(Me a)Da a in Ac ion
De elopmen s in NFDI4BIOIMAGE and I3D:bio
Susanne Kunis
Wi h he excep ion o logos and ci ed hi d-pa y con en , he con en o
hese slides is sha ed unde he e ms o he C ea i e Commons
A ibu ion License (CC-BY 4.0) unless he con en is ma ked o he wise.
22.10.2025 Susanne Kunis RDM4mic Mee ing
STATUS:
DATA SILO LEVEL:
„I I wan o sha e da a, I
coo dina e i di ec ly wi h my
colleague”
„My p ojec /g oup has ag ee o
use a speci ic pla o m o da a
managemen “
„ I should manage da a and
s i e o use app op ia e
s anda ds and ools.”
„ I ha e lea ned how o apply
da a managemen policies and
sha ing has become much
easie .”
„ I ind ha I can easily
disco e , access, combine
and publish da a".
highly indi idualized, lexible
sys em
- S uc u ed
- Collabo a i e
- Rigo ously documen ed
- Ins i u ion-wide coo dina ion
& collabo a ion
- S anda diza ion
- Accessibili y
- Secu i y
- Long- e m p ese a ion
- C oss-ins i u ional coo dina ion
& collabo a ion
- S anda diza ion &
In e ope abili y
- Signi ican in es men in
in as uc u e & expe ise
- S ong leade ship & a na ional
ision o da a-d i en
inno a ion.
- Global da a go e nance
amewo ks
- In e ope able s anda ds
- Fede a ed da a ne wo ks
- Da a sha ing ag eemen s
- Collabo a i e in as uc u e
local Cen alized o wo king g oup Cen alized local in as uc u e Na ional and domain speci ic
in as uc u e
single use Resou ce o alida e decisions Resou ce o make decisions Asse o answe u u e ques ionssingle use
INDIVIDUAL
01
PROJECT/GROUP
02
INSTITUTIONAL
03
NATIONAL
04
INTERNATIONAL
05
DATA VALUE:
Collabo a i e in as uc u e
Le els o Da amanagemen
22.10.2025 Susanne Kunis RDM4mic Mee ing
STATUS:
highly indi idualized, lexible
sys em
- S uc u ed
- Collabo a i e
- Rigo ously documen ed
- Ins i u ion-wide coo dina ion
& collabo a ion
- S anda diza ion
- Accessibili y
- Secu i y
- Long- e m p ese a ion
- C oss-ins i u ional coo dina ion
& collabo a ion
- S anda diza ion &
In e ope abili y
- Signi ican in es men in
in as uc u e & expe ise
- S ong leade ship & a na ional
ision o da a-d i en
inno a ion.
- Global da a go e nance
amewo ks
- In e ope able s anda ds
- Fede a ed da a ne wo ks
- Da a sha ing ag eemen s
- Collabo a i e in as uc u e
INDIVIDUAL
01
PROJECT/GROUP
02
INSTITUTIONAL
03
NATIONAL
04
INTERNATIONAL
05
Since 2019 2022-2025 2023-2028
Le els o Da amanagemen
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I3D:bio
Co e Mission:
Implemen he needs o ools, suppo and aining wi h ocus on OMERO and ligh
mic oscopy
4
GUIDE: S uc u ing o Da a and Me ada a
in Bioimaging: Concep s and echnical
Solu ions in he Con ex o Linked Da a
h ps://doi.o g/10.5281/zenodo.7018928
Wo kshops & T aining ma e ial
Videos:
h ps:// inyu l.com/mwykwj6h
Slides:
h ps://doi.o g/10.5281/zenodo.8323587
Zenodo Communi y:
h ps://zenodo.o g/communi ies/i3dbio/ eco ds
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I3D:bio
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h ps://doi.o g/10.1111/jmi.13317
A p ac ical guide o bioimaging esea ch da a
managemen in co e acili ies
An imaging-co e- acili y-cen ic pe spec i e ou lining he
expe ience and cu en s a egies in Ge many o acili a e he
p ac ical adop ion o he FAIR p inciples closely aligned wi h he
in e na ional bioimaging communi y
Includes ables o common issues
and p oposed solu ion o each
s age in he li e-cycle
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•ome o-au o ag, ome o- agsea ch main enance
•OMERO.web inhe i anno a ion om p ojec /da ase
•ome o-linkage- oolbox: enables linking o bioimage me ada a in OMERO wi h ELN (expe imen al
me ada a)
•Gami ica ion: “ easu e hun ” abou use o Tags and key- alues in OMERO
h ps://ome o- aining.ge bi-gmb.de/webclien /
•TiM da a managemen concep and in as uc u e
•TiM OMERO se e wi h public, anno a ed da a:
h ps://ome o- im.ge bi-gmb.de/webclien / (kindly hos ed by he NFDI4BIOIMAGE conso ium)
•Knowledge hub: h ps://ge bi-gmb.de/i3dbio/
I3D:bio wha else…
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NFDI4BIOIMAGE
Co e Mission:
Enable FAIR bioimage da a managemen o Ge man esea che s,ac oss disciplines and
embedded in he in e na ional amewo k.
7
Maximum in ensi y p ojec ion in dep h colo coding o an op ically clea ed, one mon h old zeb a ish, imaged in a ligh -shee mic oscope. (Cou esy o J.
Huisken and K. Weiss). The QR-code links o he image in an OMERO da abase.
