hub. The p ocess consis s o he ollowing s eps:
1. Access he eposi o y by isi ing h ps://gi hub.com/Da aTools4Hea /documen a ion-hub.
Page 6 o 12
2. Clone o o k he eposi o y and c ea e a dedica ed b anch o he new ool.
C ea e a olde named a e he ool, ollowing CSS naming con en ions (lowe case wo ds
sepa a ed by hyphens, e.g., my-amazing- ool).
3. Add an index.md ile in his olde con aining he main documen a ion, and include any
addi ional .md iles i needed, e e enced om he index.md.
4. Upda e he oo -le el index.md ile by inse ing a link o he new ool’s documen a ion unde
he Tools Manuals sec ion, main aining alphabe ical o de .
Commi and push all changes o he b anch o o k.
5. Open a pull eques o me ge he b anch o o k in o he main b anch o he o icial eposi o y.
Following hese s eps ensu es ha all ool documen a ion is consis en ly in eg a ed in o he
cen alized hub, main aining cla i y, accessibili y, and e sion con ol.
2.2 Ta ge Use G oups (Resea che s, Ca diologis s, Da a Manage s) (BSC, UB)
Fo clinical use s, DT4H FL pla o m in eg a es i ual assis an s, a wide ange o AI models, and
in ui i e in e aces ha allow seamless na iga ion and que y access o s uc u ed pa ien da a, isk
s a i ica ion ools, and diagnos ic models. These ea u es a e designed o suppo decision-making
p ocesses, assis in coho explo a ion, and in eg a e di ec ly in o clinical wo k lows o mo e p ecise
diagnosis and imp o ed pa ien ca e. Ca diologis s can bene i om ede a ion-enabled analy ics,
enabling collabo a i e s udies while sa egua ding pa ien p i acy. The pla o m i sel does no con ain
a speci ic in e ence in e ace, bu clinicians can easily expo hei own gene a ed AI models o be
deployed in hei clinical p ac ice ools. Manual use s o he FL pla o m include AI models explana ions
ha a e easily in e p e able o non- echnical/so wa e de elope s’ expe s.
3 Documen a ion and Use Manuals
3.1 Pla o m Documen a ion ( echnical manuals)
The Fede a ed Execu ion Manage (FEM) was designed o un and moni o da a analy ics ools ac oss
a ne wo k o emo e nodes wi hou exposing hei sensi i e da a o equi ing da a ans e om he
o iginal sou ce.
The guideline is o a esea che o da a scien is o use i hough he AI Dashboa d is loca ed a he
documen a ion hub unde he sec ion o "AI Dashboa d".
You can ind his sec ion he e: h ps://da a ools4hea .gi hub.io/documen a ion-hub/ai-dashboa d/
3.2 Vi ual Assis an Documen a ion
The Vi ual Assis an (VA) was designed o suppo clinical esea che s in ca diology by enabling
na u al language in e ac ion h ough a cha in e ace. I allows esea che s o explo e s udies, disco e
pa ien coho s, and eques me ada a in a ede a ed and p i acy-p ese ing way wi hou equi ing
da a ans e om hospi al nodes. The VA suppo s in e ac ion in se en Eu opean languages, ensu ing
accessibili y ac oss he esea ch communi y. The VA guideline is loca ed a he documen a ion hub
unde he sec ion o "Vi ual Assis an ":
h ps://da a ools4hea .gi hub.io/documen a ion-hub/ i ual-assis an /
Page 7 o 12
3.3 Me ada a Ca alogue
The Da aTools4Hea Ca alogue is an AI- eady ca diology da ase disco e y po al based on he Mica
(OBiBa) pla o m. I p o ides public access o s udy me ada a, da ase desc ip ions, and AI ea u es.
