arXiv (Cornell University),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Jan. 1, 2024
Together
with
the
molecular
knowledge
of
genes
and
proteins,
biological
images
promise
to
significantly
enhance
scientific
understanding
complex
cellular
systems
advance
predictive
personalized
therapeutic
products
for
human
health.
For
this
potential
be
realized,
quality-assured
image
data
must
shared
among
labs
at
a
global
scale
compared,
pooled,
reanalyzed,
thus
unleashing
untold
beyond
original
purpose
which
was
generated.
There
are
two
broad
sets
requirements
enable
sharing
in
life
sciences.
One
set
is
articulated
companion
White
Paper
entitled
Enabling
Global
Image
Data
Sharing
Life
Sciences,
published
parallel
addresses
need
build
cyberinfrastructure
digital
array
data.
In
Paper,
we
detail
requirements,
involves
collecting,
managing,
presenting,
propagating
contextual
information
essential
assess
quality,
understand
content,
interpret
implications,
reuse
context
experimental
details.
We
start
by
providing
an
overview
main
lessons
learned
date
through
international
community
activities,
have
recently
made
considerable
progress
toward
generating
standard
practices
imaging
Quality
Control
(QC)
metadata.
then
provide
clear
recommendations
amplifying
work.
The
driving
goal
address
remaining
challenges
democratize
access
everyday
tools
spectrum
biomedical
researchers,
regardless
their
expertise,
resources,
geographical
location.
Histochemistry and Cell Biology,
Journal Year:
2023,
Volume and Issue:
160(3), P. 223 - 251
Published: July 10, 2023
A
growing
community
is
constructing
a
next-generation
file
format
(NGFF)
for
bioimaging
to
overcome
problems
of
scalability
and
heterogeneity.
Organized
by
the
Open
Microscopy
Environment
(OME),
individuals
institutes
across
diverse
modalities
facing
these
have
designed
specification
process
(OME-NGFF)
address
needs.
This
paper
brings
together
wide
range
those
members
describe
cloud-optimized
itself-OME-Zarr-along
with
tools
data
resources
available
today
increase
FAIR
access
remove
barriers
in
scientific
process.
The
current
momentum
offers
an
opportunity
unify
key
component
domain-the
that
underlies
so
many
personal,
institutional,
global
management
analysis
tasks.
Cell,
Journal Year:
2024,
Volume and Issue:
187(25), P. 7045 - 7063
Published: Dec. 1, 2024
Cells
are
essential
to
understanding
health
and
disease,
yet
traditional
models
fall
short
of
modeling
simulating
their
function
behavior.
Advances
in
AI
omics
offer
groundbreaking
opportunities
create
an
virtual
cell
(AIVC),
a
multi-scale,
multi-modal
large-neural-network-based
model
that
can
represent
simulate
the
behavior
molecules,
cells,
tissues
across
diverse
states.
This
Perspective
provides
vision
on
design
how
collaborative
efforts
build
AIVCs
will
transform
biological
research
by
allowing
high-fidelity
simulations,
accelerating
discoveries,
guiding
experimental
studies,
offering
new
for
cellular
functions
fostering
interdisciplinary
collaborations
open
science.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: June 11, 2024
Abstract
Spatial
omics
data
allow
in-depth
analysis
of
tissue
architectures,
opening
new
opportunities
for
biological
discovery.
In
particular,
imaging
techniques
offer
single-cell
resolutions,
providing
essential
insights
into
cellular
organizations
and
dynamics.
Yet,
the
complexity
such
presents
analytical
challenges
demands
substantial
computing
resources.
Moreover,
proliferation
diverse
spatial
technologies,
as
Xenium,
MERSCOPE,
CosMX
in
spatial-transcriptomics,
MACSima
PhenoCycler
multiplex
imaging,
hinders
generality
existing
tools.
We
introduce
Sopa
(
https://github.com/gustaveroussy/sopa
),
a
technology-invariant,
memory-efficient
pipeline
with
unified
visualizer
all
image-based
omics.