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NFDI4BIOIMAGE
FAIR Digi al Objec s o
Bioimaging
Cloud- eady open ile o ma s
Me ada a s anda ds & ools
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Task A ea 1:
Image (me a)da a
o ma s &
s anda diza ion
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FDO-compa ible da a ype o
bioimaging o ensu e da a is open
and web-accessible o enable
e icien dis ibu ed p ocessing.
FAIR Digi al Objec s o Bioimaging
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La ge numbe o p op ie a y ile o ma s (PFF):
Many o ma s can only be ead co ec ly wi h speci ic manu ac u e so wa e; o he wise, hey
need o be con e ed o widely accep ed o ma s like TIF, which o en esul s in he loss o
me ada a
Di e si y in o ma s
16
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Examples o S anda ds/Recommenda ions o desc ibe echnique o /and con ex :
•OME Da a model (Technical me ada a desc ip ion o an imaging expe imen )
•REMBI (Recommended Me ada a o Biological Images)
•4DN-BINA-OME-QUAREP (BNO) ie ed me ada a guidelines
•3D-MMS (3D mic oscopy me ada a s anda d)
•BIDS (B ain Imaging Da a S uc u e) o Mic oscopy
•MITI (Minimum In o ma ion o Highly Mul iplexed Tissue Images)
•MIHCSME (Minimum In o ma ion o High Con en Sc eening Mic oscopy Expe imen s)
•MIFA (Me ada a, Incen i es, Fo ma s and Accessibili y guidelines o AI euse)
h ps://ge bi-gmb.de/2024/12/05/me ada a-s anda ds- o -bioimaging /
Di e si y in s anda ds
17
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- TIFF
TIFF
XML
The model includes image pa ame e s,
such as XYZ dimensions and pixels ype, as
well as ex ensi e me ada a on, o
example, image acquisi ion, anno a ion,
and egions o in e es (ROIs).
Linke , e al. (2010) Me ada a ma e s: access o image da a in he eal wo ld.The
Jou nal o Cell Biology 189(5), 777-782.
DOI: 10.1083/jcb.201004104
h ps://ome-model. ead hedocs.io/en/s able/ome- i /speci ica ion.h ml
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Canno ep esen all endo -
speci ic in o ma ions
No ideal o in eg a e “o he ”
da a
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Modula amewo k
20
Me ada a s anda ds & ools
22.10.2025 Susanne Kunis RDM4mic Mee ing
Me ada a s anda ds & ools
C ea ing (me a)da a ep esen a ions is easy.
The ha d pa is building a common one.
21
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.
22
Me ada a s anda ds & ools
Imp o ed da a disco e y:
Seman ic da a in eg a ion enables he
in eg a ion and ha moniza ion o da a
om a ious bioimaging sou ces and
ela ed da a.
Inc eased da a euse:
RDF acili a es linking and
combining da ase s o new insigh s.
Enhanced in e ope abili y:
Da a can be easily in eg a ed and
exchanged be ween di e en sys ems.
Machine eadabili y:
Enables au oma ed p ocessing and
analysis o me ada a
Goal: Web o me ada a
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S eps
Con e sion OMERO Da a Model
xsd -> LinkML
o p o ide URIs o each Class and
P edica e
h ps://joshmoo e.gi hub.io/ome-ld/co e/docs/Anno a ion.h ml
Me ada a s anda ds & ools
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S eps
T ansla ing OMERO-speci ic
me ada a in o RDF ia ome o- d
o ob ain a seman ically ich
ep esen a ion and simpli y
in eg a ion wi h da a o he
domains
$ ome o d Image:165854
@p e ix dca : <h p://www.w3.o g/ns/dca #> .
@p e ix dc e ms: <h p://pu l.o g/dc/ e ms/> .
@p e ix e o: <h p://www.ebi.ac.uk/e o/> .
@p e ix hi : <h p://hl7.o g/ hi /> .
@p e ix je m: <h p://je mon ology.o g/on ology/JERMOn ology#> .
@p e ix obi: <h p://pu l.obolib a y.o g/obo/OBI_> .
@p e ix ome: <h p://www.openmic oscopy.o g/Schemas/OME/2016-06#> .
@p e ix oc a e: <h ps://w3id.o g/ o/c a e/1.1/con ex > .
@p e ix sio: <h p://seman icscience.o g/ esou ce/> .
@p e ix sioc: <h p:// d s.o g/sioc/ns#>
Me ada a s anda ds & ools
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S eps
Map OMERO me ada a o Vi ual
Knowledge G aph ia OMERO-
on op-mapping
o ac as a SPARQL endpoin o
e ch da a ia SPARQL
p e ix ome ol: h ps://e olome o.e olbio.mpg.de/ d /
p e ix image: h ps://e olome o.e olbio.mpg.de/ d /Image/
p e ix ds: h ps://e olome o.e olbio.mpg.de/ d /Da ase /
p e ix omeco e: h ps://ld.openmic oscopy.o g/co e/
p e ix d s: h p://www.w3.o g/2000/01/ d -schema#
p e ix dc: h p://pu l.o g/dc/elemen s/1.1/
p e ix omekg: h ps://ld.openmic oscopy.o g/omekg#
selec dis inc ?img ? ag whe e {
?img a omeco e:Image .
alues ?img {image:9}
?img omekg: ag_anno a ion_ alue ? ag
}
Lis all image ags:
VKG Engine
Me ada a s anda ds & ools
