<s>
BisQue	B-Operating_System
is	O
a	O
free	O
,	O
open	B-License
source	I-License
web-based	O
platform	O
for	O
the	O
exchange	O
and	O
exploration	O
of	O
large	O
,	O
complex	O
datasets	O
.	O
</s>
<s>
BisQue	B-Operating_System
specifically	O
supports	O
large	O
scale	O
,	O
multi-dimensional	O
multimodal-images	O
and	O
image	B-General_Concept
analysis	I-General_Concept
.	O
</s>
<s>
Image	B-General_Concept
analysis	I-General_Concept
modules	O
can	O
be	O
added	O
to	O
perform	O
complex	O
analysis	O
tasks	O
on	O
compute	B-Architecture
clusters	I-Architecture
.	O
</s>
<s>
BisQue	B-Operating_System
can	O
be	O
easily	O
deployed	O
in	O
cloud	O
computing	O
environments	O
or	O
on	O
computer	B-Architecture
clusters	I-Architecture
for	O
scalability	O
.	O
</s>
<s>
BisQue	B-Operating_System
has	O
been	O
integrated	O
into	O
the	O
NSF	O
Cyberinfrastructure	O
project	O
CyVerse	O
.	O
</s>
<s>
The	O
user	O
interacts	O
with	O
BisQue	B-Operating_System
via	O
any	O
modern	O
web	B-Application
browser	I-Application
.	O
</s>
<s>
Project	O
BisQue	B-Operating_System
originally	O
started	O
in	O
2004	O
as	O
part	O
of	O
the	O
US	O
National	O
Science	O
Foundation	O
(	O
NSF	O
)	O
supported	O
Center	O
for	O
Bio-Image	O
Informatics	O
at	O
UCSB	O
,	O
to	O
facilitate	O
integration	O
of	O
database	O
and	O
image	B-General_Concept
analysis	I-General_Concept
methods	O
,	O
specifically	O
in	O
the	O
context	O
of	O
microscopy	O
images	O
.	O
</s>
<s>
More	O
importantly	O
,	O
there	O
was	O
also	O
a	O
need	O
for	O
maintaining	O
the	O
analysis	O
provenance	O
for	O
reproducing	O
image	B-General_Concept
analysis	I-General_Concept
results	O
.	O
</s>
<s>
Very	O
early	O
on	O
,	O
it	O
was	O
realized	O
that	O
BisQue	B-Operating_System
has	O
to	O
go	O
schema-less	O
to	O
support	O
the	O
needs	O
of	O
diverse	O
biological	O
experiments	O
—	O
each	O
experiment	O
and	O
analysis	O
results	O
are	O
unique	O
and	O
slightly	O
different	O
.	O
</s>
<s>
Further	O
,	O
from	O
the	O
beginning	O
,	O
BisQue	B-Operating_System
focused	O
on	O
using	O
the	O
web	B-Application
browser	I-Application
as	O
the	O
standard	O
interface	O
.	O
</s>
<s>
These	O
posed	O
unique	O
database	O
and	O
visualization	O
challenges	O
while	O
dealing	O
with	O
large	O
scale	O
multimodal	O
data	O
,	O
and	O
in	O
the	O
process	O
BisQue	B-Operating_System
has	O
developed	O
a	O
unique	O
and	O
novel	O
framework	O
for	O
visualizing	O
very	O
large	O
images	O
(	O
100k	O
x	O
100k	O
pixels	O
,	O
for	O
example	O
)	O
,	O
and	O
currently	O
supports	O
over	O
250	O
different	O
image	O
file	O
formats	O
.	O
</s>
<s>
Within	O
the	O
browser	B-Application
,	O
users	O
can	O
now	O
visualize	O
2D	O
,	O
3D	O
,	O
4D	O
and	O
5D	O
images	O
,	O
and	O
export	O
them	O
to	O
many	O
other	O
standardized	O
formats	O
.	O
</s>
<s>
Over	O
the	O
years	O
the	O
BisQue	B-Operating_System
team	O
has	O
closely	O
worked	O
with	O
the	O
iPlant	O
Cyberinfrastructure	O
(	O
now	O
the	O
CyVerse	O
)	O
,	O
supporting	O
the	O
image	O
database	O
management	O
