<s>
CellProfiler	B-Language
is	O
free	O
,	O
open-source	B-Application
software	I-Application
designed	O
to	O
enable	O
biologists	O
without	O
training	O
in	O
computer	O
vision	O
or	O
programming	O
to	O
quantitatively	O
measure	O
phenotypes	O
from	O
thousands	O
of	O
images	O
automatically	O
.	O
</s>
<s>
Distributions	O
are	O
available	O
for	O
Microsoft	B-Application
Windows	I-Application
,	O
macOS	B-Application
,	O
and	O
Linux	B-Application
.	O
</s>
<s>
The	O
source	O
code	O
for	O
CellProfiler	B-Language
is	O
freely	O
available	O
.	O
</s>
<s>
CellProfiler	B-Language
is	O
developed	O
by	O
the	O
Broad	O
Institute	O
's	O
Imaging	O
Platform	O
.	O
</s>
<s>
CellProfiler	B-Language
can	O
read	O
and	O
analyze	O
most	O
common	O
microscopy	O
image	O
formats	O
.	O
</s>
<s>
Biologists	O
typically	O
use	O
CellProfiler	B-Language
to	O
identify	O
objects	O
of	O
interest	O
(	O
e.g.	O
</s>
<s>
Object	O
identification	O
(	O
segmentation	B-Algorithm
)	O
is	O
performed	O
through	O
machine	O
learning	O
or	O
image	B-Algorithm
thresholding	I-Algorithm
,	O
recognition	O
and	O
division	O
of	O
clumped	O
objects	O
,	O
and	O
removal	O
or	O
merging	O
of	O
objects	O
on	O
the	O
basis	O
of	O
size	O
or	O
shape	O
.	O
</s>
<s>
These	O
measurements	O
are	O
accessible	O
by	O
using	O
built-in	O
viewing	O
and	O
plotting	O
data	O
tools	O
,	O
exporting	O
in	O
a	O
comma-delimited	O
spreadsheet	B-Application
format	O
,	O
or	O
importing	O
into	O
a	O
MySQL	B-Application
or	O
SQLite	B-Language
database	O
.	O
</s>
<s>
CellProfiler	B-Language
interfaces	O
with	O
the	O
high-performance	O
scientific	O
libraries	O
NumPy	B-Application
and	O
SciPy	B-Application
for	O
many	O
mathematical	O
operations	O
,	O
the	O
Open	O
Microscopy	O
Environment	O
Consortium	O
’s	O
Bio-Formats	O
library	O
for	O
reading	O
more	O
than	O
100	O
image	O
file	O
formats	O
,	O
ImageJ	B-Language
for	O
use	O
of	O
plugins	O
and	O
macros	O
,	O
and	O
ilastik	B-Algorithm
for	O
pixel-based	O
classification	O
.	O
</s>
<s>
While	O
designed	O
and	O
optimized	O
for	O
large	O
numbers	O
of	O
two-dimensional	O
images	O
(	O
the	O
most	O
common	O
high-content	O
screening	O
image	O
format	O
)	O
,	O
CellProfiler	B-Language
supports	O
analysis	O
of	O
small-scale	O
experiments	O
and	O
time-lapse	O
movies	O
.	O
</s>
<s>
CellProfiler	B-Language
was	O
released	O
in	O
December	O
2005	O
by	O
scientists	O
from	O
the	O
Whitehead	O
Institute	O
for	O
Biomedical	O
Research	O
and	O
Massachusetts	O
Institute	O
of	O
Technology	O
.	O
</s>
<s>
Originally	O
developed	O
in	O
MATLAB	B-Language
,	O
it	O
was	O
re-written	O
in	O
Python	B-Language
and	O
released	O
as	O
CellProfiler	B-Language
2.0	O
in	O
2010	O
.	O
</s>
<s>
CellProfiler	B-Language
4.0	O
was	O
released	O
in	O
September	O
2020	O
and	O
focused	O
on	O
speed	O
,	O
usability	O
,	O
and	O
utility	O
improvements	O
with	O
most	O
notable	O
example	O
of	O
migration	O
to	O
Python	B-Language
3	O
.	O
</s>
<s>
Because	O
CellProfiler	B-Language
is	O
a	O
free	O
,	O
open-source	B-Application
project	O
,	O
anyone	O
can	O
develop	O
their	O
own	O
image	B-Algorithm
processing	I-Algorithm
algorithms	I-Algorithm
as	O
a	O
new	O
module	O
for	O
CellProfiler	B-Language
and	O
contribute	O
it	O
to	O
the	O
project	O
.	O
</s>
<s>
The	O
CellProfiler	B-Language
website	O
contains	O
a	O
forum	O
for	O
discussion	O
where	O
new	O
users	O
can	O
have	O
their	O
questions	O
answered	O
,	O
usually	O
by	O
the	O
creators	O
of	O
the	O
project	O
.	O
</s>
