<s>
Amira	B-Algorithm
(	O
pronounce	O
:	O
Ah-meer-ah	O
)	O
is	O
a	O
software	O
platform	O
for	O
3D	O
and	O
4D	O
data	O
visualization	B-Application
,	O
processing	O
,	O
and	O
analysis	O
.	O
</s>
<s>
Amira	B-Algorithm
is	O
an	O
extendable	O
software	O
system	O
for	O
scientific	B-Application
visualization	I-Application
,	O
data	B-General_Concept
analysis	I-General_Concept
,	O
and	O
presentation	O
of	O
3D	O
and	O
4D	O
data	O
.	O
</s>
<s>
micro-CT	O
,	O
PET	B-Application
,	O
Ultrasound	B-Application
.	O
</s>
<s>
Its	O
ever-expanding	O
functionality	O
has	O
made	O
it	O
a	O
versatile	O
data	B-General_Concept
analysis	I-General_Concept
and	O
visualization	B-Application
solution	O
,	O
applicable	O
to	O
and	O
being	O
used	O
in	O
many	O
fields	O
,	O
such	O
as	O
microscopy	O
in	O
biology	O
and	O
materials	O
science	O
,	O
molecular	O
biology	O
,	O
quantum	O
physics	O
,	O
astrophysics	O
,	O
computational	O
fluid	O
dynamics	O
(	O
CFD	O
)	O
,	O
finite	B-Application
element	I-Application
modeling	O
(	O
FEM	O
)	O
,	O
non-destructive	O
testing	O
(	O
NDT	O
)	O
,	O
and	O
many	O
more	O
.	O
</s>
<s>
One	O
of	O
the	O
key	O
features	O
,	O
besides	O
data	O
visualization	B-Application
,	O
is	O
Amira	B-Algorithm
’s	O
set	O
of	O
tools	O
for	O
image	B-Algorithm
segmentation	I-Algorithm
and	O
geometry	O
reconstruction	O
.	O
</s>
<s>
This	O
allows	O
the	O
user	O
to	O
mark	O
(	O
or	O
segment	O
)	O
structures	O
and	O
regions	O
of	O
interest	O
in	O
3D	B-Algorithm
image	I-Algorithm
volumes	O
using	O
automatic	O
,	O
semi-automatic	O
,	O
and	O
manual	O
tools	O
.	O
</s>
<s>
The	O
segmentation	B-Algorithm
can	O
then	O
be	O
used	O
for	O
a	O
variety	O
of	O
subsequent	O
tasks	O
,	O
such	O
as	O
volumetric	O
analysis	O
,	O
density	O
analysis	O
,	O
shape	B-Algorithm
analysis	I-Algorithm
,	O
or	O
the	O
generation	O
of	O
3D	O
computer	B-Application
models	I-Application
for	O
visualization	B-Application
,	O
numerical	B-Application
simulations	I-Application
,	O
or	O
rapid	B-Device
prototyping	I-Device
or	O
3D	O
printing	O
,	O
to	O
name	O
a	O
few	O
.	O
</s>
<s>
Other	O
key	O
Amira	B-Algorithm
features	O
are	O
multi-planar	O
and	O
volume	O
visualization	B-Application
,	O
image	B-Algorithm
registration	I-Algorithm
,	O
filament	O
tracing	O
,	O
cell	O
separation	O
and	O
analysis	O
,	O
tetrahedral	B-Architecture
mesh	I-Architecture
generation	I-Architecture
,	O
fiber-tracking	O
from	O
diffusion	B-Algorithm
tensor	I-Algorithm
imaging	I-Algorithm
(	O
DTI	O
)	O
data	O
,	O
skeletonization	B-Algorithm
,	O
spatial	O
graph	O
analysis	O
,	O
and	O
stereoscopic	B-Algorithm
rendering	O
of	O
3D	O
data	O
over	O
multiple	O
displays	O
and	O
immersive	O
virtual	O
reality	O
environments	O
,	O
including	O
CAVEs	B-General_Concept
.	O
</s>
<s>
As	O
a	O
commercial	O
product	O
Amira	B-Algorithm
requires	O
the	O
purchase	O
of	O
a	O
license	O
or	O
an	O
academic	O
subscription	O
.	O
</s>
<s>
Amira	B-Algorithm
’s	O
roots	O
go	O
back	O
to	O
1993	O
and	O
the	O
Department	O
for	O
Scientific	B-Application
Visualization	I-Application
,	O
headed	O
by	O
Hans-Christian	O
Hege	O
at	O
the	O
Zuse	O
Institute	O
Berlin	O
(	O
ZIB	O
)	O
.	O
</s>
<s>
The	O
