bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Окт. 25, 2023
Abstract
Motivation
The
full
automation
of
digital
neuronal
reconstruction
from
light
microscopic
images
has
long
been
impeded
by
noisy
images.
Previous
endeavors
to
improve
image
quality
can
hardly
get
a
good
compromise
between
robustness
and
computational
efficiency.
Results
We
present
the
enhancement
pipeline
named
Neuronal
Image
Enhancement
through
Noise
Disentanglement
(NIEND).
Through
extensive
benchmarking
on
863
mouse
with
manually
annotated
gold
standards,
NIEND
achieves
remarkable
improvements
in
such
as
signal-background
contrast
(40-fold)
background
uniformity
(10-fold),
compared
raw
Furthermore,
automatic
reconstructions
NIEND-enhanced
have
shown
significant
both
enhanced
using
other
methods.
Specifically,
average
F1
score
is
0.88,
surpassing
original
0.78
second-ranking
method,
which
achieved
0.84.
Up
52%
outperform
all
4
methods
scores.
In
addition,
requires
only
1.6
seconds
for
processing
256×256×256-sized
images,
after
attain
substantial
compression
rate
1%
LZMA.
improves
neuron
reconstruction,
providing
potential
advancements
automated
morphology
petascale.
Availability
Implementation
study
conducted
based
Vaa3D
Python
3.10.
available
GitHub
(
https://github.com/Vaa3D
).
proposed
method
implemented
Python,
hosted
along
testing
code
data
https://github.com/zzhmark/NIEND
brains
be
found
at
BICCN’s
Brain
Library
(BIL)
https://www.brainimagelibrary.org
Asian Journal of Current Research,
Год журнала:
2024,
Номер
9(3), С. 181 - 195
Опубликована: Авг. 10, 2024
Neuroscience,
a
dynamic
field
at
the
forefront
of
scientific
exploration,
is
unravelling
complexities
human
brain.
By
merging
biology,
psychology,
physics,
and
computer
science,
researchers
are
gaining
profound
insights
into
cognition,
behaviour,
neurological
underpinnings
diseases.
Brain
mapping
key
component
recent
advancements.
Techniques
like
fMRI,
PET,
DTI
offer
unprecedented
views
brain
structure
function.
The
Human
Connectome
Project
similar
initiatives
have
produced
detailed
maps
connections,
revealing
how
different
regions
interact
to
support
cognition
behaviour.
These
crucial
for
identifying
disease
biomarkers,
predicting
treatment
responses,
developing
targeted
therapies.
Molecular
biology
genetics
also
driving
progress.
Researchers
uncovering
genetic
basis
disorders,
providing
clues
about
susceptibility
progression.
imaging
techniques
visualise
neurotransmitter
systems
cellular
processes,
shedding
light
on
mechanisms.
integration
neuroscience
with
modelling
AI
revolutionising
research.
algorithms
analyse
vast
datasets,
simulate
neural
networks,
even
decode
signals
brain-machine
interfaces.
This
has
potential
personalised
medicine
ground-breaking
treatments.
future
holds
immense
promise.
optogenetics
single-cell
will
greater
precision
in
studying
circuits.
However,
we
must
address
ethical
considerations
around
data
privacy,
cognitive
enhancement,
brain-altering
interventions.
Neuroscience
not
just
understanding
brain;
it's
improving
lives.
striving
conquer
disorders
maximize
by
pushing
boundaries
knowledge
technology
while
upholding
principles.
The
full
automation
of
digital
neuronal
reconstruction
from
light
microscopic
images
has
long
been
impeded
by
noisy
images.
Previous
endeavors
to
improve
image
quality
can
hardly
get
a
good
compromise
between
robustness
and
computational
efficiency.
Cells,
Год журнала:
2023,
Номер
12(23), С. 2753 - 2753
Опубликована: Ноя. 30, 2023
Automated
evaluation
of
all
glomeruli
throughout
the
whole
kidney
is
essential
for
comprehensive
study
function
as
well
understanding
mechanisms
disease
and
development.
