PLoS Computational Biology,
Journal Year:
2012,
Volume and Issue:
8(8), P. e1002653 - e1002653
Published: Aug. 23, 2012
A
systematic
assessment
of
global
neural
network
connectivity
through
direct
electrophysiological
assays
has
remained
technically
unfeasible
even
in
dissociated
neuronal
cultures.
We
introduce
an
improved
algorithmic
approach
based
on
Transfer
Entropy
to
reconstruct
approximations
structural
connectivities
from
activity
monitored
calcium
fluorescence
imaging.
Based
information
theory,
our
method
requires
no
prior
assumptions
the
statistics
firing
and
connections.
The
performance
algorithm
is
benchmarked
surrogate
time-series
generated
by
simulated
dynamics
a
with
known
ground-truth
topology.
find
that
effective
topology
revealed
depends
qualitatively
time-dependent
dynamic
state
(e.g.,
bursting
or
non-bursting).
thus
demonstrate
how
conditioning
respect
mean
improves
method.
[...]
Compared
other
reconstruction
strategies
such
as
cross-correlation
Granger
Causality
methods,
remarkably
more
accurate.
In
particular,
it
provides
good
clustering
coefficient,
allowing
discriminate
between
weakly
strongly
clustered
topologies,
whereas
hand
cross-correlations
would
invariantly
detect
artificially
high
levels
clustering.
Finally,
we
present
applicability
real
recordings
vitro
cortical
these
networks
are
characterized
elevated
level
compared
random
graph
(although
not
extreme)
markedly
non-local
connectivity.
Imaging
is
used
to
map
activity
across
populations
of
neurons.
Microscopes
with
cellular
resolution
have
small
(<1
millimeter)
fields
view
and
cannot
simultaneously
image
distributed
multiple
brain
areas.
Typical
large
field
microscopes
do
not
resolve
single
cells,
especially
in
the
axial
dimension.
We
developed
a
2-photon
random
access
mesoscope
(2p-RAM)
that
allows
high-resolution
imaging
anywhere
within
volume
spanning
areas
(∅
5
mm
x
1
cylinder).
2p-RAM
near
diffraction
limited
(lateral,
0.66
μm,
4.09
μm
at
center;
excitation
wavelength
=
970
nm;
numerical
aperture
0.6)
over
range
wavelengths.
A
fast
three-dimensional
scanning
system
efficient
sampling
neural
arbitrary
regions
interest
entire
volume.
illustrate
use
by
multiple,
non-contiguous
transgenic
mice
expressing
protein
calcium
sensors.
PLoS Computational Biology,
Journal Year:
2017,
Volume and Issue:
13(3), P. e1005423 - e1005423
Published: March 14, 2017
Fluorescent
calcium
indicators
are
a
popular
means
for
observing
the
spiking
activity
of
large
neuronal
populations,
but
extracting
each
neuron
from
raw
fluorescence
imaging
data
is
nontrivial
problem.
We
present
fast
online
active
set
method
to
solve
this
sparse
non-negative
deconvolution
Importantly,
algorithm
progresses
through
time
series
sequentially
beginning
end,
thus
enabling
real-time
estimation
neural
during
session.
Our
generalization
pool
adjacent
violators
(PAVA)
isotonic
regression
and
inherits
its
linear-time
computational
complexity.
gain
remarkable
increases
in
processing
speed:
more
than
one
order
magnitude
compared
currently
employed
state
art
convex
solvers
relying
on
interior
point
methods.
Unlike
these
approaches,
our
can
exploit
warm
starts;
therefore
optimizing
model
hyperparameters
only
requires
handful
passes
data.
A
minor
modification
further
improve
quality
inference
by
imposing
constraint
minimum
spike
size.
The
enables
simultaneous
$O(10^5)$
traces
whole-brain
larval
zebrafish
laptop.
Proceedings of the National Academy of Sciences,
Journal Year:
2016,
Volume and Issue:
113(49), P. 14133 - 14138
Published: Nov. 22, 2016
Significance
We
demonstrate
noninvasive
detection
of
action
potentials
with
single-neuron
sensitivity,
including
in
whole
organisms.
Our
sensor
is
composed
quantum
defects
within
a
diamond
chip,
which
detect
time-varying
magnetic
fields
generated
by
potentials.
The
biocompatible
and
can
be
brought
into
close
proximity
to
the
organism
without
adverse
effect,
allowing
for
long-term
observation
superior
resolution
neuron
fields.
Optical
also
provides
information
about
potential
propagation
that
not
easily
available
existing
methods.
technique
requires
no
labeling
or
genetic
modification,
allows
submillisecond
time
resolution,
does
bleach,
senses
through
opaque
tissue.
With
further
development,
we
expect
micrometer-scale
imaging
variety
neuronal
phenomena.
Nature,
Journal Year:
2023,
Volume and Issue:
615(7954), P. 884 - 891
Published: March 15, 2023
Abstract
Calcium
imaging
with
protein-based
indicators
1,2
is
widely
used
to
follow
neural
activity
in
intact
nervous
systems,
but
current
protein
sensors
report
at
timescales
much
slower
than
electrical
signalling
and
are
limited
by
trade-offs
between
sensitivity
kinetics.
Here
we
large-scale
screening
structure-guided
mutagenesis
develop
optimize
several
fast
sensitive
GCaMP-type
3–8
.
The
resulting
‘jGCaMP8’
sensors,
based
on
the
calcium-binding
calmodulin
a
fragment
of
endothelial
nitric
oxide
synthase,
have
ultra-fast
kinetics
(half-rise
times
2
ms)
highest
for
reported
calcium
sensor.
jGCaMP8
will
allow
tracking
large
populations
neurons
relevant
computation.
Neuron,
Journal Year:
2018,
Volume and Issue:
98(2), P. 256 - 281
Published: April 1, 2018
Tremendous
progress
has
been
made
since
Neuron
published
our
Primer
on
genetic
dissection
of
neural
circuits
10
years
ago.
Since
then,
cell-type-specific
anatomical,
neurophysiological,
and
perturbation
studies
have
carried
out
in
a
multitude
invertebrate
vertebrate
organisms,
linking
neurons
to
behavioral
functions.
New
methods
allow
systematic
classification
cell
types
provide
access
diverse
neuronal
for
connectivity
coding
during
behavior.
Here
we
evaluate
key
advances
over
the
past
decade
discuss
future
directions.
