Biostatistics,
Год журнала:
2018,
Номер
21(4), С. 709 - 726
Опубликована: Дек. 20, 2018
Summary
Calcium
imaging
data
promises
to
transform
the
field
of
neuroscience
by
making
it
possible
record
from
large
populations
neurons
simultaneously.
However,
determining
exact
moment
in
time
at
which
a
neuron
spikes,
calcium
set,
amounts
non-trivial
deconvolution
problem
is
critical
importance
for
downstream
analyses.
While
number
formulations
have
been
proposed
this
task
recent
literature,
article,
we
focus
on
formulation
recently
Jewell
and
Witten
(2018.
Exact
spike
train
inference
via
$\ell_{0}
$
optimization.
The
Annals
Applied
Statistics12(4),
2457–2482)
that
can
accurately
estimate
not
just
rate,
but
also
specific
times
spikes.
We
develop
much
faster
algorithm
be
used
deconvolve
fluorescence
trace
100
000
timesteps
less
than
second.
Furthermore,
present
modification
precludes
possibility
“negative
spike”.
demonstrate
performance
datasets
were
released
as
part
$\texttt{spikefinder}$
challenge
(http://spikefinder.codeneuro.org/).
presented
article
was
Allen
Institute
Brain
Science’s
“platform
paper”
decode
neural
activity
Observatory;
main
scientific
paper
their
resource
presented.
Our
$\texttt{C++}$
implementation,
along
with
$\texttt{R}$
$\texttt{python}$
wrappers,
publicly
available.
code
available
$\texttt{CRAN}$
$\texttt{Github}$,
wrappers
are
$\texttt{Github}$;
see
https://github.com/jewellsean/FastLZeroSpikeInference.
Neuron
activity
across
the
brain
How
is
it
that
groups
of
neurons
dispersed
through
interact
to
generate
complex
behaviors?
Three
papers
in
this
issue
present
brain-scale
studies
neuronal
and
dynamics
(see
Perspective
by
Huk
Hart).
Allen
et
al.
found
thirsty
mice,
there
widespread
neural
related
stimuli
elicit
licking
drinking.
Individual
encoded
task-specific
responses,
but
every
area
contained
with
different
types
response.
Optogenetic
stimulation
thirst-sensing
one
reinstated
drinking
previously
signaled
thirst.
Gründemann
investigated
mouse
basal
amygdala
relation
behavior
during
tasks.
Two
ensembles
showed
orthogonal
exploratory
nonexploratory
behaviors,
possibly
reflecting
levels
anxiety
experienced
these
areas.
Stringer
analyzed
spontaneous
firing,
finding
primary
visual
cortex
both
information
motor
facial
movements.
The
variability
responses
mainly
arousal
reflects
encoding
latent
behavioral
states.
Science
,
p.
eaav3932
eaav8736
eaav7893
;
see
also
236
Cell,
Год журнала:
2022,
Номер
185(7), С. 1240 - 1256.e30
Опубликована: Март 1, 2022
We
developed
a
miniaturized
two-photon
microscope
(MINI2P)
for
fast,
high-resolution,
multiplane
calcium
imaging
of
over
1,000
neurons
at
time
in
freely
moving
mice.
With
weight
below
3
g
and
highly
flexible
connection
cable,
MINI2P
allowed
stable
with
no
impediment
behavior
variety
assays
compared
to
untethered,
unimplanted
animals.
The
improved
cell
yield
was
achieved
through
optical
system
design
featuring
an
enlarged
field
view
(FOV)
microtunable
lens
increased
z-scanning
range
speed
that
allows
fast
multiple
interleaved
planes,
as
well
3D
functional
imaging.
Successive
across
multiple,
adjacent
FOVs
enabled
recordings
from
more
than
10,000
the
same
animal.
Large-scale
proof-of-principle
data
were
obtained
populations
visual
cortex,
medial
entorhinal
hippocampus,
revealing
spatial
tuning
cells
all
areas.
PLoS Computational Biology,
Год журнала:
2018,
Номер
14(5), С. e1006157 - e1006157
Опубликована: Май 21, 2018
In
recent
years,
two-photon
calcium
imaging
has
become
a
standard
tool
to
probe
the
function
of
neural
circuits
and
study
computations
in
neuronal
populations.
However,
acquired
signal
is
only
an
indirect
measurement
activity
due
comparatively
slow
dynamics
fluorescent
indicators.
Different
algorithms
for
estimating
spike
rates
from
noisy
measurements
have
been
proposed
past,
but
it
open
question
how
far
performance
can
be
improved.
Here,
we
report
results
spikefinder
challenge,
launched
catalyze
development
new
rate
inference
through
crowd-sourcing.
We
present
ten
submitted
which
show
improved
compared
previously
evaluated
methods.
Interestingly,
top-performing
are
based
on
wide
range
principles
deep
networks
generative
models,
yet
provide
highly
correlated
estimates
activity.