The
emerging
large-volume
microscopic
optical
imaging
techniques
allow
acquisition
mouse
whole-kidney
3D
datasets
at
a
high
resolution.
However,
fast
accurate
analysis
massive
data
remains
challenge.
Here,
we
propose
deep
learning-based
segmentation
method
called
FastCellpose
to
efficiently
segment
in
kidneys.
Our
framework
based
on
Cellpose,
with
optimization
network
architecture
mask
reconstruction
process.
By
means
visual
quantitative
analysis,
demonstrate
that
can
achieve
superior
performance
compared
other
state-of-the-art
cellular
methods,
processing
speed
was
12-fold
higher
than
before.
Based
this
high-performance
framework,
quantitatively
analyzed
development
changes
from
birth
maturity,
which
promising
terms
providing
new
insights
research
function.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Июль 17, 2024
Abstract
Healthy
brain
exhibits
a
rich
dynamical
repertoire,
with
flexible
spatiotemporal
patterns
replays
on
both
microscopic
and
macroscopic
scales.
How
do
fixed
structural
connections
yield
diverse
range
of
dynamic
in
spontaneous
activity?
We
hypothesize
that
the
observed
relationship
between
empirical
structure
functional
is
best
explained
when
neuronal
dynamics
close
to
critical
regime.
Using
modular
Spiking
Neuronal
Network
model
based
connectomes,
we
posit
multiple
stored
can
transiently
reoccur
system
operates
near
regime,
generating
realistic
structural-functional
relationships.
The
are
chosen
as
force
network
learn
propagate
suited
patterns.
To
test
our
hypothesis,
employ
magnetoencephalography
tractography
data
from
five
healthy
individuals.
show
regime
able
generate
features,
demonstrate
relevance
near-critical
regimes
for
physiological
activity.
Brain Communications,
Год журнала:
2024,
Номер
6(5)
Опубликована: Янв. 1, 2024
Creating
a
mouse
model
that
recapitulates
human
tau
pathology
is
essential
for
developing
strategies
to
intervene
in
tau-induced
neurodegeneration.
However,
mimicking
the
pathological
features
seen
often
involves
trade-off
with
artificial
effects
such
as
unexpected
gene
insertion
and
neurotoxicity
from
expression
system.
To
overcome
these
issues,
we
developed
rTKhomo
by
combining
transgenic
CaMKII-tTA
system
P301L
mutated
1N4R
knock-in
at
Journal of Microscopy,
Год журнала:
2024,
Номер
unknown
Опубликована: Ноя. 6, 2024
Abstract
Ex
vivo
x‐ray
angiography
provides
high‐resolution,
three‐dimensional
information
on
vascular
phenotypes
down
to
the
level
of
capillaries.
Sample
preparation
for
ex
starts
with
removal
blood
from
system,
followed
by
perfusion
an
dense
contrast
agent
mixed
a
carrier
such
as
gelatine
or
polymer.
Subsequently,
micro‐architecture
harvested
organs
is
imaged
in
intact
fixed
organ.
In
present
study,
we
novel
microscopic
dual‐energy
CT
(microDECT)
imaging
protocols
that
allow
visualise
and
analyse
microvasculature
situ
reference
morphology
hard
soft
tissue.
We
show
spectral
µAngiofil
Micropaque
barium
sulphate
perfused
specimens
allows
effective
separation
vasculature
mineralised
skeletal
tissues.
Furthermore,
demonstrate
counterstaining
using
established
agents
depict
vessels
together
Phosphotungstic
acid
(PTA)
used
counterstain
shows
excellent
both
sulphate–perfused
specimens.
A
Sorensen‐buffered
PTA
protocol
introduced
specimens,
polyurethane
polymer
susceptible
artefacts
when
conventional
staining
solutions.
Finally,
counterstained
samples
can
be
automatically
processed
into
three
separate
image
channels
(skeletal
tissue,
stained
tissue),
which
offers
multiple
new
options
data
analysis.
The
presented
microDECT
workflows
are
suited
tools
screen
quantify
implemented
various
correlative
pipelines
target
regions
interest
downstream
light
investigation.
