Wo k low o use in oduc ion in o mic oscopy, OMERO
and da a managemen a Cen e o Ad anced imaging
Ksenia K ooß, Vanessa Fuchs, Tom Boissonne , S e anie Weid kamp-Pe e s
Cen e o Ad anced imaging (CAi), Hein ich Heine Uni e si y Düsseldo
A e he mic oscope in oduc ion, he use
logs in o he i s ime on he OMERO
se e using uni e si y c eden ials.
The OMERO se e is connec ed o a
Ma e mos channel and sends a
no i ica ion abou he new use login.
Ou imaging specialis s co e a b oad ange o modali ies:
Sebas ian Hänsch: supe - esolu ion/ luo escence mic oscopy
and spec oscopy
Mi iam Bäume s: TEM and luo escence mic oscopy
Manuel Anlau : biosenso s and luo escence mic oscopy
Anna Hamache high-con en -sc eening and image analysis
The use is augh how o
ope a e a mic oscope in wo
hal -day one-on-one o small
g oup sessions. Du ing he
sessions, he use is shown
how o log in in OMERO.
A e he no i ica ion, Tom Boissonne
c ea es a playbook in Ma e mos o ack
he ollowing p ocess. Tom con ac s he
pe son ia e-mail and o e s a mee ing o
demons a e how o use OMERO. Tom
adds he use o he espec i e wo king
g oup on OMERO and poin s he use o
he HHU-Rocke Cha OMERO channels
and in e nal HHU-Wiki o suppo and
upda es.
The use akes he appoin men . In a one
hou one- o-one session, Tom explains
all main ea u es o OMERO and how o
make use o hem. This includes:
▪how o upload da a h ough
OMERO.insigh
▪wha bio- o ma s does
▪how o iew he images
▪how o gene a e igu es
▪ he possibili ies o in eg a ing image
analysis ools (e.g. Fiji) wi hin OMERO
A e he appoin men , Tom ma ks he
in oduc ion o OMERO as done in he
Ma e mos playbook and Ksenia
K ooß/Vanessa Fuchs con ac he pe son
ia e-mail and o e a mee ing o
demons a e how o o ganize and
anno a e da a on OMERO.
Indi idual link o
e e y i em
P e iew o
images
Figu e
p epa a ion
Connec ion
wi h Fiji
The use akes he appoin men . In aone
and a hal hou one- o-one session,
Ksenia/Vanessa explain he use da a
managemen on OMERO. This includes:
▪ he olde s uc u e
▪wha a da a se is
▪naming con en ions
▪how o use ags o lexible o ganiza ion
▪whe e o ind echnical me ada a
▪FAIR p inciples
▪ he REMBI able
▪how o anno a e biological me ada a
▪wha on ologies a e and whe e o ind
hem
▪da a publica ion
Du ing he appoin men , Ksenia/Vanessa
gene a e a cus om REMBI me ada a
empla e o he use acco ding o he /his
needs and esea ch opic.
A he Cen e o Ad anced Imaging (CAi), we ha e es ablished a wo k low o guide use s h ough all aspec s o bioimaging. The
p ocess begins wi h an ini ial consul a ion wi h ou imaging specialis s ega ding mic oscopy echniques o hei speci ic p ojec . Use s
hen ecei e aining in mic oscope ope a ion, ensu ing hey can handle he equipmen e ec i ely. I needed, ou specialis s also
p o ide suppo in image analysis. Nex , we in oduce use s o OMERO¹, highligh ing i s ea u es and he ad an ages o using a
bioimage da a managemen sys em. They a e hen ained o s uc u e and anno a e hei da a wi hin OMERO¹ acco ding o he
Recommended Me ada a o Biological Images (REMBI²), aking hei speci ic esea ch opics in o accoun . As use s p epa e o da a
publica ion, we assis wi h da a o ganiza ion and eposi o y uploads. Ou goal is o educa e esea che s in managing bioimage da a
h oughou i s en i e li ecycle, wi h a s ong emphasis on he FAIR³ ( indable, accessible, in e ope able, eusable) p inciples.
Tags
P ojec
- Da a se
- Image ile
Technical
me ada a
Biological
me ada a
A e he appoin men , he use ecei es he /his
cus om REMBI empla e and links o u he
in o ma ion ega ding:
▪ he REMBI able and pape
▪anno a ion ools o on ologies
▪ aining ideos on OMERO om he I3D:bio p ojec
▪image da a eposi o ies
Ksenia/Vanessa close he Ma e mos playbook.
Tag seach
1h ps://www.openmic oscopy.o g/ome o/
2Sa kans e al. (2021), Na u e Me hods
18, 1418–1422. DOI: 10.1038/s41592-
021-01166-8
3 Wilkinson e al. (2016), Scien i ic Da a 3,
160018. DOI: 10.1038/sda a.2016.18
A use con ac s CAi o a mic oscope in oduc ion wi h
one o ou imaging specialis s.
Da a impo
We encou age he use o con ac CAi membe s a any ime o help o in case o ques ions.
