Nucleic Acids Research,
Год журнала:
2023,
Номер
51(W1), С. W326 - W330
Опубликована: Май 17, 2023
Abstract
Segmentation
helps
interpret
imaging
data
in
a
biological
context.
With
the
development
of
powerful
tools
for
automated
segmentation,
public
repositories
have
added
support
sharing
and
visualizing
segmentations,
creating
need
interactive
web-based
visualization
3D
volume
segmentations.
To
address
ongoing
challenge
integrating
multimodal
data,
we
developed
Mol*
Volumes
Segmentations
(Mol*VS),
which
enables
interactive,
cellular
supported
by
macromolecular
annotations.
Mol*VS
is
fully
integrated
into
Viewer,
already
used
several
repositories.
All
EMDB
EMPIAR
entries
with
segmentation
datasets
are
accessible
via
Mol*VS,
supports
from
wide
range
electron
light
microscopy
experiments.
Additionally,
users
can
run
local
instance
to
visualize
share
custom
generic
or
application-specific
formats
including
volumes
.ccp4,
.mrc,
.map,
segmentations
EMDB-SFF
.hff,
Amira
.am,
iMod
.mod,
Segger
.seg.
open
source
freely
available
at
https://molstarvolseg.ncbr.muni.cz/.
Recent
advances
in
human
stem
cell-derived
brain
organoids
promise
to
replicate
critical
molecular
and
cellular
aspects
of
learning
memory
possibly
cognition
vitro
.
Coining
the
term
“organoid
intelligence”
(OI)
encompass
these
developments,
we
present
a
collaborative
program
implement
vision
multidisciplinary
field
OI.
This
aims
establish
OI
as
form
genuine
biological
computing
that
harnesses
using
scientific
bioengineering
an
ethically
responsible
manner.
Standardized,
3D,
myelinated
can
now
be
produced
with
high
cell
density
enriched
levels
glial
cells
gene
expression
for
learning.
Integrated
microfluidic
perfusion
systems
support
scalable
durable
culturing,
spatiotemporal
chemical
signaling.
Novel
3D
microelectrode
arrays
permit
high-resolution
electrophysiological
signaling
recording
explore
capacity
recapitulate
mechanisms
formation
and,
ultimately,
their
computational
potential.
Technologies
could
enable
novel
biocomputing
models
via
stimulus-response
training
organoid-computer
interfaces
are
development.
We
envisage
complex,
networked
whereby
connected
real-world
sensors
output
devices,
ultimately
each
other
sensory
organ
(e.g.
retinal
organoids),
trained
biofeedback,
big-data
warehousing,
machine
methods.
In
parallel,
emphasize
embedded
ethics
approach
analyze
ethical
raised
by
research
iterative,
manner
involving
all
relevant
stakeholders.
The
many
possible
applications
this
urge
strategic
development
discipline.
anticipate
OI-based
allow
faster
decision-making,
continuous
during
tasks,
greater
energy
data
efficiency.
Furthermore,
“intelligence-in-a-dish”
help
elucidate
pathophysiology
devastating
developmental
degenerative
diseases
(such
dementia),
potentially
aiding
identification
therapeutic
approaches
address
major
global
unmet
needs.
Nature Methods,
Год журнала:
2024,
Номер
21(5), С. 809 - 813
Опубликована: Апрель 11, 2024
Neuroscience
is
advancing
standardization
and
tool
development
to
support
rigor
transparency.
Consequently,
data
pipeline
complexity
has
increased,
hindering
FAIR
(findable,
accessible,
interoperable
reusable)
access.
brainlife.io
was
developed
democratize
neuroimaging
research.
The
platform
provides
standardization,
management,
visualization
processing
automatically
tracks
the
provenance
history
of
thousands
objects.
Here,
described
evaluated
for
validity,
reliability,
reproducibility,
replicability
scientific
utility
using
four
modalities
3,200
participants.
Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Янв. 4, 2024
Abstract
The
reconstruction
of
neural
circuits
from
serial
section
electron
microscopy
(ssEM)
images
is
being
accelerated
by
automatic
image
segmentation
methods.