Built
upon
universal
SpatialData
framework,
optimizes
tasks
like
segmentation,
transcript/channel
aggregation,
annotation,
geometric/spatial
analysis.
Its
output
includes
user-friendly
web
reports
files,
well
comprehensive
files
Overall,
represents
significant
step
toward
unifying
analysis,
enabling
more
understanding
interactions
organization
systems.
Molecular Systems Biology,
Journal Year:
2023,
Volume and Issue:
19(11)
Published: Oct. 16, 2023
Abstract
Spatial
omics
has
emerged
as
a
rapidly
growing
and
fruitful
field
with
hundreds
of
publications
presenting
novel
methods
for
obtaining
spatially
resolved
information
any
data
type
on
spatial
scales
ranging
from
subcellular
to
organismal.
From
technology
development
perspective,
is
highly
interdisciplinary
that
integrates
imaging
omics,
molecular
analyses,
sequencing
mass
spectrometry,
image
analysis
bioinformatics.
The
emergence
this
not
only
opened
window
into
biology,
but
also
created
multiple
opportunities,
questions,
challenges
method
developers.
Here,
we
provide
the
perspective
developers
what
makes
unique.
After
providing
brief
overview
state
art,
discuss
technological
enablers
present
our
vision
about
future
applications
impact
melting
pot.
Genome Medicine,
Journal Year:
2024,
Volume and Issue:
16(1)
Published: June 11, 2024
Abstract
The
study
of
immunology,
traditionally
reliant
on
proteomics
to
evaluate
individual
immune
cells,
has
been
revolutionized
by
single-cell
RNA
sequencing.
Computational
immunologists
play
a
crucial
role
in
analysing
these
datasets,
moving
beyond
traditional
protein
marker
identification
encompass
more
detailed
view
cellular
phenotypes
and
their
functional
roles.
Recent
technological
advancements
allow
the
simultaneous
measurements
multiple
components—transcriptome,
proteome,
chromatin,
epigenetic
modifications
metabolites—within
single
including
spatial
contexts
within
tissues.
This
led
generation
complex
multiscale
datasets
that
can
include
multimodal
from
same
cells
or
mix
paired
unpaired
modalities.
Modern
machine
learning
(ML)
techniques
for
integration
“omics”
data
without
need
extensive
independent
modelling
each
modality.
review
focuses
recent
ML
integrative
approaches
applied
immunological
studies.
We
highlight
importance
methods
creating
unified
representation
collections,
particularly
profiling
technologies.
Finally,
we
discuss
challenges
holistic
how
they
will
be
instrumental
development
common
coordinate
framework
studies,
thereby
accelerating
research
enabling
discoveries
computational
immunology
field.
Cell,
Journal Year:
2025,
Volume and Issue:
unknown
Published: March 1, 2025
The
organs
of
many
female
animals
are
remodeled
by
reproduction.
Using
the
mouse
intestine,
a
striking
and
tractable
model
organ
resizing,
we
find
that
reproductive
remodeling
is
anticipatory
distinct
from
diet-
or
microbiota-induced
resizing.
Reproductive
involves
partially
irreversible
elongation
small
intestine
fully
reversible
growth
its
epithelial
villi,
associated
with
an
expansion
isthmus
progenitors
accelerated
enterocyte
migration.
We
identify
induction
SGLT3a
transporter
in
subset
enterocytes
as
early
hallmark.
Electrophysiological
genetic
interrogations
indicate
does
not
sustain
digestive
functions
health;
rather,
it
detects
protons
sodium
to
extrinsically
support
adjacent
Fgfbp1-positive
progenitors,
promoting
villus
growth.
Our
findings
reveal
unanticipated
specificity
physiological
remodeling.
suggest
organ-
state-specific
programs
could
be
leveraged
improve
pregnancy
outcomes
prevent
maladaptive
consequences
such