The use manual o esea che s and clinicians is accessible a he documen a ion hub unde he
sec ion o "Me ada a Ca alogue". You can ind his sec ion he e:
h ps://da a ools4hea .gi hub.io/documen a ion-hub/me ada a-ca alogue/
3.4 MIP Documen a ion
The Medical In o ma ics Pla o m (MIP) is a use - iendly ede a ed lea ning and analy ics pla o m
wi h an in ui i e, g aphical use in e ace ailo ed o clinicians.
h ps://gi hub.com/KFilippopoli is/documen a ion-hub/blob/mip-doc/docs/mip/index.md
3.5 FLCo e
This lib a y p o ides a lexible and ex ensible amewo k o unning expe imen s in a ede a ed
lea ning en i onmen , enabling he aining and e alua ion o di e en machine lea ning models ac oss
dis ibu ed da ase s.
Figu e 2. Sc eensho o he Vi ual Resea ch En i onmen (VRE) o DT4H.
The ollowing me hods a e cu en ly implemen ed along wi h he lowe agg ega ion me hod used and
he code used o selec ing a speci ic me hod.
Model
Flw agg ega ion me hod
Code
Logis ic eg ession
Fede a ed A e age
logis ic_ eg ession
SGD classi ie
Fede a ed A e age
ls c
Page 8 o 12
Elas ic ne
Fede a ed A e age
elas ic_ne
Random Fo es
Cus om
weigh ed_ andom_ o es
Deep Lea ning
Fede a ed A e age
neu al_ne wo k
Pa ame e s a e p o ided using a command line in e ace and a e o ganized by ca ego y and include
hei name, ype, de aul alue, and a b ie explana ion. These a gumen s can be modi ied a un ime
o cus omize da a handling, model con igu a ion, aining se up, and in as uc u e de ails. The nex
able summa izes he a iables needed o he clien .
Pa ame e
Type
De aul alue
Desc ip ion
--da ase
s
None
Name o he
da aloade o use
–da a_id
da a_id
s
Iden i ie o he
da ase ile
–
no maliza ion_me ho
d
s
IQR
No maliza ion
me hod. Op ions:
`IQR`, `STD`,
`MIN_MAX`.
– ain_labels
lis [s ]
None
Labels used o
aining.
– a ge _label
lis [s ]
None
Ta ge label(s) o
p edic ion.
– ain_size
loa
0.8
F ac ion o da ase
used o aining.
Mus be in [0,1).
–num_clien s
in
1
Numbe o clien s in
he ede a ed se ing.
–model
s
andom_ o es
Base model o ain.
–num_ ounds
in
50
Numbe o ede a ed
aining ounds.
--
checkpoin _selec ion
_me ic
s
p ecision
Me ic used o selec
checkpoin s.
–d opou _me hod
s
None
D opou me hod
applied du ing
Page 9 o 12
aining.
–smoo h_me hod
s
None
Weigh smoo hing
me hod.
– andom_ o es
json
{"balanced_ ":
" ue"}
Pa ame e s o
aining a Random
Fo es model. The
balanced_ lag
indica es whe he o
balance he class
weigh s du ing
aining.
–
weigh ed_ andom_ o
es
json
{"balanced_ ":
" ue",
"le elO De ail":
"DecisionT ee"}
Pa ame e s o a
Weigh ed Random
Fo es . In addi ion o
balanced_ , his
a ian includes
le elO De ail,
which speci ies he
g anula i y o
decision ees.
--neu al_ne wo k
json
{"d opou _p": 0.2,
"de ice": "cpu",
"local_epochs": 10}
Con igu a ion
pa ame e s o
Neu al Ne wo ks.
Includes d opou
p obabili y
(d opou _p),
aining de ice (cpu
o cuda), and he
numbe o local
aining epochs.
–T
in
20
Numbe o Mon e
Ca lo d opou
samples used o
unce ain y
es ima ion in
Bayesian-s yle
neu al ne wo ks.
–linea _models
json
{“n_ ea u es”: 9}
Numbe o inpu
ea u es expec ed by
he linea model
--sandbox_pa h
s
/sandbox
Pa h o he sandbox
di ec o y used o
isola ed execu ion o