Segmentation
accuracy
often
limited
the
preceding
step
aligning
2D
to
create
a
3D
stack.
Precise
and
robust
alignment
in
presence
artifacts
challenging,
especially
as
datasets
are
attaining
petascale.
We
present
computational
pipeline
for
ssEM
with
several
key
elements.
Self-supervised
convolutional
nets
trained
via
metric
learning
encode
align
pairs,
they
used
initialize
iterative
fine-tuning
alignment.
A
procedure
called
vector
voting
increases
robustness
or
missing
data.
For
speedup
series
divided
into
blocks
that
distributed
workers
aligned
each
other
composing
transformations
decay,
which
achieves
global
without
resorting
time-consuming
optimization.
apply
our
whole
fly
brain
dataset,
show
improved
relative
prior
state
art.
also
demonstrate
scales
cubic
millimeter
mouse
visual
cortex.
Our
publicly
available
through
two
open
source
Python
packages.
Journal of Microscopy,
Год журнала:
2022,
Номер
287(3), С. 114 - 137
Опубликована: Июль 10, 2022
Detailed
knowledge
of
biological
structure
has
been
key
in
understanding
biology
at
several
levels
organisation,
from
organs
to
cells
and
proteins.
Volume
electron
microscopy
(volume
EM)
provides
high
resolution
3D
structural
information
about
tissues
on
the
nanometre
scale.
However,
throughput
rate
conventional
microscopes
limited
volume
size
number
samples
that
can
be
imaged.
Recent
improvements
methodology
are
currently
driving
a
revolution
EM,
making
possible
imaging
whole
small
organisms.
In
turn,
these
recent
developments
image
acquisition
have
created
or
stressed
bottlenecks
other
parts
pipeline,
like
sample
preparation,
analysis
data
management.
While
progress
is
stunning
due
advent
automatic
segmentation
server-based
annotation
tools,
challenges
remain.
Here
we
discuss
trends
emerging
methods
for
increasing
implications
Frontiers in Neural Circuits,
Год журнала:
2019,
Номер
13
Опубликована: Фев. 5, 2019
Open-source
software
development
has
skyrocketed
in
part
due
to
community
tools
like
github.com,
which
allows
publication
of
code
as
well
the
ability
create
branches
and
push
accepted
modifications
back
original
repository.
As
number
size
EM-based
datasets
increases,
connectomics
faces
similar
issues
when
we
publish
snapshot
data
corresponding
a
publication.
Ideally,
there
would
be
mechanism
where
remote
collaborators
could
modify
then
flexibly
reintegrate
results
via
moderated
acceptance
changes.
The
DVID
system
provides
web-based
API
first
steps
toward
such
distributed
versioning
approach
datasets.
Through
its
use
central
resource
for
Janelia's
FlyEM
team,
have
integrated
concepts
into
reconstruction
workflows,
allowing
support
proofreader
training
segmentation
experiments
through
branched,
versioned
data.
also
supports
persistence
variety
storage
systems
from
high-speed
local
SSDs
cloud-based
object
stores,
deployment
on
laptops
large
servers.
tailoring
backend
each
type
leads
efficient
fast
queries.
is
freely
available
open-source
with
an
increasing
supported
options.
Computer Graphics Forum,
Год журнала:
2022,
Номер
41(3), С. 573 - 607
Опубликована: Июнь 1, 2022
Abstract
The
field
of
connectomics
aims
to
reconstruct
the
wiring
diagram
Neurons
and
synapses
enable
new
insights
into
workings
brain.
Reconstructing
analyzing
Neuronal
connectivity,
however,
relies
on
many
individual
steps,
starting
from
high‐resolution
data
acquisition
automated
segmentation,
proofreading,
interactive
exploration,
circuit
analysis.
All
these
steps
have
handle
large
complex
datasets
rely
or
benefit
integrated
visualization
methods.
In
this
state‐of‐the‐art
report,
we
describe
methods
that
can
be
applied
throughout
pipeline,
We
first
define
different
pipeline
focus
how
is
currently
steps.
also
survey
open
science
initiatives
in
connectomics,
including
usable
open‐source
tools
publicly
available
datasets.