needs	O
of	O
the	O
plant	O
biology	O
community	O
.	O
</s>
<s>
Going	O
beyond	O
Bioimaging	O
applications	O
,	O
BisQue	B-Operating_System
has	O
been	O
used	O
in	O
analyzing	O
underwater	O
images	O
and	O
video	O
(	O
REF	O
here	O
)	O
and	O
in	O
medical	O
imaging	O
applications	O
.	O
</s>
<s>
The	O
current	O
BisQue	B-Operating_System
interface	O
now	O
supports	O
the	O
latest	O
DICOM	B-Algorithm
standard	O
.	O
</s>
<s>
BisQue	B-Operating_System
has	O
integrated	O
over	O
100	O
different	O
image	O
features	O
in	O
its	O
feature	O
service	O
and	O
the	O
next	O
release	O
will	O
include	O
support	O
for	O
deep	O
learning	O
methods	O
and	O
feature	O
classification	O
services	O
.	O
</s>
<s>
BisQue	B-Operating_System
provides	O
an	O
online	O
resource	O
for	O
management	O
and	O
analysis	O
of	O
5D	O
biological	O
images	O
.	O
</s>
<s>
Image	O
and	O
metadata	O
ingestion	O
is	O
the	O
first	O
step	O
in	O
using	O
BisQue	B-Operating_System
.	O
</s>
<s>
The	O
ingestion	O
can	O
either	O
happen	O
through	O
a	O
web	O
browser-based	O
interface	O
,	O
or	O
via	O
the	O
BisQue	B-Operating_System
API	B-General_Concept
.	O
</s>
<s>
To	O
date	O
,	O
BisQue	B-Operating_System
supports	O
over	O
240	O
different	O
image	O
formats	O
from	O
generic	O
JPEG	O
to	O
specialized	O
microscopy	O
image	O
formats	O
such	O
as	O
Zeiss	O
CZI	O
,	O
Imaris	O
Ims	O
,	O
and	O
Nikon	O
ND2	O
.	O
</s>
<s>
Images	O
can	O
be	O
arbitrarily	O
large	O
and	O
are	O
automatically	O
pyramided	B-Algorithm
after	O
ingestion	O
.	O
</s>
<s>
In	O
addition	O
to	O
the	O
image	O
data	O
itself	O
,	O
BisQue	B-Operating_System
also	O
captures	O
all	O
metadata	O
of	O
an	O
image	O
(	O
e.g.	O
,	O
camera	O
settings	O
,	O
geo	O
coordinates	O
,	O
etc	O
.	O
)	O
</s>
<s>
BisQue	B-Operating_System
allows	O
an	O
arbitrary	O
number	O
of	O
tags	O
per	O
resource	O
and	O
arbitrary	O
nesting	O
between	O
tags	O
,	O
similar	O
to	O
XML	B-Protocol
documents	I-Protocol
.	O
</s>
<s>
For	O
efficiency	O
and	O
reliability	O
,	O
the	O
tags	O
and	O
values	O
are	O
stored	O
in	O
an	O
indexed	O
tag/value	O
table	O
in	O
the	O
underlying	O
SQL	B-Language
database	I-Language
.	O
</s>
<s>
In	O
addition	O
to	O
be	O
searchable	O
,	O
these	O
graphical	O
annotation	O
are	O
also	O
rendered	O
in	O
BisQue	B-Operating_System
's	O
image	O
viewer	O
as	O
overlays	O
on	O
top	O
of	O
the	O
viewed	O
image	O
.	O
</s>
<s>
For	O
the	O
former	O
,	O
BisQue	B-Operating_System
provides	O
a	O
web-based	O
tag	O
organizer	O
that	O
enables	O
rapid	O
filtering	O
and	O
grouping	O
of	O
large	O
image	O
collections	O
by	O
tag	O
names	O
and	O
values	O
.	O
</s>
<s>
For	O
the	O
latter	O
,	O
BisQue	B-Operating_System
offers	O
a	O
RESTful	B-Protocol
tag	O
query	O
interface	O
to	O
find	O
images	O
with	O
specific	O
tag	O
values	O
.	O
</s>
<s>
Both	O
of	O
these	O
search	O
capabilities	O
are	O
converted	O
into	O
SQL	B-Language
queries	O
over	O
the	O
tag/value	O
table	O
behind	O
the	O
scenes	O
.	O
</s>
<s>
Besides	O
tag-centric	O
image	O