The
competition
shows
that
benchmark
challenges
drive
algorithmic
developments
neuroscience.
Fluorescent
calcium
indicators
are
often
used
to
investigate
neural
dynamics,
but
the
relationship
between
fluorescence
and
action
potentials
(APs)
remains
unclear.
Most
APs
can
be
detected
when
soma
almost
fills
microscope's
field
of
view,
image
populations
neurons,
necessitating
a
large
generating
fewer
photons
per
neuron,
compromising
AP
detection.
Here,
we
characterized
AP-fluorescence
transfer
function
in
vivo
for
48
layer
2/3
pyramidal
neurons
primary
visual
cortex,
with
simultaneous
imaging
cell-attached
recordings
from
transgenic
mice
expressing
GCaMP6s
or
GCaMP6f.
While
most
were
under
optimal
conditions,
conditions
typical
population
studies,
only
minority
1
2
events
(often
<10%
~20-30%,
respectively),
emphasizing
limits
detection
more
realistic
conditions.Neurons,
cells
that
make
up
nervous
system,
transmit
information
using
electrical
signals
known
as
spikes.
Studying
spiking
patterns
brain
is
essential
understand
perception,
memory,
thought,
behaviour.
One
way
do
by
recording
activity
microelectrodes.
Another
study
neuronal
molecules
change
how
they
interact
light
binds
them,
since
changes
concentration
indicative
spiking.
That
observed
specialized
microscopes
know
two-photon
microscopes.
Using
indicators,
it
possible
simultaneously
record
hundreds
even
thousands
neurons.
However,
spikes
not
translate
one-to-one.
In
order
interpret
data,
important
associated
individual
The
directly
measure
this
same
neuron.
extremely
challenging
experimentally,
so
type
data
rare.
To
shed
some
on
this,
Huang,
Ledochowitsch
et
al.
had
been
genetically
modified
produce
indicator
cortex
obtained
both
measurements
these
These
experiments
revealed
that,
while
majority
time
periods
containing
multi-spike
could
identified
microscopy,
average,
less
than
10%
isolated
single
detectable.
This
an
caveat
researchers
need
take
into
consideration
interpreting
results.
findings
intended
serve
guide
studies
look
at
mammalian
level.
addition,
provided
will
useful
reference
development
sensors,
benchmark
improve
computational
approaches
detecting
predicting
PLoS Computational Biology,
Год журнала:
2020,
Номер
16(9), С. e1008198 - e1008198
Опубликована: Сен. 15, 2020
Calcium
imaging
with
fluorescent
protein
sensors
is
widely
used
to
record
activity
in
neuronal
populations.
The
transform
between
neural
and
calcium-related
fluorescence
involves
nonlinearities
low-pass
filtering,
but
the
effects
of
transformation
on
analyses
populations
are
not
well
understood.
We
compared
spikes
matched
behaving
mice.
report
multiple
discrepancies
performed
two
types
data,
including
changes
single-neuron
selectivity
population
decoding.
These
were
only
partially
resolved
by
spike
inference
algorithms
applied
fluorescence.
To
model
relation
spiking
we
simultaneously
recorded
from
individual
neurons.
Using
these
recordings
developed
a
transforming
trains
synthetic-imaging
data.
recapitulated
differences
analyses.
Our
analysis
highlights
challenges
relating
electrophysiology
suggests
forward
modeling
as
an
effective
way
understand
Nature,
Год журнала:
2022,
Номер
607(7918), С. 330 - 338
Опубликована: Июль 6, 2022
Abstract
Transcriptomics
has
revealed
that
cortical
inhibitory
neurons
exhibit
a
great
diversity
of
fine
molecular
subtypes
1–6
,
but
it
is
not
known
whether
these
have
correspondingly
diverse
patterns
activity
in
the
living
brain.
Here
we
show
primary
visual
cortex
(V1)
correlates
with
brain
state,
which
are
organized
by
single
factor:
position
along
main
axis
transcriptomic
variation.
We
combined
vivo
two-photon
calcium
imaging
mouse
V1
method
to
identify
mRNA
for
72
selected
genes
ex
slices.
classified
imaged
layers
1–3
into
three-level
hierarchy
5
subclasses,
11
types
and
35
using
previously
defined
clusters
3
.
Responses
stimuli
differed
significantly
only
between
cells
Sncg
subclass
uniformly
suppressed,
other
subclasses
predominantly
excited.
Modulation
state
at
all
hierarchical
levels
could
be
largely
predicted
from
first
principal
component,
also
correlations
simultaneously
recorded
cells.
Inhibitory
fired
more
resting,
oscillatory
states
had
smaller
fraction
their
axonal
projections
layer
1,
narrower
spikes,
lower
input
resistance
weaker
adaptation
as
determined
vitro
7
expressed
cholinergic
receptors.
Subtypes
during
arousal
opposite
properties.
Thus,
simple
principle
may
explain
how
shape
state-dependent
processing.