Finally,
discuss
challenges
possible
future
directions
exciting
research
field.
Psychiatry and Clinical Neurosciences,
Год журнала:
2019,
Номер
73(7), С. 357 - 369
Опубликована: Март 13, 2019
Imaging
genetics
aims
to
identify
genetic
variants
associated
with
the
structure
and
function
of
human
brain.
Recently,
collaborative
consortia
have
been
successful
in
this
goal,
identifying
replicating
common
influencing
gross
brain
as
measured
through
magnetic
resonance
imaging.
In
review,
we
contextualize
imaging
associations
one
important
link
understanding
causal
chain
from
variant
increased
risk
for
neuropsychiatric
disorders.
We
provide
examples
other
fields
how
disease
multiple
phenotypes
along
has
revealed
a
mechanistic
risk,
implications
can
be
similarly
applied.
discuss
current
findings
research
domain,
including
that
slightly
larger
effect
on
than
disorders
like
schizophrenia,
indicating
somewhat
simpler
architecture.
Also,
measurements
share
basis
some,
but
not
all,
disorders,
invalidating
previously
held
belief
they
are
broad
endophenotypes,
yet
pinpointing
regions
likely
involved
pathology
specific
Finally,
suggest
order
build
more
detailed
effects
brain,
future
directions
will
require
observations
cellular
synaptic
beyond
resolution
expect
integrating
at
biological
levels
synapse
sulcus
reveal
pathways
impacting
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Янв. 26, 2024
Abstract
Scientific
progress
depends
on
reliable
and
reproducible
results.
Progress
can
also
be
accelerated
when
data
are
shared
re-analyzed
to
address
new
questions.
Current
approaches
storing
analyzing
neural
typically
involve
bespoke
formats
software
that
make
replication,
as
well
the
subsequent
reuse
of
data,
difficult
if
not
impossible.
To
these
challenges,
we
created
Spyglass
,
an
open-source
framework
enables
analyses
sharing
both
intermediate
final
results
within
across
labs.
uses
Neurodata
Without
Borders
(NWB)
standard
includes
pipelines
for
several
core
in
neuroscience,
including
spectral
filtering,
spike
sorting,
pose
tracking,
decoding.
It
easily
extended
apply
existing
newly
developed
datasets
from
multiple
sources.
We
demonstrate
features
context
a
cross-laboratory
replication
by
applying
advanced
state
space
decoding
algorithms
publicly
available
data.
New
users
try
out
Jupyter
Hub
hosted
HHMI
2i2c:
https://spyglass.hhmi.2i2c.cloud/
.
Frontiers in Neuroinformatics,
Год журнала:
2025,
Номер
19
Опубликована: Март 3, 2025
Introduction
The
effectiveness
of
research
and
innovation
often
relies
on
the
diversity
or
heterogeneity
datasets
that
are
Findable,
Accessible,
Interoperable
Reusable
(FAIR).
However,
global
landscape
brain
data
is
yet
to
achieve
desired
levels
can
facilitate
generalisable
outputs.
Brain
from
low-and
middle-income
countries
Africa
still
missing
in
open
science
ecosystem.
This
mean
decades
may
not
be
populations
Africa.
Methods
combined
experiential
learning
with
a
survey
questionnaire.
involved
deriving
insights
direct,
hands-on
experiences
collecting
African
view
making
it
FAIR.
was
critical
process
action,
reflection,
doing
collection.
A
questionnaire
then
used
validate
findings
provide
wider
contexts
for
these
findings.
Results
revealed
major
challenges
FAIR
categorised
as
socio-cultural,
economic,
technical,
ethical
legal
challenges.
It
also
highlighted
opportunities
growth
include
capacity
development,
development
technical
infrastructure,
funding
well
policy
regulatory
changes.
showed
neuroscience
community
believes
ranked
order
priority
follows:
Technical,
socio-cultural
Conclusion
We
conclude
researchers
need
work
together
address
way
maximise
efforts
build
thriving
ecosystem
socially
acceptable,
ethically
responsible,
technically
robust
legally
compliant.