<s>
Vaa3D	B-Algorithm
(	O
in	O
Chinese	O
‘	O
挖三维’	O
)	O
is	O
an	O
Open	O
Source	O
visualization	O
and	O
analysis	O
software	O
suite	O
created	O
mainly	O
by	O
Hanchuan	O
Peng	O
and	O
his	O
team	O
at	O
Janelia	O
Research	O
Campus	O
,	O
HHMI	O
and	O
Allen	O
Institute	O
for	O
Brain	O
Science	O
.	O
</s>
<s>
In	O
a	O
recent	O
Nature	O
Methods	O
review	O
article	O
,	O
it	O
has	O
been	O
viewed	O
as	O
one	O
of	O
the	O
leading	O
open-source	B-Application
software	I-Application
suites	O
in	O
the	O
related	O
research	O
fields	O
.	O
</s>
<s>
Vaa3D	B-Algorithm
was	O
created	O
in	O
2007	O
to	O
tackle	O
the	O
large-scale	O
brain	O
mapping	O
project	O
at	O
Janelia	O
Farm	O
of	O
the	O
Howard	O
Hughes	O
Medical	O
Institute	O
.	O
</s>
<s>
Low	O
level	O
OpenGL-based	O
3D	O
rendering	O
was	O
developed	O
to	O
provide	O
direct	O
rendering	O
of	O
multi-dimensional	O
image	O
stacks	O
.	O
</s>
<s>
C/C	O
++	O
and	O
Qt	B-Language
were	O
used	O
to	O
create	O
cross-platform	O
compatibility	O
so	O
the	O
software	O
can	O
run	O
on	O
Mac	O
,	O
Linux	O
and	O
Windows	O
.	O
</s>
<s>
Strong	O
functions	O
for	O
synchronizing	O
multiple	O
2D/3D/4D/5D	O
rendered	O
views	O
,	O
generating	O
global	O
and	O
local	O
3D	O
viewers	O
,	O
and	O
virtual	O
finger	O
,	O
allow	O
Vaa3D	B-Algorithm
be	O
able	O
to	O
streamline	O
a	O
number	O
of	O
operations	O
for	O
complicated	O
brain	O
science	O
tasks	O
,	O
for	O
example	O
,	O
brain	O
comparison	O
and	O
neuron	O
reconstruction	O
.	O
</s>
<s>
Vaa3D	B-Algorithm
also	O
provides	O
an	O
extensible	O
plugin	B-Application
interface	O
that	O
currently	O
hosts	O
dozens	O
of	O
open	O
source	O
plugins	B-Application
contributed	O
by	O
researchers	O
worldwide	O
.	O
</s>
<s>
Vaa3D	B-Algorithm
is	O
able	O
to	O
render	O
3D	O
,	O
4D	O
,	O
and	O
5D	O
data	O
(	O
X	O
,	O
Y	O
,	O
Z	O
,	O
Color	O
,	O
Time	O
)	O
quickly	O
.	O
</s>
<s>
The	O
visualization	O
is	O
made	O
fast	O
by	O
using	O
OpenGL	B-Application
directly	O
.	O
</s>
<s>
Vaa3D	B-Algorithm
handles	O
the	O
problem	O
of	O
large	O
data	O
visualization	O
via	O
several	O
techniques	O
.	O
</s>
<s>
An	O
alternative	O
method	O
used	O
in	O
Vaa3D	B-Algorithm
is	O
to	O
combine	O
both	O
global	O
and	O
local	O
3D	O
viewers	O
.	O
</s>
<s>
Virtual	O
Finger	O
,	O
or	O
3D-WYSIWYG	O
( 	O
 '	O
What	O
You	O
See	O
in	O
2D	O
is	O
What	O
You	O
Get	O
in	O
3D	O
 '	O
)	O
technique	O
allows	O
efficient	O
generation	O
and	O
use	O
of	O
the	O
3D	O
location	O
information	O
from	O
2D	O
input	O
of	O
a	O
user	O
on	O
the	O
typical	O
2D	O
display	O
or	O
touch	O
devices	O
.	O
</s>
<s>
The	O
Vaa3D	B-Algorithm
's	O
Virtual	O
Finger	O
technology	O
allows	O
instant	O
and	O
random-order	O
exploration	O
of	O
complex	O
3D	O
image	O
content	O
,	O
similar	O
to	O
using	O
real	O
fingers	O
explore	O
the	O
real	O
3D	O
world	O
using	O
a	O
single	O
click	O
or	O
stroke	O
to	O
locate	O
3D	O
objects	O
.	O
</s>
<s>
Vaa3D	B-Algorithm
displays	O
three	O
major	O
types	O
of	O
3D	O
surface	O
objects	O
:	O
</s>
<s>
Vaa3D	B-Algorithm
can	O
display	O
multiple	O
sets	O
of	O
any	O
of	O
these	O
surface	O
objects	O
,	O
which	O
can	O
also	O
be	O
overlaid	O
on	O
top	O
of	O
image	O
voxel	O
data	O
using	O
different	O
overlaying	O
relationships	O
.	O
</s>
<s>
Vaa3D	B-Algorithm
provides	O
a	O
Vaa3D-Neuron	O
package	O
to	O
reconstruct	O
,	O
quantify	O
,	O
and	O
compare	O
3D	O
morphology	O
of	O
single	O
neurons	O
of	O
a	O
number	O
of	O
species	O
.	O
</s>
<s>
Vaa3D-Neuron	O
allows	O
several	O
ways	O
of	O
neuron	O