Scientific	B-Application
Visualization	I-Application
department	O
’s	O
mission	O
is	O
to	O
help	O
solve	O
computationally	O
and	O
scientifically	O
challenging	O
tasks	O
in	O
medicine	O
,	O
biology	O
,	O
engineering	O
and	O
materials	O
science	O
.	O
</s>
<s>
For	O
this	O
purpose	O
,	O
it	O
develops	O
algorithms	O
and	O
software	O
for	O
2D	O
,	O
3D	O
,	O
and	O
4D	O
data	O
visualization	B-Application
and	O
visually	O
supported	O
exploration	O
and	O
analysis	O
.	O
</s>
<s>
At	O
that	O
time	O
,	O
the	O
young	O
visualization	B-Application
group	O
at	O
the	O
ZIB	O
had	O
experience	O
with	O
the	O
extendable	O
,	O
data	O
flow-oriented	O
visualization	B-Application
environments	O
apE	O
,	O
IRIS	O
Explorer	O
,	O
and	O
Advanced	B-Application
Visualization	I-Application
Studio	I-Application
(	O
AVS	O
)	O
,	O
but	O
was	O
not	O
satisfied	O
with	O
these	O
products’	O
interactivity	O
,	O
flexibility	O
,	O
and	O
ease-of-use	O
for	O
non-computer	O
scientists	O
.	O
</s>
<s>
Based	O
on	O
experiences	O
that	O
Tobias	O
Höllerer	O
had	O
gained	O
in	O
late	O
1993	O
with	O
the	O
new	O
graphics	O
library	O
IRIS	B-Application
Inventor	I-Application
,	O
it	O
was	O
decided	O
to	O
utilize	O
that	O
library	O
.	O
</s>
<s>
The	O
development	O
of	O
the	O
medical	O
planning	O
system	O
was	O
performed	O
by	O
Detlev	O
Stalling	O
,	O
who	O
later	O
became	O
the	O
chief	O
software	O
architect	O
of	O
Amira	B-Algorithm
.	O
</s>
<s>
The	O
software	O
was	O
based	O
on	O
libraries	O
such	O
as	O
OpenGL	B-Application
(	O
originally	O
IRIS	B-Library
GL	I-Library
)	O
,	O
Open	B-Application
Inventor	I-Application
(	O
originally	O
IRIS	B-Application
Inventor	I-Application
)	O
,	O
and	O
the	O
graphical	B-Application
user	I-Application
interface	I-Application
libraries	O
X11	B-Operating_System
,	O
Motif	B-Application
(	O
software	O
)	O
,	O
and	O
ViewKit	O
.	O
</s>
<s>
In	O
1998	O
,	O
X11/Motif/Viewkit	O
were	O
replaced	O
by	O
the	O
Qt	B-Language
toolkit	I-Language
.	O
</s>
<s>
The	O
projects	O
included	O
applications	O
in	O
medical	B-Algorithm
image	I-Algorithm
computing	I-Algorithm
,	I-Algorithm
medical	I-Algorithm
visualization	I-Algorithm
,	O
neurobiology	O
,	O
confocal	O
microscopy	O
,	O
flow	B-Application
visualization	I-Application
,	O
molecular	B-Application
analytics	I-Application
and	O
computational	O
astrophysics	O
.	O
</s>
<s>
In	O
Feb	O
1998	O
the	O
HyperPlan	O
software	O
was	O
given	O
the	O
new	O
,	O
application-neutral	O
name	O
“	O
Amira	B-Algorithm
”	O
.	O
</s>
<s>
This	O
name	O
is	O
not	O
an	O
acronym	O
,	O
but	O
was	O
chosen	O
for	O
being	O
pronounceable	O
in	O
different	O
languages	O
and	O
providing	O
a	O
suitable	O
connotation	O
,	O
namely	O
“	O
to	O
look	O
at	O
”	O
or	O
“	O
to	O
wonder	O
at	O
”	O
,	O
from	O
the	O
Latin	O
verb	O
“	O
admirare	O
”	O
(	O
to	O
admire	O
)	O
,	O
which	O
reflects	O
a	O
basic	O
situation	O
in	O
data	O
visualization	B-Application
.	O
</s>
<s>
In	O
March	O
1999	O
,	O
the	O
first	O
version	O
of	O
the	O
commercial	O
Amira	B-Algorithm
was	O
exhibited	O
at	O
the	O
CeBIT	O
tradeshow	O
in	O
Hannover	O
,	O
Germany	O
on	O
SGI	B-Operating_System
IRIX	I-Operating_System
and	O