organization	O
,	O
BisQue	B-Operating_System
also	O
provides	O
a	O
traditional	O
folder	O
view	O
that	O
allows	O
users	O
to	O
browse	O
images	O
by	O
navigating	O
folders	O
similar	O
to	O
a	O
file	B-Application
manager	I-Application
.	O
</s>
<s>
BisQue	B-Operating_System
allows	O
users	O
to	O
write	O
analysis	O
modules	O
in	O
the	O
programming	O
language	O
of	O
their	O
choice	O
(	O
e.g.	O
,	O
Matlab	B-Language
,	O
Python	B-Language
,	O
C++	B-Language
)	O
by	O
using	O
language-specific	O
APIs	B-General_Concept
.	O
</s>
<s>
Tested	O
modules	O
can	O
then	O
be	O
registered	O
in	O
the	O
BisQue	B-Operating_System
system	O
for	O
execution	O
.	O
</s>
<s>
BisQue	B-Operating_System
supports	O
different	O
execution	O
modes	O
,	O
depending	O
on	O
the	O
available	O
infrastructure	O
.	O
</s>
<s>
For	O
simple	O
modules	O
,	O
BisQue	B-Operating_System
can	O
execute	O
them	O
on	O
a	O
single	O
node	O
.	O
</s>
<s>
For	O
high-performance	O
needs	O
,	O
BisQue	B-Operating_System
can	O
leverage	O
the	O
HTCondor	B-Operating_System
high-throughput	B-Operating_System
computing	I-Operating_System
software	O
framework	O
for	O
coarse-grained	O
distributed	O
parallelization	O
.	O
</s>
<s>
In	O
the	O
latter	O
case	O
,	O
BisQue	B-Operating_System
can	O
automatically	O
parallelize	O
analysis	O
over	O
large	O
image	O
datasets	O
and	O
then	O
collect	O
the	O
results	O
in	O
a	O
single	O
BisQue	B-Operating_System
metadata	O
document	O
.	O
</s>
<s>
Metadata	O
in	O
BisQue	B-Operating_System
can	O
take	O
many	O
forms	O
:	O
text	O
,	O
objects	O
of	O
interest	O
,	O
user	O
annotations	O
or	O
another	O
web-based	O
file	O
(	O
e.g.	O
</s>
<s>
associated	O
publication	O
in	O
PDF	B-Application
)	O
.	O
</s>
<s>
The	O
most	O
recent	O
image	O
viewer	O
is	O
able	O
to	O
present	O
volumetric	O
imagery	O
in	O
3D	O
without	O
browser	B-Application
plug-ins	O
by	O
utilizing	O
modern	O
browsers	B-Application
 '	O
WebGL	B-Library
capabilities	O
.	O
</s>
<s>
In	O
BisQue	B-Operating_System
,	O
sharing	O
images	O
,	O
metadata	O
and	O
analysis	O
results	O
can	O
be	O
performed	O
through	O
the	O
web	O
.	O
</s>
<s>
The	O
system	O
contains	O
an	O
export	O
facility	O
that	O
allows	O
conversions	O
of	O
image	O
formats	O
,	O
application	O
of	O
a	O
variety	O
of	O
image-processing	O
operations	O
and	O
export	O
of	O
textual	O
or	O
graphical	O
annotations	O
as	O
XML	B-Protocol
,	O
CSV	O
or	O
to	O
Google	B-Application
Docs	I-Application
.	O
</s>
<s>
All	O
services	O
and	O
modules	O
are	O
accessible	O
via	O
standard	O
web	O
access	O
methods	O
(	O
HTTP	B-Protocol
)	O
.	O
</s>
<s>
This	O
permits	O
a	O
wide	O
variety	O
of	O
tools	O
,	O
from	O
web	B-Application
browsers	I-Application
to	O
custom	O
analysis	O
applications	O
,	O
to	O
interact	O
with	O
BisQue	B-Operating_System
.	O
</s>
<s>
Most	O
BisQue	B-Operating_System
services	O
are	O
implemented	O
using	O
the	O
RESTful	B-Protocol
design	O
pattern	O
architecture	O
that	O
exposes	O
resources	O
through	O
URIs	O
.	O
</s>
<s>
Resources	O