tracing	O
.	O
</s>
<s>
Semi-automatic	O
tracing	O
:	O
A	O
user	O
can	O
specify	O
some	O
key	O
termini	O
points	O
where	O
the	O
neuron	O
tracing	O
must	O
reach	O
as	O
prior	O
,	O
and	O
then	O
ask	O
Vaa3D	B-Algorithm
to	O
complete	O
the	O
3D	O
reconstruction	O
automatically	O
.	O
</s>
<s>
The	O
user	O
may	O
also	O
use	O
several	O
other	O
automated	O
neuron	O
tracing	O
algorithms	O
ported	O
to	O
Vaa3D	B-Algorithm
include	O
FarSight	O
Snake	O
Tracing	O
,	O
NeuTube	O
tracing	O
(	O
tube	O
fitting	O
)	O
,	O
and	O
MOST	O
ray	O
bursting	O
based	O
tracing	O
.	O
</s>
<s>
Wrapper	O
methods	O
such	O
as	O
UltraTracer	O
,	O
that	O
extend	O
any	O
of	O
these	O
base	O
tracers	O
to	O
arbitrarily	O
large	O
multidimensional	O
image	O
volumes	O
,	O
have	O
also	O
been	O
developed	O
and	O
integrated	O
in	O
Vaa3D	B-Algorithm
.	O
</s>
<s>
Vaa3D	B-Algorithm
was	O
used	O
to	O
extract	O
single	O
cells	O
from	O
several	O
studies	O
of	O
the	O
nematode	O
C	O
.	O
elegans	O
,	O
the	O
insect	O
fruitfly	O
,	O
mouse	O
,	O
and	O
other	O
species	O
.	O
</s>
<s>
The	O
primary	O
functions	O
used	O
were	O
3D	O
image	B-Algorithm
segmentation	I-Algorithm
for	O
extracting	O
and	O
quantifying	O
single	O
cells	O
 '	O
gene	O
expression	O
levels	O
,	O
and	O
fast	O
cell	O
counting	O
in	O
specific	O
brain	O
areas	O
.	O
</s>
<s>
Vaa3D	B-Algorithm
also	O
provides	O
methods	O
to	O
annotate	O
these	O
cells	O
and	O
identify	O
their	O
names	O
.	O
</s>
<s>
Vaa3D	B-Algorithm
also	O
provides	O
a	O
SRS	O
(	O
Simultaneous	O
Segmentation	B-Algorithm
and	O
Recognition	O
)	O
algorithm	O
for	O
3D	O
segmentation	B-Algorithm
of	O
complicated	O
cells	O
,	O
which	O
are	O
often	O
touching	O
each	O
other	O
.	O
</s>
<s>
SRS	O
has	O
been	O
shown	O
to	O
reduce	O
over-segmentation	O
and	O
under-segmentation	O
errors	O
compared	O
to	O
usually	O
used	O
watershed	O
segmentation	B-Algorithm
method	O
.	O
</s>
<s>
Vaa3D	B-Algorithm
has	O
been	O
used	O
in	O
several	O
brain	O
mapping	O
projects	O
,	O
in	O
terms	O
of	O
both	O
pattern	O
alignment	O
(	O
registration	O
)	O
and	O
multiplexing	O
based	O
analysis	O
.	O
</s>
<s>
Pattern	O
alignment	O
and	O
registration	O
:	O
Vaa3D	B-Algorithm
provides	O
a	O
series	O
of	O
plugins	B-Application
and	O
functions	O
to	O
align	O
3D	O
image	O
patterns	O
,	O
and	O
then	O
synchronize	O
the	O
3D	O
display	O
of	O
these	O
aligned	O
patterns	O
.	O
</s>
<s>
Multiplexing	O
based	O
analysis	O
:	O
Vaa3D	B-Algorithm
includes	O
a	O
pattern	O
Atlas	O
Manager	O
which	O
displays	O
a	O
series	O
of	O
aligned	O
image	O
patterns	O
in	O
a	O
spread-sheet	O
,	O
with	O
which	O
subsets	O
of	O
these	O
patterns	O
can	O
be	O
colored	O
in	O
different	O
ways	O
and	O
blended	O
together	O
for	O
colocalization	O
analysis	O
.	O
</s>
<s>
Vaa3D	B-Algorithm
can	O
be	O
extended	O
using	O
a	O
plugin	B-Application
interface	O
.	O
</s>
<s>
A	O
wizard	O
called	O
"	O
Plugin	B-Application
Creator	O
"	O
is	O
provided	O
to	O
generate	O
a	O
basic	O
template	O
of	O
a	O
new	O
plugin	B-Application
.	O
</s>
<s>
The	O
following	O
main	O
categories	O
of	O
plugins	B-Application
are	O
currently	O
released	O
.	O
</s>
<s>
Vaa3D	B-Algorithm
has	O
also	O
been	O
extended	O
to	O
support	O
ITK	O
,	O
Matlab	B-Language
,	O
Bioformats	O
,	O
OpenCV	B-Language
and	O
other	O
widely	O
used	O
software	O
.	O
</s>
<s>
One	O
extension	O
,	O
called	O
Vaa3D-TeraFly	O
,	O
is	O
to	O
visualize	O
terabytes	O
of	O
image	O
data	O
using	O
a	O
Google-Earth	O
style	O
dive-in	O
view	O
of	O
data	O
.	O
</s>
