T ans o ming BioImage Analysis:
The AI4Li e App oach
Ca e ina Fus e -Ba celó, PhD – ca e ina. us e ba cel[email p o ec ed]
Cell Physics – 09 h Oc obe 2025
2025 - p esen
2022 - 2025
BioImage.IO Cha bo
SAMJ
Wha ’s
Accessibili y o
AI/Deep Lea ning
Me hods
BioImage Model Zoo
Reposi o ies:
T aining and
oppo uni ies:
Open Calls: 1, 2, 3… Go!
Phase 1: Re iew
Phase 2: Consul a ions
Phase 3: P ojec s
Open Calls: 1, 2, 3… Go!
1 2 3
72 applica ions
16 e iewe s
8 p ojec s
51 applica ions
17 e iewe s
7 p ojec s
28 applica ions
13 expe s
10 consul a ions
8 p ojec s
Wound-healing ime-lapse
o epi helial monolaye s
The da a was p o ided by Madeline Lo ejoy and Ra ael Ga cia-Ma a (PhD) a Ga cia-Ma a Lab, Uni e si y o Toledo (USA).
The da a:
The p oblem:
S udy he mig a ion
o he cells o close
he inflic ed wound
A close look
The da a was p o ided by Madeline Lo ejoy and Ra ael Ga cia-Ma a (PhD) a Ga cia-Ma a Lab, Uni e si y o Toledo (USA).
Confluen 2D epi helial monolaye ;
pipe e- ip sc a ch, fluo escen
imelapse
Compa e cell lineages – need pe -cell
segmen a ion and acking plus
mo phology and mo ili y s a s.
Challenge: high confluence, a iable
con as , edge e ec s a wound, iden i y
swaps.
F om N2V o CAREamics – ooling
n2 and CAREamics a e bo h lib a ies in
py hon o image denoising, supe esolu ion
and es o a ion.
n2 is no longe main ained. Mo e o
CAREamics!
⚠ n2 is no compa ible wi h Tenso Flow 2.16
⚠
How o use CAREamics?
h ps://gi hub.com/CAREamics/ca eamics-examples/blob/main/applica ions/n2 /2D/MouseNuclei_Noise2Void.ipynb
con ig = c ea e_n2 _con igu a ion(
expe imen _name="mouse_nuclei_n2 ",
da a_ ype="a ay",
axes="SYX",
pa ch_size=(64, 64),
ba ch_size=16,
num_epochs=10,
)
ca eamis = CAREamis (sou ce=con ig)
ca eamis . ain(
ain_sou ce= ain_da a,
)
How o use CAREamics?
h ps://gi hub.com/CAREamics/ca eamics-examples/blob/main/applica ions/n2 /2D/MouseNuclei_Noise2Void.ipynb
con ig = c ea e_n2 _con igu a ion(
expe imen _name="mouse_nuclei_n2 ",
da a_ ype="a ay",
axes="SYX",
pa ch_size=(64, 64),
ba ch_size=16,
num_epochs=10,
)
ca eamis = CAREamis (sou ce=con ig)
ca eamis . ain(
ain_sou ce= ain_da a,
)
How o use CAREamics?
h ps://gi hub.com/CAREamics/ca eamics-examples/blob/main/applica ions/n2 /2D/MouseNuclei_Noise2Void.ipynb
con ig = c ea e_n2 _con igu a ion(
expe imen _name="mouse_nuclei_n2 ",
da a_ ype="a ay",
axes="SYX",
pa ch_size=(64, 64),
ba ch_size=16,
num_epochs=10,
)
ca eamis = CAREamis (sou ce=con ig)
ca eamis . ain(
ain_sou ce= ain_da a,
)
Denoising
Segmen ing
T acking
CellPose
The Pipeline
CellPose
Segmen ing
CellPose
Why segmen a ion be o e acking?
✨ We need o know exac ly whe e hey
a e a each ime- ame and how much
hey occupy
(pixel-wise)
.
✨ We need o know which cell i is
indi idually, as in ins ance segmen a ion.
Why segmen a ion be o e acking?
✨ We need o know exac ly whe e hey
a e a each ime- ame and how much
hey occupy
(pixel-wise)
.
✨ We need o know which cell i is
indi idually, as in ins ance segmen a ion.
Seman ic Ins ance
Cellpose
Pachi a iu, M., Ra iden, M., & S inge , C. (2025). Cellpose-SAM: supe human gene aliza ion o cellula segmen a ion.
I ’s e e y hing: a GUI, a lib a y, a model and e en a da ase .
om cellpose impo io, models, ain
model = models.CellposeModel()
Cellpose
Pachi a iu, M., Ra iden, M., & S inge , C. (2025). Cellpose-SAM: supe human gene aliza ion o cellula segmen a ion.
Op ion 1:
Use a Cellpose model as-is.
💡Tips:
Calib a e o he size o you nuclei.
T y on di e en magnifica ions, s ainings, …
F om segmen ed cells o ajec o ies
Fi s s hings fi s : he masks.
✨ Inpu : cen e s a e de ec ed om masks.
✨ Linking: LAP acke connec s objec s
ame- o- ame by dis ance.
✨ Gap-closing: econnec s sho
disappea ances.
✨ Segmen spli ing: link spo s o cell
di ision
F om segmen ed cells o ajec o ies
Fi s s hings fi s : he masks.
✨ Inpu : cen e s a e de ec ed om masks.
✨ Linking: LAP acke connec s objec s
ame- o- ame by dis ance.
✨ Gap-closing: econnec s sho
disappea ances.
✨ Segmen spli ing: link spo s o cell
di ision
Displaying acks
Denoising
Segmen ing
T acking
CellPose
The Pipeline
CellPose
Sha ing
FAIR Science
Reuse
Make su e ha you wo kflow
is ep oducible and you da a
can be eused.
In e ope abili y
Da a needs o be in eg a ed
wi h applica ions o wo kflows
o analysis, s o age, and
p ocessing.
Findabili y
Me ada a and da a should be
easily o find o bo h humans
and compu e s.
Accessibili y
Knowing how he da a can be
accessed, e en including
au hen ica ion and
au ho isa ion is c ucial.
A zoo o DL models in mic oscopy
…
segmen a ion denoising
image-classi ica ion
image- econs uc ion
seman ic-segmen a ion image- es o a ion
2d 3d py o ch enso low whole-slide-imaging
Model De elopmen
Model Packaging
Upload o bioimage.io
Model Accessibili y
Model Deploymen
Model Fine Tuning
De elope s
End-use s
The li e cycle o a model in he
BioImage Model Zoo
Consuming Fine- uning Expo ing
…
🐘 happy-elephan
📊S a is ics
⬇ Downloads: 109
👁 Views: 218
🏷Tags
nuclei segmen a ion epi helial cells
luo escence mic oscopy 2D
cell-segmen a ion cellpose
🔗Links
Gi Hub Reposi o y