are	O
manipulated	O
by	O
using	O
the	O
common	O
HTTP	B-Protocol
methods	O
.	O
</s>
<s>
Among	O
many	O
benefits	O
attributed	O
to	O
RESTful	B-Protocol
pattern	O
are	O
scalability	O
through	O
web	O
caches	O
and	O
the	O
use	O
of	O
client	O
side	O
state	O
and	O
processing	O
resources	O
.	O
</s>
<s>
Bisque	B-Operating_System
services	O
exchange	O
data	O
in	O
XML	B-Protocol
format	O
.	O
</s>
<s>
For	O
easy	O
integration	O
with	O
existing	O
software	O
,	O
BisQue	B-Operating_System
also	O
provides	O
an	O
API	B-General_Concept
that	O
covers	O
all	O
aspects	O
of	O
resource	O
ingestion	O
,	O
search	O
,	O
analysis	O
,	O
and	O
manipulation	O
.	O
</s>
<s>
It	O
is	O
currently	O
available	O
for	O
Python	B-Language
and	O
Matlab	B-Language
.	O
</s>
<s>
BisQue	B-Operating_System
has	O
been	O
used	O
to	O
manage	O
and	O
analyze	O
23.3	O
hours	O
(	O
884GB	O
)	O
of	O
high	O
definition	O
video	O
from	O
dives	O
in	O
Bering	O
Sea	O
submarine	O
canyons	O
to	O
evaluate	O
the	O
density	O
of	O
fishes	O
,	O
structure-forming	O
corals	O
and	O
sponges	O
and	O
to	O
document	O
and	O
describe	O
fishing	O
damage	O
.	O
</s>
<s>
An	O
image	O
processing	O
algorithm	O
developed	O
in	O
Matlab	B-Language
was	O
used	O
to	O
detect	O
laser	O
dots	O
projected	O
onto	O
the	O
seafloor	O
as	O
a	O
scale	O
reference	O
.	O
</s>
<s>
BisQue	B-Operating_System
's	O
module	O
system	O
allows	O
to	O
wrap	O
this	O
Matlab	B-Language
code	O
into	O
an	O
analysis	O
module	O
that	O
can	O
be	O
parallelized	O
across	O
a	O
compute	B-Architecture
cluster	I-Architecture
.	O
</s>
<s>
In	O
addition	O
,	O
each	O
frame	O
was	O
manually	O
annotated	O
with	O
objects	O
of	O
interest	O
(	O
e.g.	O
,	O
fishes	O
,	O
sponges	O
,	O
substrates	O
)	O
and	O
these	O
annotations	O
and	O
other	O
image	O
metadata	O
(	O
e.g.	O
,	O
pixel	O
resolution	O
,	O
GPS	O
location	O
)	O
was	O
stored	O
in	O
BisQue	B-Operating_System
's	O
flexible	O
metadata	O
store	O
.	O
</s>
<s>
The	O
BisQue	B-Operating_System
platform	O
is	O
part	O
of	O
the	O
iPlant	O
Cyberinfrastructure	O
(	O
now	O
the	O
CyVerse	O
)	O
to	O
analyze	O
plant-related	O
images	O
in	O
the	O
context	O
of	O
phenotype	O
analysis	O
.	O
</s>
<s>
BisQue	B-Operating_System
was	O
integrated	O
with	O
iPlant	O
’s	O
authentication	O
,	O
cloud	O
storage	O
,	O
and	O
high-performance	O
grid	B-Architecture
computing	I-Architecture
infrastructure	I-Architecture
and	O
configured	O
with	O
sample	O
data	O
and	O
algorithms	O
designed	O
to	O
assay	O
phenotypes	O
such	O
as	O
directional	O
root-tip	O
growth	O
or	O
comparisons	O
of	O
seed	O
size	O
differences	O
.	O
</s>
<s>
As	O
of	O
version	O
0.5.5	O
,	O
BisQue	B-Operating_System
is	O
released	O
under	O
a	O
modified	O
BSD	B-Operating_System
license	I-Operating_System
that	O
requires	O
proper	O
and	O
visible	O
attribution	O
of	O
the	O
BisQue	B-Operating_System
project	O
if	O
the	O
whole	O
or	O
parts	O
of	O
BisQue	B-Operating_System
are	O
used	O
for	O
either	O
research	O
or	O
commercial	O
purposes	O
.	O
</s>