Hewlett-Packard	B-Application
UniX	I-Application
(	O
HP-UX	B-Application
)	O
booths	O
.	O
</s>
<s>
Versions	O
for	O
Linux	B-Application
and	O
Microsoft	B-Application
Windows	I-Application
followed	O
within	O
the	O
following	O
twelve	O
months	O
.	O
</s>
<s>
Later	O
Mac	B-Device
OS	I-Device
X	I-Device
support	O
was	O
added	O
.	O
</s>
<s>
Indeed	O
–	O
Visual	O
Concepts	O
GmbH	O
selected	O
the	O
Bordeaux	O
,	O
France	O
and	O
San	O
Diego	O
,	O
United	O
States	O
based	O
company	O
TGS	O
,	O
Inc	O
.	O
as	O
the	O
worldwide	O
distributor	O
for	O
Amira	B-Algorithm
and	O
completed	O
five	O
major	O
releases	O
(	O
up	O
to	O
version	O
3.1	O
)	O
in	O
the	O
subsequent	O
four	O
years	O
.	O
</s>
<s>
In	O
2003	O
both	O
Indeed	O
–	O
Visual	O
Concepts	O
GmbH	O
,	O
as	O
well	O
as	O
TGS	O
,	O
Inc	O
.	O
were	O
acquired	O
by	O
Massachusetts-based	O
Mercury	B-Application
Computer	I-Application
Systems	I-Application
,	O
Inc	O
.	O
(	O
NASDAQ:MRCY	O
)	O
and	O
became	O
part	O
of	O
Mercury	O
’s	O
newly	O
formed	O
life	O
sciences	O
business	O
unit	O
,	O
later	O
branded	O
Visage	O
Imaging	O
.	O
</s>
<s>
In	O
2009	O
,	O
Mercury	B-Application
Computer	I-Application
Systems	I-Application
,	O
Inc	O
.	O
spun	O
off	O
Visage	O
Imaging	O
again	O
and	O
sold	O
it	O
to	O
Melbourne	O
,	O
Australia	O
based	O
Promedicus	O
Ltd	O
(	O
ASX:PME	O
)	O
,	O
a	O
leading	O
provider	O
of	O
radiology	O
information	O
systems	O
and	O
medical	O
IT	O
solutions	O
.	O
</s>
<s>
During	O
this	O
time	O
,	O
Amira	B-Algorithm
continued	O
to	O
be	O
developed	O
in	O
Berlin	O
,	O
Germany	O
and	O
in	O
close	O
collaboration	O
with	O
the	O
ZIB	O
,	O
still	O
headed	O
by	O
the	O
original	O
creators	O
of	O
Amira	B-Algorithm
.	O
</s>
<s>
TGS	O
,	O
located	O
in	O
Bordeaux	O
,	O
France	O
was	O
sold	O
by	O
Mercury	B-Application
Computer	I-Application
systems	I-Application
to	O
a	O
French	O
investor	O
and	O
renamed	O
to	O
Visualization	B-Application
Sciences	O
Group	O
(	O
VSG	O
)	O
.	O
</s>
<s>
VSG	O
continued	O
the	O
work	O
on	O
a	O
complementary	O
product	O
named	O
Avizo	B-Algorithm
,	O
based	O
on	O
the	O
same	O
source	O
code	O
but	O
customized	O
for	O
material	O
sciences	O
.	O
</s>
<s>
In	O
August	O
2012	O
,	O
FEI	O
,	O
to	O
that	O
date	O
the	O
largest	O
OEM	O
reseller	O
of	O
Amira	B-Algorithm
,	O
purchased	O
VSG	O
and	O
the	O
Amira	B-Algorithm
business	O
from	O
Promedicus	O
.	O
</s>
<s>
This	O
brought	O
the	O
two	O
software	O
sisters	O
Amira	B-Algorithm
and	O
Avizo	B-Algorithm
back	O
into	O
one	O
hand	O
.	O
</s>
<s>
In	O
August	O
2013	O
,	O
Visualization	B-Application
Sciences	O
Group	O
(	O
VSG	O
)	O
became	O
a	O
business	O
unit	O
of	O
FEI	O
.	O
</s>
<s>
Amira	B-Algorithm
and	O
Avizo	B-Algorithm
are	O
still	O
being	O
marketed	O
as	O
two	O
different	O
products	O
;	O
Amira	B-Algorithm
for	O
life	O
sciences	O
and	O
Avizo	B-Algorithm
for	O
materials	O
science	O
,	O
but	O
the	O
development	O
efforts	O
are	O
now	O
joined	O
once	O
again	O
.	O
</s>
<s>
In	O
the	O
meantime	O
,	O
the	O
number	O
of	O
scientific	O
articles	O
using	O
the	O
Amira	B-Algorithm
/	O
Avizo	B-Algorithm
software	I-Algorithm
,	O
is	O
in	O
the	O
order	O
of	O
10	O
thousands	O
.	O
</s>
